Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSI-high metastatic colorectal cancer

BACKGROUND

Microsatellite instability (MSI) is a biomarker for response to immune checkpoint inhibitors (ICPIs). PD-1 inhibitors in metastatic colorectal carcinoma (mCRC) with MSI-high (MSI-H) have demonstrated a high disease control rate and favorable progression-free survival (PFS); however, reported response rates to pembrolizumab and nivolumab are variable and often <50%, suggesting that additional predictive biomarkers are needed.

METHODS

Clinicopathologic data were collected from patients with MSI-H mCRC confirmed by hybrid capture-based next-generation sequencing (NGS) treated with PD-1/L1 inhibitors at five institutes. Tumor mutational burden (TMB) was determined on 0.8-1.1 Mb of sequenced DNA and reported as mutations/Mb. Potential biomarkers of response and time to progression were analyzed by univariate and multivariate analyses. Once TMB was confirmed as a predictive biomarker, a larger dataset of 18 140 unique CRC patients was analyzed to define the relevance of the identified TMB cut-point.

RESULTS

A total of 22 patients were treated with PD-1/L1 inhibitors including 19 with pembrolizumab monotherapy. Among tested variables, TMB showed the strongest association with objective response (OR; P < 0.001) and PFS, by univariate (P < 0.001) and multivariate analysis (P < 0.01). Using log-rank statistics, the optimal predictive cut-point for TMB was estimated between 37 and 41 mutations/Mb. All 13 TMBhigh cases responded, while 6/9 TMBlow cases had progressive disease. The median PFS for TMBhigh has not been reached (median follow-up >18 months) while the median PFS for TMBlow was 2 months. A TMB of 37.4 mutations/Mb in a large MSI-H mCRC population (821/18, 140 cases; 4.5%) evaluated by NGS corresponded to the 35th percentile cut-point.

CONCLUSIONS

TMB appears to be an important independent biomarker within MSI-H mCRC to stratify patients for likelihood of response to ICPIs. If validated in prospective studies, TMB may play an important role in guiding the sequencing and/or combinations of ICPIs in MSI-H mCRC.

Abstract PD3-05: Co-occurring gain-of-function mutations in HER2 and HER3 cooperate to enhance HER2/HER3 binding, HER-dependent signaling, and breast cancer growth

ERBB2, the gene encoding HER2, is mutated in 2-4% of breast cancers. The HER2 tyrosine kinase inhibitor neratinib has shown clinical activity against breast cancers harboring HER2 activating mutations, suggesting these tumors depend on HER2 signaling. Co-occurring HER2 and HER3 (ERBB3) mutations have been reported in patients who respond to neratinib (Hanker et al., Cancer Discov. 2017) suggesting the possibility of cooperativity of both oncogenes. Co-expression of the mutant intracellular domains of HER2 and HER3 in HEK293 cells enhanced phosphorylation of HER3 and ERK compared to expression of either mutant alone, which was blocked by 100 nM neratinib. Interrogation of TCGA, METABRIC, Project GENIE, and Foundation Medicine datasets revealed that gain-of-function mutations in ERBB2 and ERBB3 co-occur with a statistically significant frequency. For example, in GENIE, ERBB2 mutations co-occur with mutations in ERBB3 (8.3% of ERBB2-mutant vs 2.3% of ERBB2 WT; q=1.37x10-10).

We hypothesized that co-occurring mutations in HER2 and HER3 cooperate to enhance HER2 signaling and dependence and breast cancer progression.

Thirty-four unique breast cancers were found to harbor co-occurring mutations in HER2 and HER3, the most common of which were ERBB2L755S/ERBB3E928G (n=10), ERBB2V777L/ERBB3E928G(n=6), and ERBB2L869R/Q/ERBB3E928G (n=4). Using co-immunoprecipitation assays with HER2 and HER3 antibodies in transfected HEK293 cells, we found that co-expression of HER3E928G with wild type (WT) HER2, or co-expression of HER2L755S or HER2L869R with HER3WT, slightly increased HER2-HER3 dimerization. However, binding was strongest between double mutants. This was accompanied by the highest levels of Y1289 p-HER3 in cells expressing both HER3E928G and each HER2L755S, HER2V777L, or HER2L869R compared to cells expressing each HER2 or HER3 mutant with a respective WT heterodimer partner. Structural modeling of the HER2L869R/HER3E928G double-mutant predicted that the HER3 mutation, located at the dimer interface, may enhance heterodimerization of the kinase domains through decreased bulk and electrostatic repulsion. We also noted that the HER2L755S mutation is predicted to be in close proximity to HER3E928G (&lt;4 Å) and may impact binding affinity. Investigation of the structural basis for the enhanced binding of other double mutants is in progress.

MCF7 “knock-in” cells incorporating HER2L755S, HER2V777L, or HER2L869R (or HER2WT) were stably transduced with HER3E928G or HER3WT. Co-expression of double mutants strongly enhanced estrogen-independent growth in 3D Matrigel over cells expressing either mutant alone. We are currently testing inhibitors of HER2/HER3 signaling, including neratinib ± trastuzumab, trastuzumab + pertuzumab, and the ERBB1-3 antibody mixture Sym013, to determine therapeutic strategies to block the cooperative growth induced by co-occurring HER2 and HER2 mutations.

Conclusions: Co-expression of mutant HER2 and mutant HER3 promotes HER2/HER binding, HER3 phosphorylation, and breast tumor cell proliferation. We aim to identify therapeutic vulnerabilities for patients with co-occurring HER2 and HER3 mutations.

Citation Format: Hanker AB, Koch JP, Ye D, Sliwoski G, Sheehan J, Kinch LN, Red Brewer M, He J, Miller VA, Lalani AS, Cutler, Jr. RE, Croessmann S, Zabransky DJ, Meiler J, Arteaga CL. Co-occurring gain-of-function mutations in HER2 and HER3 cooperate to enhance HER2/HER3 binding, HER-dependent signaling, and breast cancer growth [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD3-05.

Abstract P3-06-18: Comprehensive genomic profiling of carcinosarcomas of the breast

Background:

Carcinosarcomas of the breast (BCSC) are exceptionally rare and the underlying genomic drivers are still being elucidated. Comprehensive genomic profiling (CGP) determines the tumor mutation burden (TMB) and identifies all four classes of genomic alterations (GA) that have potential to direct personalized treatment strategies.

Methods:

CGP by hybridization capture of exons from up to 315 cancer-related genes and select introns of 28 genes commonly rearranged in cancer was applied to ≥ 50ng of DNA extracted from 9 consecutive BCSC and sequenced to high, uniform median coverage (&gt;500X). Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined by principal components analysis of optimized loci.

Results:

The 9 BCSC patients had a median age of 57 yrs (range 49-78 yrs). CGP was performed on the primary BCSC in 4 cases and on metastasis biopsies in 5 cases (4 lung and 1 lymph node). The mean GA/tumor was 6.6 and clinically relevant GA (CRGA)/tumor was 1.3. The most frequent non-CRGA were in TP53 (89%), MYC (56%) and LYN (40%). The most frequent CRGA were in PIK3CA (33%), and NF1, BRCA1, PTEN, RICTOR, FGFR1, AKT2 and STK11 (all at 11%). The median TMB for all BCSC was 2.4 mut/Mb with 1 (11%) tumor with a TMB &gt; 20 mut/Mb and 8 BCSC (88%) with TMB &lt; 5 mut/Mb. Five of 5 BCSC (100%) that were available for MSI status testing were microsatellite stable.

Conclusions:

On CGP, BCSC feature a high frequency of GA, but only a modest frequency of CRGA and high TMB. However, when the CRGA and TMB positive cases are combined (77.8% overall in this series), the opportunity for personalized targeted and immunotherapies are significant. Thus, further investigation of precision therapies for BCSC in the clinical trial setting appear warranted.

Citation Format: Gay LM, Elvin JA, Vergilio J-A, Killian JK, Ramkissoon S, Severson E, Daniel S, Hammerich A, Sokol E, Frampton G, Chung J, Trabucco S, Ali S, Reddy P, Schrock AB, Miller VA, Ross JS. Comprehensive genomic profiling of carcinosarcomas of the breast [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-18.

Abstract PD8-01: CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies

Background: Typically defined by negative IHC staining for E-cadherin, classic (CILC) and pleomorphic (PILC) are often combined as a single breast cancer subtype. We queried whether patients with relapsed metastatic disease, mCILC and mPILC, would harbor contrasting genomic alterations (GA)and that molecular information could further differentiate the 2 tumor types and thereby influence therapy selection.

Methods: DNA was extracted from 40 µm of FFPE sections of 10,784 invasive breast carcinomas. 454 (4%) CDH1 mutated mILC were selected including 428 classic mCILC (94%) and 26 mPLIC (6%) subtypes. Comprehensive genomic profiling (CGP) was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth &gt;600X for up to 315 cancer-related genes. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA.

Results: mCILC and mPILC patients featured a median age of 63 years (Table). Slide based ER+ status and HER2+ status was significantly different in both groups (P&lt;0.0001). The frequency of base substitutions in ESR1 was significantly higher in mCILC, and this difference was also significantly higher in mCILC metastasis biopsies exposed to hormonal therapy than in pre-treatment primary tumors (P&lt;0.0001). ERBB2 (HER2) GA (amp + non-amp) detected by CGP were higher in mPILC than mCILC in both pre-and post-treatment samples (P&lt;0.0001 for both). The ERBB2 GA frequency was nearly twice as high after hormonal therapy in both mCILC and mPILC. ESR1 and ERBB2 GA were mutually exclusive overall and especially in the mCILC group. PIK3CA GA were the most frequent GA in both mCILC and mPILC. TP53 GA were significantly more frequent in mPILC than mCILC. At 19%, the frequency of TMB &gt; 15 mutations/MB in mPILC was more than twice as frequent than in mCILC (P=0.046). All (100%) of both the CILC and PILC groups were negative for mis-match repair deficiency or MSI high status. mCILC and mPILC patients with post primary therapy associated ESR1 and ERBB2 GA responding to targeted and immunotherapies will be presented.

Contrasting Clinical and Genomic Features of CILC and PILC Classic CILC (428 cases)Pleomorphic PILC (26 cases)Median Age6363*ER+98%74%*HER2 IHC/FISH+12 (3%)6 (22%)ESR1 GA Primary Pre-Rx6%0%ESR1 GA Metastatic Post-Rx17%0%ERBB2 GA Primary Pre-Rx7%18%ERBB2 GA Metastatic Post-Rx12%34%Other Significant GAPIK3CA (55%), CCND1 (21%), TP53 (17%), ARID1A, AKT3, MDM4, PTEN (all 11%)PIK3CA (58%), TP53 (30%), AKT1 22%), FGFR4, CCND1, PTEN (all 17%)TMB median (mut/Mb)2.73.6TMB &gt; 15%8%19%*when clinical status available

Conclusions: CGP of mCILC and mPILC reveals significant differences in the panorama of GA both in pre-treatment primary and metastatic disease lesions especially in therapy-impacting GA in ESR1 and ERBB2. mCILC is more often driven by ESR1 GA and mPILC by ERBB2 GA. Although both mCILC and mPILC feature subsets of tumors with high TMB, this is more frequent for mPILC likely indicating different potentials for immunotherapies to benefit these patients.

Citation Format: Ross JS, Chung J, Elvin JE, Vergilio J-A, Ramkissoon S, Suh J, Severson E, Daniel S, Frampton GM, Fabrizio D, Hartmaier RJ, Albacker LA, Ali SM, Schrock AB, Miller VA, Stephens PJ, Gay LM. CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies [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 PD8-01.

Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer

BACKGROUND

Genomic changes that occur in breast cancer during the course of disease have been informed by sequencing of primary and metastatic tumor tissue. For patients with relapsed and metastatic disease, evolution of the breast cancer genome highlights the importance of using a recent sample for genomic profiling to guide clinical decision-making. Obtaining a metastatic tissue biopsy can be challenging, and analysis of circulating tumor DNA (ctDNA) from blood may provide a minimally invasive alternative.

PATIENTS AND METHODS

Hybrid capture-based genomic profiling was carried out on ctDNA from 254 female patients with estrogen receptor-positive breast cancer. Peripheral blood samples were submitted by clinicians in the course of routine clinical care between May 2016 and March 2017. Sequencing of 62 genes was carried out to a median unique coverage depth of 7503×. Genomic alterations (GAs) in ctDNA were evaluated and compared with matched tissue samples and genomic datasets of tissue from breast cancer.

RESULTS

At least 1 GA was reported in 78% of samples. Frequently altered genes were TP53 (38%), ESR1 (31%) and PIK3CA (31%). Temporally matched ctDNA and tissue samples were available for 14 patients; 89% of mutations detected in tissue were also detected in ctDNA. Diverse ESR1 GAs including mutation, rearrangement and amplification, were observed. Multiple concurrent ESR1 GAs were observed in 40% of ESR1-altered cases, suggesting polyclonal origin; ESR1 compound mutations were also observed in two cases. ESR1-altered cases harbored co-occurring GAs in PIK3CA (35%), FGFR1 (16%), ERBB2 (8%), BRCA1/2 (5%), and AKT1 (4%).

CONCLUSIONS

GAs relevant to relapsed/metastatic breast cancer management were identified, including diverse ESR1 GAs. Genomic profiling of ctDNA demonstrated sensitive detection of mutations found in tissue. Detection of amplifications was associated with ctDNA fraction. Genomic profiling of ctDNA may provide a complementary and possibly alternative approach to tissue-based genomic testing for patients with estrogen receptor-positive metastatic breast cancer.

Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker

The purpose of this study is to identify prognostic markers and treatment targets using a clinically certified sequencing panel in multiple myeloma. We performed targeted sequencing of 578 individuals with plasma cell neoplasms using the FoundationOne Heme panel and identified clinically relevant abnormalities and novel prognostic markers. Mutational burden was associated with maf and proliferation gene expression groups, and a high-mutational burden was associated with a poor prognosis. We identified homozygous deletions that were present in multiple myeloma within key genes, including CDKN2C, RB1, TRAF3, BIRC3 and TP53, and that bi-allelic inactivation was significantly enriched at relapse. Alterations in CDKN2C, TP53, RB1 and the t(4;14) were associated with poor prognosis. Alterations in RB1 were predominantly homozygous deletions and were associated with relapse and a poor prognosis which was independent of other genetic markers, including t(4;14), after multivariate analysis. Bi-allelic inactivation of key tumor suppressor genes in myeloma was enriched at relapse, especially in RB1, CDKN2C and TP53 where they have prognostic significance.

Abstract P6-07-04: Comprehensive genomic profiling to assess tumor mutation burden in &gt;8,000 breast cancer cases: Implications for immunotherapy

This abstract was withdrawn by the authors.

Abstract P1-05-07: Comprehensive genomic profiling of clinically malignant phyllodes tumors of the breast reveals frequent mutation of NF1 and other genes associated with PI3K and RAS pathway activation

Background: Malignant or metastatic breast phyllodes tumors (MPT) are exceptionally rare, and the underlying genomic drivers are still being elucidated. Recent studies report frequent mutations in the RAS and PI3K pathways but have not commonly reported mutations in NF1. Comprehensive genomic profiling (CGP) can measure mutation load (TMB) and identifies all four classes of oncogenic alterations, including rearrangements and copy number loss that commonly affect tumor suppressors such as NF1, and can direct personalized treatment strategies.

Methods: CGP using hybridization capture of 3,769 exons from up to 315 cancer-related genes and select introns of 28 genes commonly rearranged in cancer was applied to ≥50ng of DNA extracted from 21 consecutive MPT and sequenced to high, uniform median coverage (&gt;400X). TMB was determined as mutations/Mb on 1.1 Mb of sequenced DNA.

Results: The 21 MPT featured a median age of 51 yrs (range 14-70 yrs). CGP was performed on the primary MPT in 15 cases and on metastasis biopsies in 6 cases. TMB for all MPT was low (&lt;10 mut/Mb), and all evaluable tumors (17/21) were microsatellite stable (MSS). The most commonly mutated genes were TP53 (57.1%), TERT (56.3%), NF1 (52.4%), MED12 (38.1%), CDKN2A/B (33.3%), and MLL2 (33.3%). 19/21 (90.5%) MPT harbored clinically relevant genomic alterations (CRGA) associated with therapies available on the market or under investigation in late stage clinical trials. Additional alterations in the PI3K/AKT/MTOR, RAS/RAF/MEK, and FGFR pathways were identified (see table); the PI3K/ATK/MTOR pathway was mutated in 10/21 (47.6%) of samples. Although CDKN2A/B loss was found in 6/11 tumors with NF1 mutation and only 1/10 NF1 wild-type samples, the co-occurrence was not significant (p&lt;0.07). No significant correlation exists between the occurrence of NF1 mutations and mutation of MED12, TERT, the PI3K pathway, or other genes in the RAS/RAF pathway (NRAS, BRAF, EGFR). Targetable KIAA1549-BRAF or FGFR3-TACC3 fusions were identified in 2/21 (9.5%) tumors. Responses to targeted treatments will be presented.

Conclusions: More than 90% of MPT feature CRGA, including alteration of NF1, which was by far the most common targetable GA in this study. 52.4% of MPT had alterations predicted to result in loss of NF1 activity. NF1 mutation does not significantly co-occur with mutations in any other gene or pathway commonly altered in MPT. Other tumors with underlying NF1 mutations have responded to the MEK inhibitor selumetinib, suggesting MEK inhibitors may be relevant for the treatment of MPT. Other targetable alterations, including known gene fusions, are common in MPT. Thus, MPT may benefit from combination targeted therapy, warranting further investigation in the clinical trial setting.

  Total Mutation NumberPathwayTotal Cases (n=21)Short VariantsCopy NumberRearrangementsRAS/RAF/MEK    NF111 (52.4%)722BRAF3 (14.3%)301NRAS2 (9.5%)300PI3K/AKT/MTOR    PIK3CA4 (19%)310PTEN4 (19%)130STK112 (9.5%)110AKT11 (4.8%)100FBXW71 (4.8%)001TSC21 (4.8%)010PIK3R11 (4.8%)100FGFR    FGFR11 (4.8%)100FGFR31 (4.8%)001Other    EGFR2 (9.5%)020BRCA21 (4.8%)100PDGFRA1 (4.8%)010KIT1 (4.8%)010

Citation Format: Gay LM, Elvin JA, Vergilio J-A, Suh J, Ramkissoon S, Ali S, Schrock A, Hirshfield K, Ganesan S, Miller VA, Stephens PJ, Ross JS. Comprehensive genomic profiling of clinically malignant phyllodes tumors of the breast reveals frequent mutation of NF1 and other genes associated with PI3K and RAS pathway activation [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 P1-05-07.

Abstract P2-12-01: Comprehensive genomic profiling of 34 cases of breast angiosarcoma

Background: Angiosarcoma of the breast (BAS) is a rare but lethal neoplasia, either arising de novo or secondary to radiation therapy, with incidence of the latter disease increasing. We queried a database of more than 70,000 advanced cancer patients assayed with comprehensive genomic profiling (CGP) in the course of clinical care to uncover the frequency, type and associated genomic alterations (GA) in BAS and to highlight possible routes to benefit from targeted therapy.

Methods: CGP was performed for 34 BAS cases using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of &gt;500X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes. RNA sequencing for 265 genes was also performed for 24 cases. Limited clinical histories from submitted pathology reports were reviewed under IRB permission.

Results: Clinical specimens from 34 BAS patients, all females, were assayed. The cases harbored 87 total GA for a mean of 2.59 per case, 25% of which were copy number amplifications. The most commonly altered genes were MYC (41%, 14/34), PIK3CA (26%, 9/34), and KDR (26%, 9/34). All MYC alterations were amplifications with a mean copy number of 39, and alterations in other MYC family members (MYCN and MYCL1) were not observed. KDR was recurrently altered as T771R (7/9) and T771K (1/9) and amplified in one case (1/9).

MYC and KDR alterations were mutually exclusive (p&lt;0.0001). 6/14 MYC amplified cases had prior histories of breast carcinoma, with 3/6 noted as being treated with radiation therapy. For the remainder of MYC amplified cases (8/14), no relevant clinical history was available.

Two cases harboring gene fusions were identified including CIC-MEGF8 and NTRK1-PEAR1. Two rearrangements of potential functional significance including CIC-DEDD2 and HT-ALK (exon1 HT - exon5-29 ALK including kinase domain) were also observed. The case harboring HT-ALK also had MYC amplification and known prior radiation therapy. Two other MYC amplified cases also harbored targetable kinase alterations, including FLT4 amplification (described as targetable in Ravi et al JNCCN 2016) and FGFR3 S249C, a known activating mutation.

Conclusions: MYC amplification defines over 40% (14/34) of advanced BAS cases. Of MYC amplified cases, 28% (4/14) harbored targetable alterations of tyrosine kinases including a potential novel ALK fusion. FLT4 amplification only co-occurred with MYC amplification, but this result was not statistically significant in this small series. KDR and MYC alteration were mutually exclusive, and 45% of non-MYC altered cases (9/20) harbored KDR alterations, which were predominantly mutations of T771. Further clinico-pathologic correlation, particularly history of radiation therapy, will be explored in this series, as well defining BAS that harbor neither MYC nor KDR alterations.

Citation Format: Ravi V, Madison R, Schrock AB, Cote G, Millis S, Alvarez R, Choy E, Katz D, Chung J, Gay L, Miller VA, Ross JS, Ali SM, Schnitt S. Comprehensive genomic profiling of 34 cases of breast angiosarcoma [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 P2-12-01.

Abstract P1-05-08: Comprehensive genomic profiling of 8,654 breast carcinoma reveals therapeutically targetable molecular subtypes beyond those defined by hormone-receptor expression

Background: Breast carcinomas (BC) are commonly classified into 4 subtypes based on hormone receptor expression: basal, luminal A, luminal B, and HER2 overexpressed. Comprehensive genomic profiling (CGP) reveals targetable genomic alterations (GA) across all four mutation classes, as well measuring tumor mutational burden (TMB), and can redefine BC classification into therapeutically relevant subtypes. Testing with immunohistochemistry or hotspot testing can miss a substantial number of targetable alterations and cannot measure TMB.

Methods: DNA was extracted from 40 µm of FFPE sections for 8654 consecutive BCs. CGP was performed on hybridization-captured, adaptor ligation-based libraries (mean coverage &gt;500X) for up to 315 cancer-related genes and select introns from up to 28 genes frequently rearranged in cancer. Sequences were analyzed for substitutions, small insertions/deletions, copy number changes, and rearrangements. TMB was determined by counting non-driver, non-germline alterations across 1.1 Mbp of sequenced DNA. Clinically relevant GA (CRGA) are GA linked to therapies on the market or under evaluation in clinical trials. Immunotherapy (IO) sensitivity is defined as TMB &gt;20 mut/Mbp or mutation of specific DNA repair pathways.

Results: The table below outlines 7 distinct functional or signal transduction pathways commonly altered in BC. Several are targetable with therapies that are FDA approved for an oncology indication. Mutations can also be found in other targetable kinases such as RET, ROS1, and RAF. 6959 (80.4%) tumors harbor a GA in at least one pathway, and 2697 (31.2%) BC harbor alterations in just one pathway (unique cases). Only 9.8% of BC would be HER2-positive by IHC. Almost 4% (352/8654) of cases harbor rearrangements or gene fusions that may not be detectable with other assays. Mutations in ESR1 characterize an eighth category of tumors with acquired resistance to endocrine therapy; 796/8654 (9%) samples harbor ESR1 alterations.

Conclusions: CGP can identify CRGA and TMB that can stratify tumors by predicted sensitivity to a variety of therapies, including HER2- or mTOR-targeted therapies, immunotherapies, and other kinase inhibitors. 80% of BC harbor targetable GA, and 30% of samples harbor mutations in only one pathway. CGP can provide crucial information for identifying which of several treatment modalities is most appropriate for these 30% of patients. High levels of TMB and most GA would not be identified by IHC or hotspot testing, but can be detected by next-generation sequencing. CGP is a powerful tool for guiding treatment across therapeutically distinct, but targetable, pathways.

 PI3K/AKT/mTOR pathwayFGFR pathwayCDK pathwayERBB pathwayHR deficientIO sensitiveOther kinasesTotal Cases43752650268512941266419424% Total Cases51%31%31%15%15%5%5%Unique Cases14422262312743094858% Unique Cases17%3%3%3%4%1%1%TherapiesEverolimus, TemsirolimusPazopanib, PonatinbPalbociclibTrastuzumab, Pertuzumab, Afatinib, Lapatinib, NeratinibOlaparibPembrolizumab, Nivolumab, Atezolizumab, IpilumumabSorafenib, Regorafenib, Dabrafenib, Vemurafenib, Crizotinib, Cabozantinib, Sunitinib

Citation Format: Ross JS, Gay LM, Elvin JA, Suh J, Vergilio J-A, Ramkissoon S, Schrock A, Ali S, Miller VA, Stephens PJ. Comprehensive genomic profiling of 8,654 breast carcinoma reveals therapeutically targetable molecular subtypes beyond those defined by hormone-receptor expression [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 P1-05-08.

Patient-derived xenotransplants can recapitulate the genetic driver landscape of acute leukemias

Genomic studies have identified recurrent somatic mutations in acute leukemias. However, current murine models do not sufficiently encompass the genomic complexity of human leukemias. To develop pre-clinical models, we transplanted 160 samples from patients with acute leukemia (AML, MLL, B-ALL and T-ALL) into immunodeficient mice. Of these, 119 engrafted with expected immunophenotype. Targeted sequencing of 374 genes and 265 frequently rearranged RNAs detected recurrent and novel genetic lesions in 48 paired primary tumor (PT) and patient-derived xenotransplant (PDX) samples. Overall, the frequencies of 274 somatic variant alleles correlated between PT and PDX samples, although the data were highly variable for variant alleles present at 0-10%. 17% of variant alleles were detected in either PT or PDX samples only. Based on variant allele frequency changes, 24 PT-PDX pairs were classified as concordant while the other 24 pairs showed various degree of clonal discordance. There was no correlation of clonal concordance with clinical parameters of diseases. Significantly more bone marrow samples than peripheral blood samples engrafted discordantly. These data demonstrate the utility of developing PDX banks for modeling human leukemia, and emphasize the importance of genomic profiling of PDX and patient samples to ensure concordance before performing mechanistic or therapeutic studies.

Comprehensive genomic profiling of anal squamous cell carcinoma reveals distinct genomically defined classes

BACKGROUND

Squamous cell cancers of the anal canal (ASCC) are increasing in frequency and lack effective therapies for advanced disease. Although an association with human papillomavirus (HPV) has been established, little is known about the molecular characterization of ASCC. A comprehensive genomic analysis of ASCC was undertaken to identify novel genomic alterations (GAs) that will inform therapeutic choices for patients with advanced disease.

PATIENTS AND METHODS

Hybrid-capture-based next-generation sequencing of exons from 236 cancer-related genes and intronic regions from 19 genes commonly rearranged in cancer was performed on 70 patients with ASCC. HPV status was assessed by aligning tumor sequencing reads to HPV viral genomes. GAs were identified using an established algorithm and correlated with HPV status.

RESULTS

Sixty-one samples (87%) were HPV-positive. A mean of 3.5 GAs per sample was identified. Recurrent alterations in phosphoinositol-3-kinase pathway (PI3K/AKT/mTOR) genes including amplifications and homozygous deletions were present in 63% of cases. Clinically relevant GAs in genes involved in DNA repair, chromatin remodeling, or receptor tyrosine kinase signaling were observed in 30% of cases. Loss-of-function mutations in TP53 and CDKN2A were significantly enhanced in HPV-negative cases (P < 0.0001).

CONCLUSIONS

This is the first comprehensive genomic analysis of ASCC, and the results suggest new therapeutic approaches. Differing genomic profiles between HPV-associated and HPV-negative ASCC warrants further investigation and may require novel therapeutic and preventive strategies.

Abstract P6-03-12: Comprehensive genomic profiling of clinically advanced mucinous carcinoma of the breast

Background: Mucinous carcinoma of the breast (mucBC) is generally associated with a favorable prognosis, but on occasion, may have an aggressive clinical course in which it is commonly refractory to cytotoxic chemotherapy. The low incidence of mucBC (∼2% of breast cancers) precludes the development of consensus based guidelines for management of these relapsed/refractory cases. We performed hybrid-capture based comprehensive genomic profiling (CGP) to identify potential therapy targets not routinely searched for in clinical management of metastatic mucBC.

Methods: DNA was extracted from 40 microns of FFPE sections from 22 cases of stage IV mucBC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation based next generation sequencing assay to a mean coverage depth of &gt;550X. The results were analyzed for all classes of genomic alterations (GA) including base substitutions, insertions and deletions, select rearrangements, and copy number changes. Clinically relevant genomic alterations (CRGA) were defined as those identifying anti-cancer drugs on the market or in registered clinical trials.

Results: The median age of the 22 mucBC patients was 57 years (range 32 to 79 years). Samples were from breast (11), lymph nodes (3), chest wall (2), liver (2), soft tissue (2), bone (1) and pleura (1). Three mucBC were grade 1, 17 were grade 2 and 2 were grade 3. Twenty-one (95%) mucBC were ER+, 19 (86%) were PR+ and 4 (18%) were HER2+ by IHC and/or FISH. There were 129 GA identified on the 22 mucBC (5.9 per tumor) including 51 CRGA with a mean of 2.3 per tumor. Amplifications of FGFR1 and ZNF703 were found in 8 out of 22 cases (36%) on the same amplicon. Other most frequently altered genes were TP53 (32%), CCND1 and FGF3/4/19 often co-amplified together (27%). ERBB2/HER2 alterations were found on 5 cases (23%) including amplifications on all 4 HER2+ cases by IHC and/or FISH, and ERBB2 substitution D769Y on one additional mucBC. CRGA were found on some other 20 genes included PIK3CA (5), BRCA1 (1), TSC2 (1), STK11 (1), AKT3 (1), and ESR1 (1).

Conclusions: The subset of relapsed/refractory mucBC presents a management challenge, but comprehensive genomic profiling offers avenues for benefit from targeted therapy. MucBC relative to breast cancer is predominantly ER+, enriched for FGFR1 amplification, 36% vs 11% from TCGA ER+ breast cancer (N=601) with Fisher's test p-value &lt;0.005. Moreover, metastatic mucBC appears more often to have ERBB2/HER2 alterations (23%) than typical mucBC cured by local treatments. Comprehensive genomic profiling uncovers a variety of genomic targets in metastatic mucBC that could facilitate the introduction of targeted therapies for patients with this challenging disease.

Citation Format: Wang K, Ali SM, Khaira D, Elvin JA, Vergilio J-A, Suh J, Yelensky R, Lipson D, Chmielecki J, Miller VA, Stephens PJ, Ross JS. Comprehensive genomic profiling of clinically advanced mucinous carcinoma of the breast. [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 P6-03-12.

Abstract P3-07-05: Non-amplification ERBB2 genomic alterations in 5,605 cases of refractory and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies

Background: Non-amplification ERBB2 alterations (ERBB2 mut) in advanced/metastatic breast cancer (mBC) are not detected by IHC or FISH, but when detected by DNA sequencing assays can lead to clinical responses to anti-HER2 targeted therapy. We queried a database of more than 43,000 clinical cases to uncover the frequency, type and associated genomic alterations (GA) in mBC driven by ERBB2 mut and highlight clinical responses to small molecule drug and antibody-based anti-HER2 therapeutics.

Methods: DNA was extracted from 40 microns of FFPE sections from 5,605 mBC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of &gt;600X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes.

Results: 698 (12.5%) of 5,605 mBC featured ERBB2 alterations. 596 (10.6%) featured ERBB2 amplifications and 137 (2.4%) featured ERBB2mut. 35 (0.6%) of total mBC had both ERBB2amp and ERBB2mut, which accounted for 5.0% of all ERBB2 altered mBC. The 137 ERBB2mut mBC cases had a median age of 61 years (range 29 to 93 years) and were sequenced to a mean depth of 600X. Samples utilized for CGP included 52 (38%) from the patient's primary BC and 85 (62%) from metastatic sites including bone/soft tissue/skin (12%), liver (20%), LN (14%), serous cavities (6%), lung (4%) and miscellaneous sites (6%). 71 (52%) mBC were submitted as carcinoma NOS, 44 (32%) as IDC, 22 (16%) as ILC and 1 (1%) as mucinous mBC. Of the 137 ERBB2mut cases, 8 featured more than 1 ERBB2 mut. There were 124 (85%) ERBB2 kinase domain mutations and 15 (10%) extra-cellular domain ERBB2mut. The most common genes co-altered in ERBB2mut mBC were TP53 (49%), PIK3CA (42%), CDH1 (37%), MYC (17%), and CCND1 (16%). The enrichment of ERBB2mut in CDH1 mut mBR was significant (p=0.0006) and associated with relapsed lobular mBC. Multiple case examples of kinase domain and extra-cellular domain ERBB2mut mBC responding to a variety of anti-HER2 targeted therapies will be presented.

Conclusions: In this large series of 5,605 mBC, 20% of the total ERBB2 alterations were non-amplification ERBB2mut not detectable by standard of care IHC and FISH slide-based HER2 tests. Given the demonstration of ERBB2mut driven mBC responsive to anti-HER2 targeted therapies in this study, expansion of clinical trials designed to detect these ERBB2mut cases with CGP and optimize the targeted therapies for these patients is strongly recommended.

Citation Format: Ross JS, Wang K, Ali SM, Chumsri S, Elvin JA, Vergilio J-A, Suh J, Yelensky R, Lipson D, Chmielecki J, Miller VA, Stephens PJ. Non-amplification ERBB2 genomic alterations in 5,605 cases of refractory and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies. [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 P3-07-05.

Abstract P6-07-06: Clinicopathologic characterization and comprehensive genomic profiling (CGP) of advanced breast cancer patients with fibroblast growth factor receptor (FGFR) alterations

BACKGROUND: FGFR family members are infrequently mutated but are frequently overexpressed in breast cancer and often accompanied by increased, or altered, expression of FGF ligands. In this retrospective study, we reviewed a large series of FGFR altered breast cancer cases that received comprehensive genomic profiling (CGP) in the course of clinical care.

MATERIAL AND METHODS: CGP was performed on hybridization-captures, adaptor ligation-based libraries using DNA extracted from 40 μm formalin-fixed paraffin-embedded (FFPE) section cut at 10 μm performed in a CLIA-certified lab (Foundation Medicine, Inc.). The pathologic diagnosis of each case was confirmed on routine hematoxylin and eosin-stained slides, and all samples forwarded for DNA extraction contained a minimum of 20% of DNA derived from tumor cells. The FoundationOne test sequences the full coding regions of up to 315 cancer-related genes, and up to 28 genes that are frequently altered in cancer to detect all classes of genomic alterations including base substitutions, indels, copy-number alterations (CNA), and fusions/rearrangements. The average depth of coverage is greater than 600X. The genomic profiles of 2,617 patients with diverse advanced malignancies who were evaluated at Cancer Treatment Centers of America between 12/24/12 and 03/11/15 were reviewed. 176 FGFR alterations (7.8%) were detected, of which 76 (43.5%) were found in breast cancer cases out of 434 (16.5%). The study was carried out in accordance with WIRB Institutional Review Board.

RESULTS: A total of 76 female breast cancer patients, having a median age 50 (range, 28-69), with FGFR alterations were reviewed. All patients had metastatic/relapsed advanced breast cancer. 54 patients were Estrogen Receptor-positive (70%), and 15 were HER2+ (20%). 6 patients had gBRCA deleterious mutations. 84% of the samples (n=67) tissue block were analyzed, and the anatomic sites represented by the samples were 24 breast primary tumor (31%), 15 liver (19%), 10 lymph nodes (13%), and other sites (37%). The median number of chemotherapies cycles was 4 (range, 1-12), and the median time to metastasis was 31 months (range, 0-175). At the time of this report, 31 patients (40%) were deceased. 79 FGFR gene alterations were identified in 76 patients, including FGFR1 (65), FGFR2 (6), FGFR3 (2), and FGFR4 (4), with all but 7 of these being amplifications. The most co-existent altered gene was TP53 (66%), and other altered genes included PIK3CA (37%), MYC (28%), FGF3/4/19 (17%), CCND1 (17%), and CCNE1 (16%). The subset of co-amplified FGF3/4/19 and FGFR amplified patients were all (7) ER+ except for 1 patient.

CONCLUSIONS: FGFR genomic alterations in breast cancer patients are predominantly amplifications and are most commonly observed in ER+ patients. Further review of treatment history will be performed to evaluate the hypothesis that alterations of FGFR is a modifier of response to endocrine therapy, and co-amplified FGF3/4/19 and FGFR breast cancer cases may be a distinct clinic-pathologic entity. Any patients in this series initiated on anti-FGFR targeted therapy will also be reported.

Citation Format: Alvarez RH, Thomas JW, Kramer K, Niu J, Ahn E, McKnight JE, Dhillon N, Pabbathi H, Johnson AT, Wang K, Ross JS, Miller VA, Stephens PJ, Daneker GW, Ali S, Markman M. Clinicopathologic characterization and comprehensive genomic profiling (CGP) of advanced breast cancer patients with fibroblast growth factor receptor (FGFR) alterations. [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 P6-07-06.

Abstract A32: MCL1 gene amplification in breast cancer is associated with TNBC status and can respond to a sorafenib/vorinostat regimen

Background: MCL1 encodes the induced myeloid leukemia cell differentiation protein Mcl-1, a member of the BCL-2 family which functions to inhibit apoptosis. Mcl-1 over-expression has been associated with high tumor grade and adverse prognosis in triple negative breast cancer (TNBC) but therapies specifically leading to inhibition of MCL-1 have not been identified.

Methods: Comprehensive genomic profiling (CGP) using hybridization capture of 3,769 exons from 315 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer was applied to ≥50ng of DNA extracted from 2,824 consecutive BC and sequenced to high, uniform median coverage (&gt;600X). The original primary BC was assayed in 44% of cases and a sample from a metastatic focus was assayed in 56% of cases.

Results: Of 2824 consecutive BC cases, 200 (7.1%) cases harbored MCL1 amplification. Of these MCL1-amplified cases, 146 (73%) were TNBC and 54 were non-TNBC (p&lt;0.0001). Twelve of the latter cases (22%) were ERBB2 (HER2) amplified and slide-based HER2 status concordance with CGP was 99%. MCL1 amplification was also observed in the TCGA dataset for 32/123 (26%) of TNBC (p=0.008). Of the MCL1 amplified TNBC cases, 88% were high grade and 98% were stage IV at the time of CGP. Genes co-altered within MCL1 amplified TNBC included TP53 (86%), MYC (41%), MYST3 (21%), LYN (20%), CCNE1 (19%), PIK3CA (18%), and AKT3 (15%). Two MCL1 amplified TNBC patients were treated with a multi-drug regimen based on sorafenib and vorinostat and experienced significant clinical benefit.

Conclusions: MCL1 amplification is a frequent feature in advanced stage and high grade TNBC, and correspondingly such MCL1 amplified tumors very seldom harbor co-amplifications of ERBB2. Clinical observation suggests that treatment with sorafenib and vorinostat in heavily pre-treated MCL1 amplified patients may be correlated with clinical benefit, consistent with historic preclinical investigation. These preliminary findings suggest that MCL1 amplified TNBC may be able to benefit from combination targeted therapy, and warrant further systematic investigation.

Citation Format: JS Ross, K Wang, A Johnson, J Watson, C Hatzis, L Pusztai, J Chmielecki, R Yelensky, D Lipson, JA Elvin, J Vergilio, J Suh, VA Miller, K Dicke, PJ Stephens, SM Ali. MCL1 gene amplification in breast cancer is associated with TNBC status and can respond to a sorafenib/vorinostat regimen. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A32.

Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing

BACKGROUND

To determine genomic alterations in head and neck squamous cell carcinoma (HNSCC) using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine clinical practice, selected cancer-related genes were evaluated and compared with alterations seen in frozen tumors obtained through research studies.

PATIENTS AND METHODS

DNA samples obtained from 252 FFPE HNSCC were analyzed using next-generation sequencing-based (NGS) clinical assay to determine sequence and copy number variations in 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. Human papillomavirus (HPV) status was determined by presence of the HPV DNA sequence in all samples and corroborated with high-risk HPV in situ hybridization (ISH) and p16 immunohistochemical (IHC) staining in a subset of tumors. Sequencing data from 399 frozen tumors in The Cancer Genome Atlas and University of Chicago public datasets were analyzed for comparison.

RESULTS

Among 252 FFPE HNSCC, 84 (33%) were HPV positive and 168 (67%) were HPV negative by sequencing. A subset of 40 tumors with HPV ISH and p16 IHC results showed complete concordance with NGS-derived HPV status. The most common genes with genomic alterations were PIK3CA and PTEN in HPV-positive tumors and TP53 and CDKN2A/B in HPV-negative tumors. In the pathway analysis, the PI3K pathway in HPV-positive tumors and DNA repair-p53 and cell cycle pathways in HPV-negative tumors were frequently altered. The HPV-positive oropharynx and HPV-positive nasal cavity/paranasal sinus carcinoma shared similar mutational profiles.

CONCLUSION

The genomic profile of FFPE HNSCC tumors obtained through routine clinical practice is comparable with frozen tumors studied in research setting, demonstrating the feasibility of comprehensive genomic profiling in a clinical setting. However, the clinical significance of these genomic alterations requires further investigation through application of these genomic profiles as integral biomarkers in clinical trials.

Next-generation sequencing reveals frequent consistent genomic alterations in small cell undifferentiated lung cancer

Aims

Small cell lung cancer (SCLC) carries a poor prognosis, and the systemic therapies currently used as treatments are only modestly effective, as demonstrated by a low 5-year survival at only ∼5%. In this retrospective collected from March 2013 to study, we performed comprehensive genomic profiling of 98 small cell undifferentiated lung cancer (SCLC) samples to identify potential targets of therapy not currently searched for in routine clinical practice.

Methods

DNA from 98 SCLC was sequenced to high, uniform coverage (Illumina HiSeq 2500) and analysed for all classes of genomic alterations.

Results

A total of 386 alterations were identified for an average of 3.9 alterations per tumour (range 1–10). Fifty-two (53%) of cases harboured at least 1 actionable alteration with the potential to personalise therapy including base substitutions, amplifications or homozygous deletions in RICTOR (10%), KIT (7%), PIK3CA (6%), EGFR (5%), PTEN (5%), KRAS (5%), MCL1 (4%), FGFR1 (4%), BRCA2, (4%), TSC1 (3%), NF1 (3%), EPHA3 (3%) and CCND1. The most common non-actionable genomic alterations were alterations in TP53 (86% of SCLC cases), RB1 (54%) and MLL2 (17%).

Conclusions

Greater than 50% of the SCLC cases harboured at least one actionable alteration. Given the limited treatment options and poor prognosis of patients with SCLC, comprehensive genomic profiling has the potential to identify new treatment paradigms and meet an unmet clinical need for this disease.

Next-generation sequencing of adrenocortical carcinoma reveals new routes to targeted therapies

Aims

Adrenocortical carcinoma (ACC) carries a poor prognosis and current systemic cytotoxic therapies result in only modest improvement in overall survival. In this retrospective study, we performed a comprehensive genomic profiling of 29 consecutive ACC samples to identify potential targets of therapy not currently searched for in routine clinical practice.

Methods

DNA from 29 ACC was sequenced to high, uniform coverage (Illumina HiSeq) and analysed for genomic alterations (GAs).

Results

At least one GA was found in 22 (76%) ACC (mean 2.6 alterations per ACC). The most frequent GAs were in TP53 (34%), NF1 (14%), CDKN2A (14%), MEN1 (14%), CTNNB1 (10%) and ATM (10%). APC, CCND2, CDK4, DAXX, DNMT3A, KDM5C, LRP1B, MSH2 and RB1 were each altered in two cases (7%) and EGFR, ERBB4, KRAS, MDM2, NRAS, PDGFRB, PIK3CA, PTEN and PTCH1 were each altered in a single case (3%). In 17 (59%) of ACC, at least one GA was associated with an available therapeutic or a mechanism-based clinical trial.

Conclusions

Next-generation sequencing can discover targets of therapy for relapsed and metastatic ACC and shows promise to improve outcomes for this aggressive form of cancer.

Abstract S3-06: Emergence of constitutively active estrogen receptor mutations in advanced estrogen receptor positive breast cancer

Introduction: The lack of estrogen receptor (ER) expression is the primary cause of de novo resistance of breast cancers to endocrine therapy. In contrast, in most cases of acquired endocrine resistance, ER is expressed and other mechanisms of resistance have been proposed, such as ER mutations. Pre-clinical studies demonstrated a small number of specific point mutations that can enhance ER function. However, the studies on clinical samples performed in the 1990's were limited by small sample size, lack of detailed clinical correlation and lacked the sensitivity of next-generation sequencing (NGS). Therefore, in this study we sought to comprehensively investigate the frequency and functional significance of ER mutations throughout the progression of breast cancer from primary disease to advanced metastatic disease using targeted NGS.

Methods: In this retrospective study, a total of 249 tumor specimens were analyzed. The specimens include 134 ER positive and, as controls, 115 estrogen receptor negative tumors. The estrogen receptor positive samples consist of 58 primary breast cancers and 76 metastatic sample. All tumors were sequenced with high coverage using NGS targeting the coding sequence of ER and an additional 181 cancer-related genes.

Results: Recurring somatic mutations at codons 537 and 538 within the ligand-binding domain of the estrogen receptor were detected in ER positive metastatic tumors. Overall, the frequency of these mutations was 12% (95% CI 6%-21%) in metastatic patients compared with none in the primary cases. In total there were 9 recurring somatic mutations; Y537C (11%), Y537N (33%), Y537S (22%) and D538G (33%). In addition in a small number of paired primary and metastatic samples from the same patient, these mutations were found only in the metastatic specimens. In a subset of heavily pre-treated patients the frequency was 20% (5/25, 95% CI 7%-41%). ER activating mutations were not detected in any stage of ER negative disease. ER alterations were not mutually exclusive with any of the other commonly altered genes and of the most frequently altered genes, all but ER alterations displayed similar frequencies across primary and metastatic specimens. Functional studies in cell line models demonstrated that these ER mutations render ER constitutively active and confer resistance to hormone deprivation, tamoxifen and fulvestrant.

Conclusions: Herein, we reveal functional ER mutations as potential drivers of endocrine resistance during the progression of ER positive breast cancer. The absence of detectable mutations in the primary tumors suggests clonal evolution as the mechanism of resistance. Thus, these mutations have the potential to be an important genetic biomarker of endocrine resistance in ER positive metastatic breast cancer and could assist in clinical decision making as disease progresses. Our findings also underscore the value of repeated biopsies of metastatic lesions. Lastly, since the frequencies of these mutations are substantial when sensitive testing methods are used in the correct clinical context, pre-clinical and clinical studies to identify novel therapeutics that can overcome this resistance are warranted.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S3-06.

Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer

We identified novel gene fusions in patients with lung cancer harboring the kinase domain of the NTRK1 gene that encodes the TRKA receptor. Both the MPRIP-NTRK1 and CD74-NTRK1 fusions lead to constitutive TRKA kinase activity and are oncogenic. Treatment of cells expressing NTRK1 fusions with inhibitors of TRKA kinase activity inhibited autophosphorylation of TRKA and cell growth. Three of 91 lung cancer patients (3.3%), without known oncogenic alterations, assayed by NGS or FISH demonstrated evidence of NTRK1 gene fusions.

Comprehensive genomic profiling of epithelial ovarian cancer by next generation sequencing-based diagnostic assay reveals new routes to targeted therapies

OBJECTIVE

Targeted next generation sequencing (NGS) was evaluated for its ability to identify unanticipated targetable genomic alterations (GA) for patients with relapsed ovarian epithelial carcinoma (OC).

METHODS

DNA sequencing was performed for 3320 exons of 182 cancer-related genes and 37 introns of 14 genes frequently rearranged in cancer on indexed, adaptor ligated, hybridization-captured libraries using DNA isolated from FFPE sections from 48 histologically verified relapsed OC specimens. The original primary tumor was sequenced in 26 (54%) of the cases and recurrent/metastatic tumor site biopsies were sequenced in 22 (46%) of the cases. Actionability was defined as: GA that predict sensitivity or resistance to approved or standard therapies or are inclusion or exclusion criteria for specific experimental therapies in NCI registered clinical trials.

RESULTS

There were 38 (80%) serous, 5 (10%) endometrioid, 3 (6%) clear cell, 1 mucinous (2%) and 1 (2%) undifferentiated carcinomas. 141 GA were identified with an average of 2.9 GA (range 0-8) per tumor, of which 67 were actionable for an average of 1.4 actionable GA per patient (range 0-5). 33/48 (69%) of OC patient samples harbored at least one actionable GA. Most common GA were TP53 (79%); MYC (25%); BRCA1/2 (23%); KRAS (16.6%) and NF1 (14.5%). One tumor featured an ERBB2 point mutation. One of 3 (33%) of clear cell tumors featured cMET amplification validated by both FISH and IHC.

CONCLUSIONS

NGS assessment of therapy resistant OC identifies an unexpectedly high frequency of GA that could influence targeted therapy selection for the disease.

Abstract S3-6: Profiling of triple-negative breast cancers after neoadjuvant chemotherapy identifies targetable molecular alterations in the treatment-refractory residual disease

Background: Neoadjuvant chemotherapy (NAC) is increasingly used in patients with triple-negative breast cancer (TNBC). NAC can induce a pathologic complete response (pCR) in ∼30% of patients which portends a favorable prognosis. In contrast, patients with residual disease (RD) in the breast at surgical resection exhibit worse outcomes.

Objective: We hypothesized that profiling residual TNBCs after NAC would identify molecularly targetable lesions in the chemotherapy-resistant component of the tumor and that the persistent tumor cells would mirror micro-metastases which ultimately recur in such patients.

Methods: We utilized targeted next generation sequencing (NGS) for 182 oncogenes and tumor suppressors in a CLIA certified lab (Foundation Medicine, Cambridge, MA) and gene expression profiling (NanoString) of the RD after NAC in 102 patients with TNBC. The RD was stained for Ki67, which has been reported to predict outcome after NAC in unselected breast cancers.

Results: Thirteen tumors were not evaluable due to low tumor cellularity. Of 89 evaluable post-NAC tumors, 57 (64%) were basal-like; 19% HER2-enriched; 6% luminal A; 6% luminal B and 5% normal-like. Mean depth of coverage was 635 (range: 135–1207). Of 81 tumors evaluated by NGS, 72/81 (89%) demonstrated mutations in TP53, 22 were MCL1-amplified (27%), and 17 were MYC-amplified (21%). Alterations in the PI3K/mTOR pathway (AKT1-3, PIK3CA, PIK3R1, RAPTOR, PTEN, and TSC1) were identified in 27 tumors (33%). Cell cycle genes were altered in 25 tumors (31%), including amplifications of CDK2, CDK4, and CDK6, CCND1-3, and CCNE1 as well as RB loss. Alterations in the DNA repair pathway (BRCA1/2, ATM; 16 tumors; 20%) and the Ras/MAPK pathway (KRAS, RAF1, NF1; 10 tumors; 12%) were also common. Sporadic growth factor receptor amplifications occurred in EGFR, KIT, PDGFRA, PDGFRB, MET, FGFR1, FGFR2, and IGF1R. NGS identified 7 patients with ERBB2 gene amplification in the RD which was confirmed by FISH in both the pre- and post-treatment tissue, suggesting NGS could assist in the identification of ERBB2-overexpressing tumors misclassified at the time of diagnosis. In general, the gene amplifications identified by NGS corresponded to enhanced gene expression levels. Amplifications of MYC were independently associated with poor recurrence-free survival (RFS) and overall survival (OS). An interaction effect on survival was observed between MEK activation (assayed by a gene expression signature) and MYC amplification, suggesting cooperation between these pathways. Alterations in DNA repair also identified a subgroup with poor RFS and OS. In contrast, high post-NAC Ki67 score did not predict poor RFS or OS in this predominantly TNBC cohort.

Conclusions: The diversity of lesions in residual TNBCs after NAC underscores the need for powerful and broad molecular approaches to identify actionable molecular alterations and, in turn, better inform personalized therapy of this aggressive disease. Incorporation of this platform into clinical studies and eventually standards of care should aid in the prioritization of patients with RD after NAC into rational adjuvant studies.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S3-6.

A randomized, double-blind, placebo-controlled, phase IIIb trial (ATLAS) comparing bevacizumab (B) therapy with or without erlotinib (E) after completion of chemotherapy with B for first-line treatment of locally advanced, recurrent, or metastatic non-small cell lung cancer (NSCLC)

LBA8002

Background: B when added to chemotherapy, and E alone, each lead to improved survival in the treatment of patients (pts) with NSCLC (Sandler et al, NEJM 2006, 355:2542–2550; Shepherd et al, NEJM 2005, 353:123–132). Pre-clinical and clinical data (Herbst, J Clin Oncol 2007, 25: 4743–4750) suggest that the combination of B and E may improve the efficacy of NSCLC treatment. This potential was demonstrated in the BETA (B in combination with E compared with E alone for treatment of advanced NSCLC after failure of standard first-line chemotherapy) trial, a phase III trial in which progression free survival (PFS) was improved for patients treated with B + E (Hainsworth, Thoracic Oncol 2008, 3(11) Supp. 4:S302). Methods: The ATLAS study was designed to evaluate B + E (150 mg daily) versus B alone, following B + platin-containing doublet chemotherapy, in pts with stage IIIb/IV NSCLC. Enrolled pts were B-eligible, including pts with treated brain metastases, and pts anticoagulated with low molecular weight heparin(s). Pts with peripheral and/or extra-thoracic squamous tumors were also eligible. Pts received 4 cycles of B (15 mg/kg every 3 weeks) with chemotherapy. Pts who had not experienced disease progression (DP) or significant toxicity were then randomized to receive B + E or B + placebo (P). The primary objective of ATLAS was to compare PFS in pts receiving B + E versus B + placebo. Secondary objectives included the assessment of safety, and overall survival. A data safety monitoring committee (DSMC) monitored safety and efficacy. Results: 1,160 patients were enrolled and 768 randomized from May 2005 to May 2008. The DSMC recommended stopping the trial at the second planned interim efficacy analysis, because it met the primary endpoint. The median PFS after randomization was 4.8 mos for (B + E) vs. 3.7 mos for (B + P), HR= 0.722 (95% CI: 0.592–0.881), p = 0.0012. The safety profile for B + E was consistent with known profiles for B and E. Conclusions: E added to B treatment after chemotherapy with B significantly improves the PFS of patients treated in the first-line setting for locally advanced, recurrent, or metastatic NSCLC.

[Table: see text]

A randomized, double-blind, placebo-controlled, phase IIIb trial (ATLAS) comparing bevacizumab (B) therapy with or without erlotinib (E) after completion of chemotherapy with B for first-line treatment of locally advanced, recurrent, or metastatic non-small cell lung cancer (NSCLC)

LBA8002

The full, final text of this abstract will be available in Part II of the 2009 ASCO Annual Meeting Proceedings, distributed onsite at the Meeting on May 30, 2009, and as a supplement to the June 20, 2009, issue of the Journal of Clinical Oncology.

[Table: see text]

Rebiopsy of patients (pts) with acquired resistance to epidermal growth factor tyrosine kinase inhibitors (EGFR-TKIs) in non-small cell lung cancer (NSCLC)

8025

Background: The EGFR-TKIs erlotinib and gefitinib produce dramatic regressions of tumor in ∼ 70% of NSCLC patients with activating mutations in the EGFR-TK domain. After a median time to progression of ∼1 year, most pts have progressive disease. We undertook this study to search for mechanisms of “acquired resistance” to EGFR-TKIs, to determine the spectrum and frequency of secondary EGFR mutations which arose, and to determine the feasibility of rebiopsy in this setting. Methods: All pts had metastatic or recurrent NSCLC and prior treatment with EGFR-TKI and progressive disease while on EGFR-TKI. Pts must also have had an activating EGFR mutation OR radiographic response (RECIST or WHO) to EGFR-TKI OR significant and durable improvement in cancer-related symptoms as judged by patient's physician. Core biopsies were performed and studied for EGFR mutation (exons 18–21 including PCR-based test for T790M) and MET amplification. Results: From 8/04–12/08 98 pts were consented for rebiopsy and 85 underwent the procedure. Demographics Female/Male=59/39; median age 62 (range 28–88); smoking: never=59, former/current=39. Primary EGFR mutation was exon 19 del-39; exon 21 L858R-11, other/WT-28, pending-7. Median time on EGFR-TKI before biopsy was 12 months (7–28 months). Secondary EGFR mutations: T790M-33, other-2, none detected-31, indeterminate-10, pending-9. MET amplification in 2/16 studied to date. Conclusions: 1) Rebiopsy of patients with NSCLC and acquired resistance to EGFR TKIs is feasible and well-received by pts. 2) Knowledge of EGFR genotype including EGFR T790M and MET status can inform clinical trials of targeted therapies in this population 3) More complete annotation of MET status and exploratory analyses of profiles of specimens by metastatic sites and prior EGFR-TKI versus chemo and EGFR-TKI is ongoing. Supported by the Doris Duke Foundation, the LaBrecque Foundation, Steps for Breath, NIH, and an anonymous donor.

No significant financial relationships to disclose.

A phase II trial of salirasib in patients with stage IIIB/IV lung adenocarcinoma enriched for KRAS mutations

8012

Background: KRAS mutations are present in 30% of lung adenocarcinomas and are associated with primary resistance to erlotinib and gefitinib. Salirasib severs RAS proteins from the membrane, decreasing function of all RAS isoforms. Salirasib inhibits KRAS-dependent growth in cell lines and xenograft models. This phase II study was designed to determine the activity of salirasib in patients (pts) with advanced NSCLC enriched for KRAS mutations. Methods: Two cohorts of pts with stage IIIB/IV NSCLC were eligible. Group A: pts with KRAS mutations previously treated with chemotherapy. Group B: previously-untreated pts with ≥15 pack-year smoking history. Salirasib was given orally, for days 1–28 of a 35 day cycle, with response assessment on day 28, day 63, and every 10 weeks (wks) thereafter. The primary endpoint was rate of RECIST non-progression at 10 wks. Secondary endpoints were response rate (RR), time to progression (TTP), overall survival (OS) and toxicity. Results: From August 2007-December 2008, 33 pts were enrolled (20 women); median age 68 (range 46–79). Pts in Group A had received a median of 2 lines of prior chemotherapy. All 23 pts in Group A and 7/10 pts in Group B had KRAS mutations. Of the 30 pts with KRAS mutations, 7 were never smokers or smoked ≤15 pack-years. Three pts withdrew due to drug-related diarrhea in the first 10 wks of therapy. Four pts have not reached 10 wks of therapy. After 10 wks of salirasib, 5/18 (28%) previously treated pts with KRAS mutations and 3/8 (38%) previously untreated pts showed no progression. The RR in pts was 0/18 for Group A and 0/8 in Group B. For all pts with KRAS mutations, the RR was 0/23. The median TTP was 1 month (mo) and 2 mo in Groups A and B, respectively. The median OS was 13 mo for Group B and not reached in Group A (median follow-up 3 mo). Grade 3 diarrhea and fatigue were the most common toxicities. Conclusions: After 10 wks of salirasib, 28% of previously treated pts with KRAS mutations and 38% of untreated pts had stable disease. No partial or complete responses were seen in pts with KRAS mutations. The successful enrollment over 15 months of 29 pts with tumors with known KRAS mutations demonstrates that trials of a KRAS-specific genotype in lung cancer are feasible, and should be standard in future studies targeting the KRAS pathway.

[Table: see text]

Impact on disease-free survival of adjuvant erlotinib or gefitinib in patients with resected lung adenocarcinomas that harbor epidermal growth factor receptor (EGFR) mutations

7523

Background: Patients with stage IV adenocarcinoma whose tumors harbor EGFR mutations have high rates of response (∼ 75%) and prolonged progression free survival after EGFR tyrosine kinase inhibitor (TKI) treatment. Adjuvant cisplatin-based chemotherapy improves disease free survival (DFS) and overall survival (OS) in patients with resected stages IB-IIIA NSCLC. To see if adjuvant treatment with EGFR TKI (gefitinib or erlotinib) improves DFS in patients with EGFR mutation NSCLC, we conducted a retrospective review of patients with resected lung adenocarcinoma harboring EGFR mutations, some of whom received EGFR TKIs postoperatively. Methods: With Institutional Review Board approval, clinical information was obtained on all patients with stage I-III lung adenocarcinoma harboring EGFR exon 19 or 21 mutations that underwent resection at MSKCC between May 2002 and August 2008. Age, gender, type of surgery, histology, EGFR mutation status (exon 19 deletions and exon 21 L858R), stage, perioperative therapy and survival were recorded. Kaplan-Meier analysis and Cox regression analysis were performed. Results: We studied 150 patients (112 women, 38 men) with completely resected stage I-III lung adenocarcinoma whose resection specimens contained EGFR activating mutations in exon 19 or 21. Median age was 69. Forty two patients (28%) received cytotoxic chemotherapy. Forty eight (32%) received either erlotinib (n=26) or gefitinib (n=22) postoperatively. The median time on TKI was 16 months. The median DFS was 43 months in the group that received a TKI vs. 31 months for those that did not. After controlling for stage, individuals who received adjuvant gefitinib or erlotinib had a better DFS (HR=0.38, 95%CI: 0.16–0.90) than the non-TKI group (p=0.03). The median overall survival has not been reached. Conclusions: These data indicate that the adjuvant use of either gefitinib or erlotinib improves DFS in patients with completely resected stage I -III lung adenocarcinomas with mutations in EGFR exons 19 and 21. These data justify a randomized trial in similar patients.

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A phase II study of BIBW 2992, a novel irreversible dual EGFR and HER2 tyrosine kinase inhibitor (TKI), in patients with adenocarcinoma of the lung and activating EGFR mutations after failure of one line of chemotherapy (LUX-Lung 2)

8013

Background: EGFR mutations are associated with exquisite sensitivity to EGFR TKIs in NSCLC. A phase II trial evaluating the efficacy of BIBW 2992 (Tovok), a novel, potent, irreversible, dual EGFR and HER2 TKI with preclinical activity in cell lines harboring activating (H3255, IC50=0.7 nM) and resistant (H1975, IC50=99 nM) EGFR mutations, is reported. Methods: Objective response rate is the primary endpoint of this 2-stage trial. Based on 16 or more unconfirmed PRs in an interim analysis of the first 40 2nd line patients (pts) completing 1 course (28 days), accrual will continue to a total of 120 1st and 2nd line pts (expected completion of accrual by May 2009. Data on 2nd line pts only are presented). Eligible pts have stage IIIB/IV lung adenocarcinoma, EGFR mutation in exons 18–21 (tested by direct sequencing), measurable disease, ECOG PS 0–2 and adequate end organ function. Pts receive 50 mg BIBW 2992 qd until progression. Tumor assessments are performed every 4 weeks for 12 weeks, then every 8 weeks. Results: Since Oct 2007, samples from 289 pts (222 from Taiwan and 67 from the US) have been sequenced. 100 had detectable EGFR mutations including del19 (n=39), L858R (n=45) and others (n=16). 69 pts have started treatment. The trial was moved to stage 2 after 21 of the first 38 treated pts had objective response at 28 days. Of 55 evaluable 2nd line pts, 29 (53%) had PR, and 23 (42%) had SD. Median follow up is 5.1 months. Most common related AEs were diarrhea and skin-related AEs, reported in 87% and 88% of pts, respectively. 27 pts (42.9 %) had dose reduction to 40 mg and 7 pts (11%) to 30 mg but only 1 pt permanently discontinued due to AEs. Diarrhea and rash were main causes of dose reduction. Conclusions: In the 2nd line setting, BIBW 2992 shows efficacy in NSCLC harboring EGFR activating mutations. Diarrhea and skin disorders, the most frequently observed AEs, are manageable with supportive care and dose reduction. Updated response and disease control rates and preliminary progression-free survival data will be presented. An international Phase III trial program investigating BIBW 2992 in NSCLC, LUX-Lung, is now recruiting.

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Phase II study of induction and adjuvant bevacizumab in patients with stage IB-IIIA non-small cell lung cancer (NSCLC) receiving induction docetaxel and cisplatin

7531

Background: VEGF supports growth of NSCLC and is blocked by bevacizumab. Bevacizumab with chemotherapy is an established treatment for advanced NSCLC. We conducted this study to assess the efficacy and toxicity of induction bevacizumab (Bev) with cisplatin (C) and docetaxel (D) in patients with resectable NSCLC. Methods: All patients (pts) had resectable Stage IB-IIIA NSCLC and received up to 4 cycles of D 75 mg/m2 and C 75 mg/m2 followed by surgery. Pts with non-squamous NSCLC also received 3 cycles of Bev 15 mg/kg along with induction DC (Bev-DC). Bev was not given in pre-operative cycle 4. Pts with squamous or central tumors or hemoptysis received 4 cycles of DC only (DC). All resected pts were eligible for adjuvant Bev 15 mg/kg q3 weeks for 1 year. The primary endpoint was rate of downstaging from pre-operative clinical stage to pathologic stage. Results: From Aug 2005 - Nov 2008, 47 pts were enrolled: 27 women; median age 62; Stage 1B -15%, Stage II-17%, Stage IIIA-68%. Of 36 pts given Bev-DC, 15/30 (50%) who have completed surgery were downstaged. Of 11 pts given DC, 3/11 (27%) were downstaged. In Bev-DC group, 22/33 (67%) completed all 4 cycles of DC without a dose reduction and 28/33 pts (85%) completed all 3 planned cycles of Bev. Pts received <3 cycles due to: hemoptysis (n=3), consent withdrawal (n=1), hypertension (n=1), and sepsis (n=1). For DC, 6/11 pts (55%) completed all 4 cycles of DC without a dose reduction. 42/43 patients were resected. R0 resection rate: 29/31 for Bev-DC and 9/11 for DC. Grade 3/4 surgical complications were seen in 5/31 pts (16%) in Bev-DC and 1/11 (9%) in DC. Only 17/41 (41%) who completed surgery received adjuvant bev (median 6 cycles), and 7/41 (17%) completed all adjuvant Bev. Pts did not receive adjuvant Bev due to: POD prior to adjuvant Bev (n=9), POD during adjuvant Bev (n=6), toxicity (n=4), consent withdrawal (n=1), RT for unresectable disease (n=1), surgical complications (n=4), chemotherapy complications (n=4). No treatment related deaths. Conclusions: Induction chemotherapy with Bev-DC in NSCLC is feasible and is associated with an improved rate of downstaging compared with historical controls (33%). In patients treated with DC-Bev, grade 3/4 surgical complications were increased by 7%.

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