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Sokol ES, Feng YX, Jin DX, Basudan A, Lee AV, Atkinson JM, Chen J, Stephens PJ, Frampton GM, Gupta PB, Ross JS, Chung JH, Oesterreich S, Ali SM, Hartmaier RJ. Loss of function of NF1 is a mechanism of acquired resistance to endocrine therapy in lobular breast cancer. Ann Oncol 2020; 30:115-123. [PMID: 30423024 PMCID: PMC6336006 DOI: 10.1093/annonc/mdy497] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Background Invasive lobular carcinoma (ILC) as a disease entity distinct from invasive ductal carcinoma (IDC) has merited focused studies of the genomic landscape, but those to date are largely limited to the assessment of early-stage cancers. Given that genomic alterations develop as acquired resistance to endocrine therapy, studies on refractory ILC are needed. Patients and methods Tissue from 336 primary-enriched, breast-biopsied ILC and 485 estrogen receptor (ER)-positive IDC and metastatic biopsy specimens from 180 ILC and 191 ER-positive IDC patients was assayed with hybrid-capture-based comprehensive genomic profiling for short variant, indel, copy number variants, and rearrangements in up to 395 cancer-related genes. Results Whereas ESR1 alterations are enriched in the metastases of both ILC and IDC compared with breast specimens, NF1 alterations are enriched only in ILC metastases (mILC). NF1 alterations are predominantly under loss of heterozygosity (11/14, 79%), are mutually exclusive with ESR1 mutations [odds ratio = 0.24, P < 0.027] and are frequently polyclonal in ctDNA assays. Assessment of paired specimens shows that NF1 alterations arise in the setting of acquired resistance. An in vitro model of CDH1 mutated ER-positive breast cancer demonstrates that NF1 knockdown confers a growth advantage in the presence of 4-hydroxy tamoxifen. Our study further identified a significant increase in tumor mutational burden (TMB) in mILCs relative to breast ILCs or metastatic IDCs (8.9% >20 mutations/mb; P < 0.001). Most TMB-high mILCs harbor an APOBEC trinucleotide signature (14/16; 88%). Conclusions This study identifies alteration of NF1 as enriched specifically in mILC. Mutual exclusivity with ESR1 alterations, polyclonality in relapsed ctDNA, and de novo acquisition suggest a role for NF1 loss in endocrine therapy resistance. Since NF1 loss leads to RAS/RAF kinase activation, patients may benefit from a matched inhibitor. Moreover, for an independent subset of mILC, TMB was elevated relative to breast ILC, suggesting possible benefit from immune checkpoint inhibitors.
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Affiliation(s)
- E S Sokol
- Foundation Medicine Inc., Cambridge.
| | - Y X Feng
- Department of Biology, Massachusetts Institute of Technology, Cambridge
| | - D X Jin
- Foundation Medicine Inc., Cambridge; Department of Biology, Massachusetts Institute of Technology, Cambridge
| | - A Basudan
- University of Pittsburgh, Pittsburgh; Womens Cancer Research Center, Department of Genetics, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh
| | - A V Lee
- University of Pittsburgh, Pittsburgh; Womens Cancer Research Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh
| | - J M Atkinson
- University of Pittsburgh, Pittsburgh; Womens Cancer Research Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh
| | - J Chen
- University of Pittsburgh, Pittsburgh; Womens Cancer Research Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh
| | | | | | - P B Gupta
- Department of Biology, Massachusetts Institute of Technology, Cambridge
| | - J S Ross
- Foundation Medicine Inc., Cambridge; Upstate Medical University, Syracuse, USA
| | | | - S Oesterreich
- University of Pittsburgh, Pittsburgh; Womens Cancer Research Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh
| | - S M Ali
- Foundation Medicine Inc., Cambridge
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Hartmaier RJ, Trabucco SE, Priedigkeit N, Chung JH, Parachoniak CA, Vanden Borre P, Morley S, Rosenzweig M, Gay LM, Goldberg ME, Suh J, Ali SM, Ross J, Leyland-Jones B, Young B, Williams C, Park B, Tsai M, Haley B, Peguero J, Callahan RD, Sachelarie I, Cho J, Atkinson JM, Bahreini A, Nagle AM, Puhalla SL, Watters RJ, Erdogan-Yildirim Z, Cao L, Oesterreich S, Mathew A, Lucas PC, Davidson NE, Brufsky AM, Frampton GM, Stephens PJ, Chmielecki J, Lee AV. Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer. Ann Oncol 2019; 29:872-880. [PMID: 29360925 PMCID: PMC5913625 DOI: 10.1093/annonc/mdy025] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer. Patients and methods To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots. Results We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations. Conclusions Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.
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Affiliation(s)
- R J Hartmaier
- Foundation Medicine Inc., Cambridge; Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA.
| | | | - N Priedigkeit
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | | | | | | | - S Morley
- Foundation Medicine Inc., Cambridge
| | | | - L M Gay
- Foundation Medicine Inc., Cambridge
| | | | - J Suh
- Foundation Medicine Inc., Cambridge
| | - S M Ali
- Foundation Medicine Inc., Cambridge
| | - J Ross
- Foundation Medicine Inc., Cambridge
| | - B Leyland-Jones
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - B Young
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - C Williams
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - B Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, USA
| | - M Tsai
- Minnesota Oncology, Minneapolis, USA
| | - B Haley
- UT Southwestern Medical Center, Dallas, USA
| | - J Peguero
- Oncology Consultants Research Department, Houston, USA
| | | | | | - J Cho
- New Bern Cancer Care, New Bern, USA
| | - J M Atkinson
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - A Bahreini
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA; Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A M Nagle
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - S L Puhalla
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - R J Watters
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, USA
| | - Z Erdogan-Yildirim
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA
| | - L Cao
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Central South University Xiangya School of Medicine, China
| | - S Oesterreich
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - A Mathew
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - P C Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
| | - N E Davidson
- Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - A M Brufsky
- Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | | | | | | | - A V Lee
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
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Pietrantonio F, Di Nicolantonio F, Schrock AB, Lee J, Morano F, Fucà G, Nikolinakos P, Drilon A, Hechtman JF, Christiansen J, Gowen K, Frampton GM, Gasparini P, Rossini D, Gigliotti C, Kim ST, Prisciandaro M, Hodgson J, Zaniboni A, Chiu VK, Milione M, Patel R, Miller V, Bardelli A, Novara L, Wang L, Pupa SM, Sozzi G, Ross J, Di Bartolomeo M, Bertotti A, Ali S, Trusolino L, Falcone A, de Braud F, Cremolini C. RET fusions in a small subset of advanced colorectal cancers at risk of being neglected. Ann Oncol 2019. [PMID: 29538669 DOI: 10.1093/annonc/mdy090] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Recognition of rare molecular subgroups is a challenge for precision oncology and may lead to tissue-agnostic approval of targeted agents. Here we aimed to comprehensively characterize the clinical, pathological and molecular landscape of RET rearranged metastatic colorectal cancer (mCRC). Patients and methods In this case series, we compared clinical, pathological and molecular characteristics of 24 RET rearranged mCRC patients with those of a control group of 291 patients with RET negative tumors. RET rearranged and RET negative mCRCs were retrieved by systematic literature review and by taking advantage of three screening sources: (i) Ignyta's phase 1/1b study on RXDX-105 (NCT01877811), (ii) cohorts screened at two Italian and one South Korean Institutions and (iii) Foundation Medicine Inc. database. Next-generation sequencing data were analyzed for RET rearranged cases. Results RET fusions were more frequent in older patients (median age of 66 versus 60 years, P = 0.052), with ECOG PS 1-2 (90% versus 50%, P = 0.02), right-sided (55% versus 32%, P = 0.013), previously unresected primary tumors (58% versus 21%, P < 0.001), RAS and BRAF wild-type (100% versus 40%, P < 0.001) and MSI-high (48% versus 7%, P < 0.001). Notably, 11 (26%) out of 43 patients with right-sided, RAS and BRAF wild-type tumors harbored a RET rearrangement. At a median follow-up of 45.8 months, patients with RET fusion-positive tumors showed a significantly worse OS when compared with RET-negative ones (median OS 14.0 versus 38.0 months, HR: 4.59; 95% CI, 3.64-32.66; P < 0.001). In the multivariable model, RET rearrangements were still associated with shorter OS (HR: 2.97; 95% CI, 1.25-7.07; P = 0.014), while primary tumor location, RAS and BRAF mutations and MSI status were not. Conclusions Though very rare, RET rearrangements define a new subtype of mCRC that shows poor prognosis with conventional treatments and is therefore worth of a specific management.
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Affiliation(s)
- F Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.
| | - F Di Nicolantonio
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - A B Schrock
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - J Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - F Morano
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - G Fucà
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - P Nikolinakos
- Medical Oncology, University Cancer & Blood Center, Athens
| | - A Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - K Gowen
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - G M Frampton
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - P Gasparini
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - D Rossini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Gigliotti
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - S T Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - M Prisciandaro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - J Hodgson
- Medical Oncology, University Cancer & Blood Center, Athens
| | - A Zaniboni
- Department of Medical Oncology, Fondazione Poliambulanza, Brescia, Italy
| | - V K Chiu
- Department of Internal Medicine, University of New Mexico, Albuquerque, USA
| | - M Milione
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - R Patel
- Department of Diagnostics, Ignyta, Inc., San Diego, USA
| | - V Miller
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - A Bardelli
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - L Novara
- ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - L Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, USA
| | - S M Pupa
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - G Sozzi
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - J Ross
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - M Di Bartolomeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A Bertotti
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - S Ali
- Clinical Development, Foundation Medicine, Inc., Cambridge, USA
| | - L Trusolino
- Department of Oncology, University of Torino, Candiolo, Italy; ECMO, Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - A Falcone
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - F de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - C Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Sokol ES, Frampton GM, Ross J, Ali S, Chung J, Oesterreich S. Abstract P3-10-05: BRCA1/2 alterations are present at significant rates across breast cancer subtypes and are associated with a high genome-wide loss of heterozygosity signature. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-10-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
The recent approval of PARP inhibitor, olaparib, in HER2-negative breast cancer expands the therapeutic options for patients with germline BRCA1/2 alterations. The role of somatic BRCA alteration as a predictive biomarker in breast cancer is currently unclear. NCCN guidelines call for germline testing in all young patients (<46 yrs) and patients with triple negative breast cancer (TNBC) (< 61 yrs) with a personal history of breast cancer. Here we examined the landscape of BRCA mutations to assess whether additional populations may have potential benefit from PARP inhibitors.
Methods
Hybrid-capture based comprehensive genomic profiling of 395 cancer-related genes using the FoundationOne assay (Foundation Medicine, MA) was performed on 12,508 breast carcinomas. Somatic/germline/zygosity status for BRCA1/2 variants was analyzed as described in Sun, 2018 (PMID: 29415044). High genome-wide loss-of-heterozygosity (gLOH) was classified as ≥16% LOH. Subgroups were analyzed on histological {Invasive Ductal Carcinoma (IDC), Invasive Lobular Carcinoma (ILC)} and molecular subtypes [ER-positive (ER+), HER2-amplified (HER2+), TNBC], patient age [≤45, 46-60, 61+], and gender.
Results
Consistent with previous reports, the frequency of BRCA1/2 alterations was highest in young patients (<46; 15%), TNBC (10%), and male breast cancer (14%); BRCA1/2 alterations were also identified in HER2+, ILC, and ER+ tumors (5.3%, 6.5%, 8.3%). Overall, BRCA1 was more frequently mutated in TNBC and young patients (67%), whereas BRCA2 was more frequently mutated in ER+, HER2+, ILC, and male breast cancer (63%, 57%, 79%, 100%).
The fraction of somatic BRCA mutations (sBRCA) was 38%, with the lowest fraction of sBRCA in TNBC and young patients (30%, 30% overall, 36%, 42% for BRCA1) and highest in HER2+, ILC, and older patients (46%, 52%, 51%); the absolute frequency of sBRCA is approximately 3.5%. In tumors with ESR1 mutations, we detected concurrent BRCA mutation in 6.4% (85/1319), with 48% predicted somatic.
Almost all tumors with BRCA mutations had biallelic inactivation, with LOH of the second allele irrespective of predicted germline status (90% of gBRCA and 86% of sBRCA under LOH). gLOH score was used as a phenotypic measure of homologous recombination deficiency (HRD): patients harboring biallelic BRCA alterations had elevated rates of gLOH with 89% of gBRCA and 84% of sBRCA tumors harboring a high gLOH score, vs 47% with heterozygous BRCA, 34% with no BRCA alteration, and 80% for patients with BRCA deletion.
Conclusions
Thirty-eight percent of deleterious BRCA alterations in breast are predicted somatic, including 36% of BRCA1 alterations in TNBC. Germline testing would miss these alterations even though they are frequently under LOH and are associated with high gLOH, a biomarker with predictive value in ovarian cancer. While patients with ER+ and HER2+ tumors have low rates of gBRCA alterations, the overall BRCA mutation rate, including somatic alterations, is appreciable at 8.3% and 5.3%. Our findings demonstrate that sBRCA alterations are associated with a comparable HRD phenotype to gBRCA altertions and suggests that PARP inhibitors may have potential value for a wider range of breast cancer patients.
Citation Format: Sokol ES, Frampton GM, Ross J, Ali S, Chung J, Oesterreich S. BRCA1/2 alterations are present at significant rates across breast cancer subtypes and are associated with a high genome-wide loss of heterozygosity signature [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 P3-10-05.
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Affiliation(s)
- ES Sokol
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - GM Frampton
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - J Ross
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - S Ali
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - J Chung
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - S Oesterreich
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
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5
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Sokol ES, Basudan A, Lee AV, Stephens PJ, Frampton GM, Oesterreich S, Hartmaier RJ. Abstract PD8-05: Genomic profiling of metastatic invasive lobular carcinoma reveals unique genomics and therapeutic opportunities. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pd8-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Invasive lobular carcinoma (ILC) is a common breast cancer histological subtype comprising ˜10-15% of all cases. ILC possesses many unique features when compared to invasive ductal carcinoma (IDC). First, ILC has distinct genomic alterations expanding beyond the defining event of CDH1 loss to other genes such as TBX3, FOXA1, and AKT signaling related genes. Second, ILC responds differently to chemotherapeutics and endocrine therapies despite similar clinical staging. Third, ILC tumors spread to a distinct set of organs compared to IDC tumors, commonly forming distant metastases in the ovary, colon, omentum, and stomach. However, the genomics of metastatic ILC have yet to be fully explored.
Methods
Comprehensive hybrid-capture based genomic analysis of 286-395 cancer related genes was performed on 5523 histologically defined ILC (n=613) and IDC (n=4910) tumors. Of these, 29% and 21% were from distant metastatic sites for ILC and IDC, respectively. Additionally, histology based ER-status was available for a subset of tumors allowing a subgroup of ER-positive, HER2-negative IDC (ER-IDC) samples to be identified (n=655).
Results
We examined the genetic differences between ILC and IDC in the context of both local and metastatic disease. Overall, the genomic profiles of ILC are enriched for alterations in CDH1, TBX3, PIK3CA, and RUNX1 in agreement with previous studies. Alterations in genes involved in AKT signaling (PIK3CA, PTEN, and AKT1) are also enriched in ILC (64% v. 49%; p<10-7). Interestingly, NF1 loss of function alterations are enriched in metastatic ILC compared to ER-IDC (12.2% v. 3.6%, p<0.001) but not in local disease (4.8% v. 4.1%, p=0.72). NF1 is a negative regulator of RAS-cyclic AMP pathway and suggests that NF1 driven RAS signaling is an important driver of metastasis in ILC.
We next examined metastatic ILC samples for alterations enriched at specific metastatic tissue sites. Two metastatic sites were exclusive to ILC samples compared to ER-IDC: GI (19.4%) and the female reproductive tract (11.7%). Within metastatic ILC, alterations in ESR1 showed strong tissue site bias towards liver metastases with 29% harboring an alteration in ESR1 (range: 8-13% in other sites, excluding ovary). Interestingly, ESR1 alterations were never observed in 14 ovary metastases, potentially reflecting an effect of local estrogen production on ILC ovarian metastases. In support of this, ILC ovarian metastases occur in younger women with a median age of 53.5 compared to 63.5 across all other sites.
Lastly, high tumor mutation burden (TMB) is strongly associated with metastatic ILC with 8.9% of metastatic ILC classified as TMB-high (320 mutations/Mb) compared to 2.1% of ILC in the breast. A similar but less pronounced finding was also observed for ER-IDC (1.6% versus 0.8%). This suggests that checkpoint blockage therapies may be a more common option in metastatic ILC than previously appreciated.
Conclusions
Genomic profiling of metastatic ILC reveals numerous potential therapeutic options enriched in this disease. Inhibition of RAS signaling driven by NF1 loss and TMB-high directed immunotherapeutics may be potential therapeutic options for a substantial portion of metastatic ILC patients.
Citation Format: Sokol ES, Basudan A, Lee AV, Stephens PJ, Frampton GM, Oesterreich S, Hartmaier RJ. Genomic profiling of metastatic invasive lobular carcinoma reveals unique genomics and therapeutic opportunities [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 PD8-05.
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Affiliation(s)
- ES Sokol
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - A Basudan
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - AV Lee
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - PJ Stephens
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - GM Frampton
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - S Oesterreich
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
| | - RJ Hartmaier
- Foundation Medicine, Cambridge, MA; University of Pittsburgh, Pittsburgh, PA
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6
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Ross JS, Chung J, Elvin JE, Vergilio JA, 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. Abstract PD8-01: CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pd8-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
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 >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<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<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<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 > 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 > 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.
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Affiliation(s)
- JS Ross
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - J Chung
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - JE Elvin
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - J-A Vergilio
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - S Ramkissoon
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - J Suh
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - E Severson
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - S Daniel
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - GM Frampton
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - D Fabrizio
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - RJ Hartmaier
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - LA Albacker
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - SM Ali
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - AB Schrock
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - VA Miller
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - PJ Stephens
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
| | - LM Gay
- Albany Medical College, Albany, NY; Foundation Medicine, Cambridge, MA
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7
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Chung JH, Pavlick D, Hartmaier R, Schrock AB, Young L, Forcier B, Ye P, Levin MK, Goldberg M, Burris H, Gay LM, Hoffman AD, Stephens PJ, Frampton GM, Lipson DM, Nguyen DM, Ganesan S, Park BH, Vahdat LT, Leyland-Jones B, Mughal TI, Pusztai L, O'Shaughnessy J, Miller VA, Ross JS, Ali SM. Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer. Ann Oncol 2017; 28:2866-2873. [PMID: 28945887 PMCID: PMC5834148 DOI: 10.1093/annonc/mdx490] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- J H Chung
- Foundation Medicine, Inc., Cambridge.
| | - D Pavlick
- Foundation Medicine, Inc., Cambridge
| | | | | | - L Young
- Foundation Medicine, Inc., Cambridge
| | - B Forcier
- Foundation Medicine, Inc., Cambridge
| | - P Ye
- Avera Cancer Institute, Sioux Falls
| | - M K Levin
- Baylor University Medical Center, Texas Oncology, US Oncology, Dallas
| | | | - H Burris
- Sarah Cannon Research Institute, Nashville
| | - L M Gay
- Foundation Medicine, Inc., Cambridge
| | | | | | | | | | - D M Nguyen
- Sutter Medical Group of the Redwoods, Santa Rosa
| | - S Ganesan
- Division of Medical Oncology, Department of Medicine, Rutgers Cancer Institute of New Jersey, New Brunswick
| | - B H Park
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore
| | - L T Vahdat
- Weill Cornell Breast Center, Weill Cornell Medicine, New York
| | | | - T I Mughal
- Foundation Medicine, Inc., Cambridge; Tufts University Medical Center, Boston
| | - L Pusztai
- Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven
| | - J O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, US Oncology, Dallas
| | | | - J S Ross
- Foundation Medicine, Inc., Cambridge; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, USA. mailto:
| | - S M Ali
- Foundation Medicine, Inc., Cambridge
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Frampton GM, Connelly C, Fabrizio D, Miller VA, Stephens PJ. Abstract P6-07-04: Comprehensive genomic profiling to assess tumor mutation burden in >8,000 breast cancer cases: Implications for immunotherapy. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p6-07-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
This abstract was withdrawn by the authors.
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9
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Wang K, Sanchez-Martin M, Wang X, Knapp KM, Koche R, Vu L, Nahas MK, He J, Hadler M, Stein EM, Tallman MS, Donahue AL, Frampton GM, Lipson D, Roels S, Stephens PJ, Sanford EM, Brennan T, Otto GA, Yelensky R, Miller VA, Kharas MG, Levine RL, Ferrando A, Armstrong SA, Krivtsov AV. Patient-derived xenotransplants can recapitulate the genetic driver landscape of acute leukemias. Leukemia 2016; 31:151-158. [PMID: 27363283 PMCID: PMC5203983 DOI: 10.1038/leu.2016.166] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022]
Abstract
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.
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Affiliation(s)
- K Wang
- Foundation Medicine, Cambridge, MA, USA
| | - M Sanchez-Martin
- Institute for Cancer Genetics Columbia University, New York, NY, USA
| | - X Wang
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - K M Knapp
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - R Koche
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - L Vu
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M K Nahas
- Foundation Medicine, Cambridge, MA, USA
| | - J He
- Foundation Medicine, Cambridge, MA, USA
| | - M Hadler
- Foundation Medicine, Cambridge, MA, USA
| | - E M Stein
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M S Tallman
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - D Lipson
- Foundation Medicine, Cambridge, MA, USA
| | - S Roels
- Foundation Medicine, Cambridge, MA, USA
| | | | | | - T Brennan
- Foundation Medicine, Cambridge, MA, USA
| | - G A Otto
- Foundation Medicine, Cambridge, MA, USA
| | | | | | - M G Kharas
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - R L Levine
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ferrando
- Institute for Cancer Genetics Columbia University, New York, NY, USA
| | - S A Armstrong
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A V Krivtsov
- Center for Epigenetic Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Chung JH, Sanford E, Johnson A, Klempner SJ, Schrock AB, Palma NA, Erlich RL, Frampton GM, Chalmers ZR, Vergilio J, Rubinson DA, Sun JX, Chmielecki J, Yelensky R, Suh JH, Lipson D, George TJ, Elvin JA, Stephens PJ, Miller VA, Ross JS, Ali SM. Comprehensive genomic profiling of anal squamous cell carcinoma reveals distinct genomically defined classes. Ann Oncol 2016; 27:1336-41. [PMID: 27052656 DOI: 10.1093/annonc/mdw152] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/22/2016] [Indexed: 01/03/2023] Open
Abstract
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.
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Affiliation(s)
| | | | | | - S J Klempner
- Division of Hematology-Oncology, University of California Irvine, Irvine
| | | | | | | | | | | | | | - D A Rubinson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston
| | - J X Sun
- Foundation Medicine, Cambridge
| | | | | | - J H Suh
- Foundation Medicine, Cambridge
| | | | - T J George
- Division of Hematology-Oncology, University of Florida, Gainesville
| | | | | | | | - J S Ross
- Foundation Medicine, Cambridge Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, USA
| | - S M Ali
- Foundation Medicine, Cambridge
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11
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Chung CH, Guthrie VB, Masica DL, Tokheim C, Kang H, Richmon J, Agrawal N, Fakhry C, Quon H, Subramaniam RM, Zuo Z, Seiwert T, Chalmers ZR, Frampton GM, Ali SM, Yelensky R, Stephens PJ, Miller VA, Karchin R, Bishop JA. Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Ann Oncol 2015; 26:1216-1223. [PMID: 25712460 PMCID: PMC4516044 DOI: 10.1093/annonc/mdv109] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/23/2015] [Accepted: 02/18/2015] [Indexed: 01/07/2023] Open
Abstract
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.
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Affiliation(s)
- C H Chung
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery.
| | - V B Guthrie
- Department of Biomedical Engineering, Institute for Computational Medicine
| | - D L Masica
- Department of Biomedical Engineering, Institute for Computational Medicine
| | - C Tokheim
- Department of Biomedical Engineering, Institute for Computational Medicine
| | | | - J Richmon
- Department of Otolaryngology-Head and Neck Surgery
| | - N Agrawal
- Department of Otolaryngology-Head and Neck Surgery
| | - C Fakhry
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery; Department of Milton J. Dance Head and Neck Center, Baltimore
| | - H Quon
- Department of Radiation Oncology
| | - R M Subramaniam
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery; Department of Radiology and Radiological Sciences
| | - Z Zuo
- Department of Medicine, University of Chicago, Chicago
| | - T Seiwert
- Department of Medicine, University of Chicago, Chicago
| | | | | | - S M Ali
- Foundation Medicine, Inc., Cambridge, USA
| | - R Yelensky
- Foundation Medicine, Inc., Cambridge, USA
| | | | - V A Miller
- Foundation Medicine, Inc., Cambridge, USA
| | - R Karchin
- Department of Oncology; Department of Biomedical Engineering, Institute for Computational Medicine
| | - J A Bishop
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore
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12
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Chalmers ZR, Ali SM, Frampton GM, Chmielecki J, Palma NA, Elvin JA, Johnson A, Yelensky R, Ross JS, Stephens PJ, Miller VA, Waanders AJ, Crawford J. GE-04 * COMPREHENSIVE GENOMIC PROFILING (CGP) OF PEDIATRIC GLIOMAS REVEALS A HIGH FREQUENCY OF CLINICALLY RELEVANT GENOMIC ALTERATIONS (CRGA) ASSOCIATED WITH BENEFIT FROM TARGETED THERAPY. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov061.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Chalmers ZR, Ali SM, Ohgami RS, Campregher PV, Frampton GM, Yelensky R, Elvin JA, Palma NA, Erlich R, Vergilio JA, Chmielecki J, Ross JS, Stephens PJ, Hermann R, Miller VA, Miles CR. Comprehensive genomic profiling identifies a novel TNKS2-PDGFRA fusion that defines a myeloid neoplasm with eosinophilia that responded dramatically to imatinib therapy. Blood Cancer J 2015; 5:e278. [PMID: 25658984 PMCID: PMC4349257 DOI: 10.1038/bcj.2014.95] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
| | - S M Ali
- Foundation Medicine Inc., Cambridge, MA, USA
| | - R S Ohgami
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - P V Campregher
- 1] Foundation Medicine Inc., Cambridge, MA, USA [2] Clinical Laboratory, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | - R Yelensky
- Foundation Medicine Inc., Cambridge, MA, USA
| | - J A Elvin
- Foundation Medicine Inc., Cambridge, MA, USA
| | - N A Palma
- Foundation Medicine Inc., Cambridge, MA, USA
| | - R Erlich
- Foundation Medicine Inc., Cambridge, MA, USA
| | - J-A Vergilio
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - J S Ross
- 1] Foundation Medicine Inc., Cambridge, MA, USA [2] Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY, USA
| | | | - R Hermann
- Northwest Georgia Oncology Centers, Jasper Cancer Center, Jasper, GA, USA
| | - V A Miller
- Foundation Medicine Inc., Cambridge, MA, USA
| | - C R Miles
- Northwest Georgia Oncology Centers, Jasper Cancer Center, Jasper, GA, USA
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