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Zhou K, Zhang M, Zhai D, Wang Z, Liu T, Xie Y, Shi Y, Shi H, Chen Q, Li X, Xu J, Cai Z, Zhang Y, Shao N, Lin Y. Genomic and transcriptomic profiling of inflammatory breast cancer reveals distinct molecular characteristics to non-inflammatory breast cancers. Breast Cancer Res Treat 2024:10.1007/s10549-024-07437-0. [PMID: 39030466 DOI: 10.1007/s10549-024-07437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
PURPOSE Inflammatory breast cancer (IBC), a rare and highly aggressive form of breast cancer, accounts for 10% of breast cancer-related deaths. Previous omics studies of IBC have focused solely on one of genomics or transcriptomics and did not discover common differences that could distinguish IBC from non-IBC. METHODS Seventeen IBC patients and five non-IBC patients as well as additional thirty-three Asian breast cancer samples from TCGA-BRCA were included for the study. We performed whole-exon sequencing (WES) to investigate different somatic genomic alterations, copy number variants, and large structural variants between IBC and non-IBC. Bulk RNA sequencing (RNA-seq) was performed to examine the differentially expressed genes, pathway enrichment, and gene fusions. WES and RNA-seq data were further investigated in combination to discover genes that were dysregulated in both genomics and transcriptomics. RESULTS Copy number variation analysis identified 10 cytobands that showed higher frequency in IBC. Structural variation analysis showed more frequent deletions in IBC. Pathway enrichment and immune infiltration analysis indicated increased immune activation in IBC samples. Gene fusions including CTSC-RAB38 were found to be more common in IBC. We demonstrated more commonly dysregulated RAS pathway in IBC according to both WES and RNA-seq. Inhibitors targeting RAS signaling and its downstream pathways were predicted to possess promising effects in IBC treatment. CONCLUSION We discovered differences unique in Asian women that could potentially explain IBC etiology and presented RAS signaling pathway as a potential therapeutic target in IBC treatment.
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Affiliation(s)
- Kaiwen Zhou
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengmeng Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Duanyang Zhai
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zilin Wang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ting Liu
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yawei Shi
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qianjun Chen
- Department of Breast Oncology, Traditional Chinese Medicine Hospital of Guangdong Province, Guangzhou, Guangdong, China
| | - Xiaoping Li
- Department of Breast Oncology, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Juan Xu
- Department of Breast Oncology, Maternal and Child Health Care Hospital of Guangdong Province, Guangzhou, China
| | - Zhenhai Cai
- Department of Breast Oncology, Jieyang People's Hospital, Jieyang, Guangdong, China
| | - Yunjian Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Nan Shao
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
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2
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Priedigkeit N, Harrison B, Shue R, Hughes M, Li Y, Kirkner GJ, Spurr LF, Remolano MC, Strauss S, Files J, Feeney AM, Grant L, Mohammed-Abreu A, Garrido-Castro A, Sousa RB, Bychkovsky B, Nakhlis F, Bellon JR, King TA, Winer EP, Lindeman N, Johnson BE, Sholl L, Dillon D, Overmoyer B, Tolaney SM, Cherniack A, Lin NU, Lynce F. Clinicogenomic characterization of inflammatory breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592972. [PMID: 38766070 PMCID: PMC11100693 DOI: 10.1101/2024.05.07.592972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Inflammatory breast cancer (IBC) is a rare and poorly characterized type of breast cancer with an aggressive clinical presentation. The biological mechanisms driving the IBC phenotype are relatively undefined-partially due to a lack of comprehensive, large-scale genomic studies and limited clinical cohorts. Patients and Methods A retrospective analysis of 2457 patients with metastatic breast cancer who underwent targeted tumor-only DNA-sequencing was performed at Dana-Farber Cancer Institute. Clinicopathologic, single nucleotide variant (SNV), copy number variant (CNV) and tumor mutational burden (TMB) comparisons were made between clinically confirmed IBC cases within a dedicated IBC center versus non-IBC cases. Results Clinicopathologic differences between IBC and non-IBC cases were consistent with prior reports-including IBC being associated with younger age at diagnosis, higher grade, and enrichment with hormone receptor (HR)-negative and HER2-positive tumors. The most frequent somatic alterations in IBC involved TP53 (72%), ERBB2 (32%), PIK3CA (24%), CCND1 (12%), MYC (9%), FGFR1 (8%) and GATA3 (8%). A multivariate logistic regression analysis revealed a significant enrichment in TP53 SNVs in IBC; particularly in HER2-positive and HR-positive disease which was associated with worse outcomes. Tumor mutational burden (TMB) did not differ substantially between IBC and non-IBC cases and a pathway analysis revealed an enrichment in NOTCH pathway alterations in HER2-positive disease. Conclusion Taken together, this study provides a comprehensive, clinically informed landscape of somatic alterations in a large cohort of patients with IBC. Our data support higher frequency of TP53 mutations and a potential enrichment in NOTCH pathway activation-but overall; a lack of major genomic differences. These results both reinforce the importance of TP53 alterations in IBC pathogenesis as well as their influence on clinical outcomes; but also suggest additional analyses beyond somatic DNA-level changes are warranted.
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Affiliation(s)
- Nolan Priedigkeit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Beth Harrison
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Robert Shue
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Melissa Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Yvonne Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Gregory J. Kirkner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F. Spurr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | | | - Sarah Strauss
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Janet Files
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anne-Marie Feeney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Libby Grant
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ana Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | | | - Brittany Bychkovsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Faina Nakhlis
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jennifer R. Bellon
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Tari A. King
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Eric P. Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Neal Lindeman
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Bruce E. Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lynette Sholl
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Deborah Dillon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Beth Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Andrew Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Nancy U. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
| | - Filipa Lynce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston MA, USA
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3
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Bertucci F, Lerebours F, Ceccarelli M, Guille A, Syed N, Finetti P, Adélaïde J, Van Laere S, Goncalves A, Viens P, Birnbaum D, Mamessier E, Callens C, Bedognetti D. Mutational landscape of inflammatory breast cancer. J Transl Med 2024; 22:374. [PMID: 38637846 PMCID: PMC11025259 DOI: 10.1186/s12967-024-05198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) is the most pro-metastatic form of BC. Better understanding of its enigmatic pathophysiology is crucial. We report here the largest whole-exome sequencing (WES) study of clinical IBC samples. METHODS We retrospectively applied WES to 54 untreated IBC primary tumor samples and matched normal DNA. The comparator samples were 102 stage-matched non-IBC samples from TCGA. We compared the somatic mutational profiles, spectra and signatures, copy number alterations (CNAs), HRD and heterogeneity scores, and frequencies of actionable genomic alterations (AGAs) between IBCs and non-IBCs. The comparisons were adjusted for the molecular subtypes. RESULTS The number of somatic mutations, TMB, and mutational spectra were not different between IBCs and non-IBCs, and no gene was differentially mutated or showed differential frequency of CNAs. Among the COSMIC signatures, only the age-related signature was more frequent in non-IBCs than in IBCs. We also identified in IBCs two new mutational signatures not associated with any environmental exposure, one of them having been previously related to HIF pathway activation. Overall, the HRD score was not different between both groups, but was higher in TN IBCs than TN non-IBCs. IBCs were less frequently classified as heterogeneous according to heterogeneity H-index than non-IBCs (21% vs 33%), and clonal mutations were more frequent and subclonal mutations less frequent in IBCs. More than 50% of patients with IBC harbored at least one high-level of evidence (LOE) AGA (OncoKB LOE 1-2, ESCAT LOE I-II), similarly to patients with non-IBC. CONCLUSIONS We provide the largest mutational landscape of IBC. Only a few subtle differences were identified with non-IBCs. The most clinically relevant one was the higher HRD score in TN IBCs than in TN non-IBCs, whereas the most intriguing one was the smaller intratumor heterogeneity of IBCs.
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Affiliation(s)
- François Bertucci
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
| | - Florence Lerebours
- Department of Medical Oncology, Institut Curie Saint-Cloud, Paris, France
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, USA
- Department of Public Health Sciences, University of Miami, Miami, USA
| | - Arnaud Guille
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Najeeb Syed
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Pascal Finetti
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - José Adélaïde
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium
| | - Anthony Goncalves
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Patrice Viens
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Daniel Birnbaum
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Emilie Mamessier
- Département d'Oncologie Médicale, Predictive Oncology Laboratory, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, 232, Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Céline Callens
- Department of Medical Oncology, Institut Curie Saint-Cloud, Paris, France
| | - Davide Bedognetti
- Tumor Biology and Immunology Laboratory, Research Branch, Sidra Medicine, Doha, Qatar
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4
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Rypens C, Van Berckelaer C, Berditchevski F, van Dam P, Van Laere S. Deciphering the molecular biology of inflammatory breast cancer through molecular characterization of patient samples and preclinical models. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 384:77-112. [PMID: 38637101 DOI: 10.1016/bs.ircmb.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Inflammatory breast cancer is an aggressive subtype of breast cancer with dismal patient prognosis and a unique clinical presentation. In the past two decades, molecular profiling technologies have been used in order to gain insight into the molecular biology of IBC and to search for possible targets for treatment. Although a gene signature that accurately discriminates between IBC and nIBC patient samples and preclinical models was identified, the overall genomic and transcriptomic differences are small and ambiguous, mainly due to the limited sample sizes of the evaluated patient series and the failure to correct for confounding effects of the molecular subtypes. Nevertheless, data collected over the past 20 years by independent research groups increasingly support the existence of several IBC-specific biological characteristics. In this review, these features are classified as established, emerging and conceptual hallmarks based on the level of evidence reported in the literature. In addition, a synoptic model is proposed that integrates all hallmarks and that can explain how cancer cell intrinsic mechanisms (i.e. NF-κB activation, genomic instability, MYC-addiction, TGF-β resistance, adaptive stress response, chromatin remodeling, epithelial-to-mesenchymal transition) can contribute to the establishment of the dynamic immune microenvironment associated with IBC. It stands to reason that future research projects are needed to further refine (parts of) this model and to investigate its clinical translatability.
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Affiliation(s)
- Charlotte Rypens
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; CellCarta N V, Wilrijk, Belgium
| | - Christophe Van Berckelaer
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Peter van Dam
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; Multidisciplinary Oncological Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, Edegem, Belgium
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium.
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5
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Chamorro DF, Somes LK, Hoyos V. Engineered Adoptive T-Cell Therapies for Breast Cancer: Current Progress, Challenges, and Potential. Cancers (Basel) 2023; 16:124. [PMID: 38201551 PMCID: PMC10778447 DOI: 10.3390/cancers16010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Breast cancer remains a significant health challenge, and novel treatment approaches are critically needed. This review presents an in-depth analysis of engineered adoptive T-cell therapies (E-ACTs), an innovative frontier in cancer immunotherapy, focusing on their application in breast cancer. We explore the evolving landscape of chimeric antigen receptor (CAR) and T-cell receptor (TCR) T-cell therapies, highlighting their potential and challenges in targeting breast cancer. The review addresses key obstacles such as target antigen selection, the complex breast cancer tumor microenvironment, and the persistence of engineered T-cells. We discuss the advances in overcoming these barriers, including strategies to enhance T-cell efficacy. Finally, our comprehensive analysis of the current clinical trials in this area provides insights into the future possibilities and directions of E-ACTs in breast cancer treatment.
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Affiliation(s)
- Diego F. Chamorro
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; (D.F.C.); (L.K.S.)
| | - Lauren K. Somes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; (D.F.C.); (L.K.S.)
| | - Valentina Hoyos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; (D.F.C.); (L.K.S.)
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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6
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Johnson KC, Grimm M, Sukumar J, Schnell PM, Park KU, Stover DG, Jhawar SR, Gatti-Mays M, Wesolowski R, Williams N, Sardesai S, Pariser A, Sudheendra P, Tozbikian G, Ramaswamy B, Doto D, Cherian MA. Survival outcomes seen with neoadjuvant chemotherapy in the management of locally advanced inflammatory breast cancer (IBC) versus matched controls. Breast 2023; 72:103591. [PMID: 37871527 PMCID: PMC10598404 DOI: 10.1016/j.breast.2023.103591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Inflammatory breast cancer (IBC) poses an ongoing challenge as rates of disease recurrence and mortality remain high compared to stage-matched controls. However, frontline therapy has evolved through the years, including the widespread use of neoadjuvant chemotherapy (NAC) given the prognostic importance of pathologic complete response (pCR). Due to these sweeping changes, we need new data to assess current recurrence and survival outcomes for locally advanced IBC in the context of matched non-inflammatory controls. We conducted a retrospective analysis of institutional IBC data from 2010 to 2016 with the primary objective of comparing overall survival (OS), relapse-free survival (RFS), and distant relapse-free survival (DRFS). We matched IBC patients to non-inflammatory controls based on age, receptor status, tumor grade, clinical stage, and receipt of prior NAC. Secondary objectives included assessing pCR rates and identifying prognostic factors. Among NAC recipients, we observed similar pCR rates (47.6 % vs. 49.4 %, p = 0.88) between IBC (n = 84) and matched non-IBC (n = 81) cohorts. However, we noted a significant worsening of OS (p = 0.0001), RFS (p = 0.0001), and DRFS (p = 0.001) in the IBC group. Specifically, 5-year OS in the IBC cohort was 58.9 % vs. 86.7 % for matched controls (p = 0.0003). Older age was a weak negative predictor for OS (HR 1.03, p = 0.001) and RFS (HR 1.02, p = 0.01). For DRFS, older age was also a weak negative predictor (HR 1.02, p = 0.02), whereas the use of NAC was a positive predictor (HR 0.47, p = 0.02). Despite no clear difference in pCR, survival outcomes remain poor for IBC compared to matched non-inflammatory controls.
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Affiliation(s)
- Kai Cc Johnson
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Michael Grimm
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Jasmine Sukumar
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Patrick M Schnell
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Ko Un Park
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA; Division of Surgical Oncology, Department of Surgery, The Ohio State University, Columbus, OH, USA
| | - Daniel G Stover
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Sachin R Jhawar
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Margaret Gatti-Mays
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Robert Wesolowski
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Nicole Williams
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Sagar Sardesai
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Ashley Pariser
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Preeti Sudheendra
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Gary Tozbikian
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Bhuvaneswari Ramaswamy
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Dureti Doto
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Mathew A Cherian
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
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7
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Richard F, De Schepper M, Maetens M, Leduc S, Isnaldi E, Geukens T, Van Baelen K, Nguyen HL, Vermeulen P, Van Laere S, Bertucci F, Ueno N, Dirix L, Floris G, Biganzoli E, Desmedt C. Comparison of the genomic alterations present in tumor samples from patients with metastatic inflammatory versus non-inflammatory breast cancer reveals AURKA as a potential treatment target. Breast 2023:S0960-9776(23)00010-3. [PMID: 36717329 DOI: 10.1016/j.breast.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/02/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Inflammatory breast cancer (IBC) is a rare but aggressive subtype of breast cancer, mainly characterized using primary tumor samples. Here, using public datasets, we compared the genomic alterations in primary and metastatic samples from patients with metastatic IBC versus patients with metastatic non-IBC. We observed a higher frequency of AURKA amplification in IBC. We further showed that AURKA amplification was associated with increased AURKA mRNA expression, which we demonstrated was higher in IBC. Finally, higher protein expression of AURKA was associated with worse prognosis in patients with IBC. These findings deserve further investigation given the existence of AURKA-inhibitors.
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Affiliation(s)
- François Richard
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Maxim De Schepper
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Marion Maetens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Sophia Leduc
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Edoardo Isnaldi
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium; Department of Internal Medicine and Medical Specialties, University of Genoa, IT-16132, Genoa, Italy
| | - Tatjana Geukens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Karen Van Baelen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Ha-Linh Nguyen
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Peter Vermeulen
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium; Department of Oncological Research, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Belgium
| | - François Bertucci
- Institut Paoli Calmettes, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille Université, Marseille, France
| | - Naoto Ueno
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Dirix
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium; Department of Oncological Research, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Giuseppe Floris
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, KU Leuven, 3000, Leuven, Belgium
| | - Elia Biganzoli
- Unit of Medical Statistics, Biometry and Epidemiology, Department of Biomedical and Clinical Sciences (DIBIC) & DSRC, Ospedale "L. Sacco" LITA Campus, Università degli Studi di Milano, 20157, Milan, Italy
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, 3000, Leuven, Belgium.
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8
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Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K. JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer Res 2023; 83:264-284. [PMID: 36409824 PMCID: PMC9845989 DOI: 10.1158/0008-5472.can-22-0423] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/23/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Inflammatory breast cancer (IBC) is a difficult-to-treat disease with poor clinical outcomes due to high risk of metastasis and resistance to treatment. In breast cancer, CD44+CD24- cells possess stem cell-like features and contribute to disease progression, and we previously described a CD44+CD24-pSTAT3+ breast cancer cell subpopulation that is dependent on JAK2/STAT3 signaling. Here we report that CD44+CD24- cells are the most frequent cell type in IBC and are commonly pSTAT3+. Combination of JAK2/STAT3 inhibition with paclitaxel decreased IBC xenograft growth more than either agent alone. IBC cell lines resistant to paclitaxel and doxorubicin were developed and characterized to mimic therapeutic resistance in patients. Multi-omic profiling of parental and resistant cells revealed enrichment of genes associated with lineage identity and inflammation in chemotherapy-resistant derivatives. Integrated pSTAT3 chromatin immunoprecipitation sequencing and RNA sequencing (RNA-seq) analyses showed pSTAT3 regulates genes related to inflammation and epithelial-to-mesenchymal transition (EMT) in resistant cells, as well as PDE4A, a cAMP-specific phosphodiesterase. Metabolomic characterization identified elevated cAMP signaling and CREB as a candidate therapeutic target in IBC. Investigation of cellular dynamics and heterogeneity at the single cell level during chemotherapy and acquired resistance by CyTOF and single cell RNA-seq identified mechanisms of resistance including a shift from luminal to basal/mesenchymal cell states through selection for rare preexisting subpopulations or an acquired change. Finally, combination treatment with paclitaxel and JAK2/STAT3 inhibition prevented the emergence of the mesenchymal chemo-resistant subpopulation. These results provide mechanistic rational for combination of chemotherapy with inhibition of JAK2/STAT3 signaling as a more effective therapeutic strategy in IBC. SIGNIFICANCE Chemotherapy resistance in inflammatory breast cancer is driven by the JAK2/STAT3 pathway, in part via cAMP/PKA signaling and a cell state switch, which can be overcome using paclitaxel combined with JAK2 inhibitors.
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Affiliation(s)
- Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Callahan M Wilde
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Renee C Geck
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Natalie L Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vanessa Almendro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alanna L Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | | | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Ningxuan Zhou
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Walker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Salas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - David A Frank
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth A Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
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9
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Allouchery V, Perdrix A, Calbrix C, Berghian A, Lequesne J, Fontanilles M, Leheurteur M, Etancelin P, Sarafan-Vasseur N, Di Fiore F, Clatot F. Circulating PIK3CA mutation detection at diagnosis in non-metastatic inflammatory breast cancer patients. Sci Rep 2021; 11:24041. [PMID: 34911971 PMCID: PMC8674263 DOI: 10.1038/s41598-021-02643-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/11/2021] [Indexed: 01/04/2023] Open
Abstract
Inflammatory breast cancer (IBC) is an aggressive BC subtype with poor outcomes. A targetable somatic PIK3CA mutation is reported in 30% of IBC, allowing for treatment by PI3Kα-specific inhibitors, such as alpelisib. The aim of this study was to evaluate the detection rate of circulating PIK3CA mutation in locally-advanced IBC (LAIBC) patients harbouring a PIK3CA mutation on initial biopsy. This monocentric retrospective study was based on available stored plasma samples and tumour biopsies at diagnosis from all LAIBC patients treated with neo-adjuvant chemotherapy (NCT) between 2008 and 2018 at the Centre Henri Becquerel. PIK3CA mutations (E542K, E545K, H1047R/L) were assessed by droplet digital PCR (ddPCR) in plasma samples and tumoral tissue at diagnosis. A total of 55 patients were included. Overall, 14/55 patients (25%) had a PIK3CA mutation identified on baseline biopsy (H1047R = 8; H1047L = 3; E545K = 2; E542K = 1). Among them, 11 (79%) patients had enough DNA for circulating DNA analyses, and corresponding circulating PIK3CA mutations were found in 6/11 (55%). Among the 41 patients without PIK3CA mutations on biopsy, 32 (78%) had enough DNA for circulating DNA analysis, and no circulating PIK3CA mutation was identified. Our results revealed no prognostic or predictive value of PIK3CA mutations at the diagnosis of non-metastatic IBC but highlighted the prognostic value of the cfDNA rate at diagnosis. Our study showed that a corresponding circulating PIK3CA mutation was identified in 55% of LAIBC patients with PIK3CA-mutated tumours, while no circulating mutation was found among patients with PI3KCA wild-type tumours.
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Affiliation(s)
- Violette Allouchery
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.
| | - Anne Perdrix
- IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Céline Calbrix
- IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Anca Berghian
- Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Justine Lequesne
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - Maxime Fontanilles
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.,IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France
| | - Marianne Leheurteur
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France
| | | | - Nasrin Sarafan-Vasseur
- IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.,IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France
| | - Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.,IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France
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10
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Luo R, Chong W, Wei Q, Zhang Z, Wang C, Ye Z, Abu-Khalaf MM, Silver DP, Stapp RT, Jiang W, Myers RE, Li B, Cristofanilli M, Yang H. Whole-exome sequencing identifies somatic mutations and intratumor heterogeneity in inflammatory breast cancer. NPJ Breast Cancer 2021; 7:72. [PMID: 34075047 PMCID: PMC8169683 DOI: 10.1038/s41523-021-00278-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
Inflammatory breast cancer (IBC) is the most aggressive form of breast cancer. Although it is a rare subtype, IBC is responsible for roughly 10% of breast cancer deaths. In order to obtain a better understanding of the genomic landscape and intratumor heterogeneity (ITH) in IBC, we conducted whole-exome sequencing of 16 tissue samples (12 tumor and four normal samples) from six hormone-receptor-positive IBC patients, analyzed somatic mutations and copy number aberrations, and inferred subclonal structures to demonstrate ITH. Our results showed that KMT2C was the most frequently mutated gene (42%, 5/12 samples), followed by HECTD1, LAMA3, FLG2, UGT2B4, STK33, BRCA2, ACP4, PIK3CA, and DNAH8 (all nine genes tied at 33% frequency, 4/12 samples). Our data indicated that PTEN and FBXW7 mutations may be considered driver gene mutations for IBC. We identified various subclonal structures and different levels of ITH between IBC patients, and mutations in the genes EIF4G3, IL12RB2, and PDE4B may potentially generate ITH in IBC.
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Affiliation(s)
- Rui Luo
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Weelic Chong
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Qiang Wei
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Zhenchao Zhang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Chun Wang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhong Ye
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maysa M Abu-Khalaf
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Daniel P Silver
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Robert T Stapp
- Department of Pathology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Wei Jiang
- Department of Pathology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ronald E Myers
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Massimo Cristofanilli
- Division of Hematology Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hushan Yang
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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11
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Bertucci F, Boudin L, Finetti P, Van Berckelaer C, Van Dam P, Dirix L, Viens P, Gonçalves A, Ueno NT, Van Laere S, Birnbaum D, Mamessier E. Immune landscape of inflammatory breast cancer suggests vulnerability to immune checkpoint inhibitors. Oncoimmunology 2021; 10:1929724. [PMID: 34104544 PMCID: PMC8158040 DOI: 10.1080/2162402x.2021.1929724] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background. Anti-PD1/PDL1 immune checkpoint inhibitors (ICIs) showed promising results in breast cancer, and exploration of additional actionable immune checkpoints is ongoing. Inflammatory breast cancer (IBC) is an aggressive form of disease, the immune tumor microenvironment (TME) of which is poorly known. We aimed at providing the first comprehensive immune portrait of IBCs. Methods. From the gene expression profiles of 137 IBC and 252 non-IBC clinical samples, we measured the fractions of 22 immune cell types, expression of signatures associated with tertiary lymphoid structures (TLS) and with the response to ICIs (T cell-inflamed signature: TIS) and of 18 genes coding for major actionable immune checkpoints. The IBC/non-IBC comparison was adjusted upon the clinicopathological variables. Results. The immune profiles of IBCs were heterogeneous. CIBERSORT analysis showed profiles rich in macrophages, CD8+ and CD4 + T-cells, with remarkable similarity with melanoma TME. The comparison with non-IBCs showed significant enrichment in M1 macrophages, γδ T-cells, and memory B-cells. IBCs showed higher expression of TLS and TIS signatures. The TIS signature displayed values in IBCs close to those observed in other cancers sensitive to ICIs. Two-thirds of actionable immune genes (HAVCR2/TIM3, CD27, CD70, CTLA4, ICOS, IDO1, LAG3, PDCD1, TNFRSF9, PVRIG, CD274/PDL1, and TIGIT) were overexpressed in IBCs as compared to normal breast and two-thirds were overexpressed in IBCs versus non-IBCs, with very frequent co-overexpression. For most of them, the overexpression was associated with better pathological response to chemotherapy. Conclusion. Our results suggest the potential higher vulnerability of IBC to ICIs. Clinical trials.
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Affiliation(s)
- François Bertucci
- Predictive Oncology Laboratory, "Equipe Labellisée Ligue Contre Le Cancer", Centre De Recherche En Cancérologie De Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille Université, Marseille, France.,Department of Medical Oncology, CRCM, Institut Paoli-Calmettes, Marseille, France
| | - Laurys Boudin
- Predictive Oncology Laboratory, "Equipe Labellisée Ligue Contre Le Cancer", Centre De Recherche En Cancérologie De Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille Université, Marseille, France
| | - Pascal Finetti
- Predictive Oncology Laboratory, "Equipe Labellisée Ligue Contre Le Cancer", Centre De Recherche En Cancérologie De Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille Université, Marseille, France
| | - Christophe Van Berckelaer
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp Belgium
| | - Peter Van Dam
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp Belgium
| | - Luc Dirix
- Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium.,Department of Oncological Research, Oncology Center, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Patrice Viens
- Department of Medical Oncology, CRCM, Institut Paoli-Calmettes, Marseille, France
| | - Anthony Gonçalves
- Predictive Oncology Laboratory, "Equipe Labellisée Ligue Contre Le Cancer", Centre De Recherche En Cancérologie De Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille Université, Marseille, France.,Department of Medical Oncology, CRCM, Institut Paoli-Calmettes, Marseille, France
| | - Naoto T Ueno
- Breast Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp Belgium.,Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, "Equipe Labellisée Ligue Contre Le Cancer", Centre De Recherche En Cancérologie De Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille Université, Marseille, France
| | - Emilie Mamessier
- Predictive Oncology Laboratory, "Equipe Labellisée Ligue Contre Le Cancer", Centre De Recherche En Cancérologie De Marseille (CRCM), Institut Paoli-Calmettes, INSERM UMR1068, CNRS UMR725, Aix-Marseille Université, Marseille, France
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12
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Li X, Kumar S, Harmanci A, Li S, Kitchen RR, Zhang Y, Wali VB, Reddy SM, Woodward WA, Reuben JM, Rozowsky J, Hatzis C, Ueno NT, Krishnamurthy S, Pusztai L, Gerstein M. Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. Genome Med 2021; 13:70. [PMID: 33902690 PMCID: PMC8077918 DOI: 10.1186/s13073-021-00879-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases. METHODS We performed WGS of 20 IBC samples and paired normal blood DNA to identify genomic alterations. For comparison, we used 23 matched non-IBC samples from the Cancer Genome Atlas Program (TCGA). We also validated our findings using WGS data from the International Cancer Genome Consortium (ICGC) and the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We examined a wide selection of genomic features to search for differences between IBC and conventional breast cancer. These include (i) somatic and germline single-nucleotide variants (SNVs), in both coding and non-coding regions; (ii) the mutational signature and the clonal architecture derived from these SNVs; (iii) copy number and structural variants (CNVs and SVs); and (iv) non-human sequence in the tumors (i.e., exogenous sequences of bacterial origin). RESULTS Overall, IBC has similar genomic characteristics to non-IBC, including specific alterations, overall mutational load and signature, and tumor heterogeneity. In particular, we observed similar mutation frequencies between IBC and non-IBC, for each gene and most cancer-related pathways. Moreover, we found no exogenous sequences of infectious agents specific to IBC samples. Even though we could not find any strongly statistically distinguishing genomic features between the two groups, we did find some suggestive differences in IBC: (i) The MAST2 gene was more frequently mutated (20% IBC vs. 0% non-IBC). (ii) The TGF β pathway was more frequently disrupted by germline SNVs (50% vs. 13%). (iii) Different copy number profiles were observed in several genomic regions harboring cancer genes. (iv) Complex SVs were more frequent. (v) The clonal architecture was simpler, suggesting more homogenous tumor-evolutionary lineages. CONCLUSIONS Whole-genome sequencing of IBC manifests a similar genomic architecture to non-IBC. We found no unique genomic alterations shared in just IBCs; however, subtle genomic differences were observed including germline alterations in TGFβ pathway genes and somatic mutations in the MAST2 kinase that could represent potential therapeutic targets.
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Affiliation(s)
- Xiaotong Li
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center Houston, Houston, TX USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Robert R. Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Yan Zhang
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH USA
- The Ohio State University Comprehensive Cancer Center (OSUCCC – James), Columbus, OH USA
| | - Vikram B. Wali
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Sangeetha M. Reddy
- Division of Hematology/Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX USA
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Wendy A. Woodward
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - James M. Reuben
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Christos Hatzis
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Naoto T. Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lajos Pusztai
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Computer Science, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Statistics and Data Science, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
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13
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Checkpoint Inhibitors and Hepatotoxicity. Biomedicines 2021; 9:biomedicines9020101. [PMID: 33494227 PMCID: PMC7909829 DOI: 10.3390/biomedicines9020101] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
Uncontrolled immune response to a pathogen or any protein can lead to tissue damage and autoimmune diseases, that represent aberrant immune responses of the individual to its own cells and/or proteins. The immune checkpoint system is the regulatory mechanism that controls immune responses. Tumor cells escape the immune surveillance mechanism, avoiding immune detection and elimination by activating these checkpoints and suppressing the anti-tumor response, thus allowing formation of tumors. Antigenic modulation facilitates masking and contributes to the escape of tumor cells. In addition, there are growing cell promoters, like transforming growth factor β (TGF-β), contributing to escape mechanisms. Targeting the immunological escape of malignant cells is the basis of immune oncology. Checkpoint inhibitors, cytokines and their antibodies may enhance the immune system’s response to tumors. Currently, immunomodulatory agents have been designed, evaluated in clinical trials and have been approved by both European and United States Drug Agencies. The present review is a reflection of the increasingly important role of the checkpoint inhibitors. Our aim is to review the side effects with the emphasis on hepatic adverse reactions of these novel biological drug interventions.
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14
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Dobiasova B, Mego M. Biomarkers for Inflammatory Breast Cancer: Diagnostic and Therapeutic Utility. BREAST CANCER-TARGETS AND THERAPY 2020; 12:153-163. [PMID: 33116817 PMCID: PMC7569067 DOI: 10.2147/bctt.s231502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022]
Abstract
Inflammatory breast cancer (IBC) is a rare and highly aggressive subtype of advanced breast cancer. The aggressive behavior, resistance to chemotherapy, angiogenesis, and high metastatic potential are key intrinsic characteristics of IBC caused by many specific factors. Pathogenesis and behavior of IBC are closely related to tumor surrounding inflammatory and immune cells, blood vessels, and extracellular matrix, which are all components of the tumor microenvironment (TME). The tumor microenvironment has a crucial role in the local immune r09esponse. The communication between intrinsic and extrinsic components of IBC and the abundance of cytokines and chemokines in the TME strongly contribute to the aggressiveness and high angiogenic potential of this tumor. Critical modes of interaction are cytokine-mediated communication and direct intercellular contact between cancer cells and tumor microenvironment with a variety of pathway crosstalk. This review aimed to summarize current knowledge of predictive and prognostic biomarkers in IBC.
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Affiliation(s)
- Barbora Dobiasova
- 2 Department of Oncology, Comenius University, Faculty of Medicine, National Cancer Institute, Bratislava, Slovak Republic
| | - Michal Mego
- 2 Department of Oncology, Comenius University, Faculty of Medicine, National Cancer Institute, Bratislava, Slovak Republic
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15
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Faldoni FLC, Villacis RAR, Canto LM, Fonseca-Alves CE, Cury SS, Larsen SJ, Aagaard MM, Souza CP, Scapulatempo-Neto C, Osório CABT, Baumbach J, Marchi FA, Rogatto SR. Inflammatory Breast Cancer: Clinical Implications of Genomic Alterations and Mutational Profiling. Cancers (Basel) 2020; 12:cancers12102816. [PMID: 33007869 PMCID: PMC7650681 DOI: 10.3390/cancers12102816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Inflammatory breast cancer (IBC) is an aggressive disease with high mortality rates. Nowadays, there is no targeted treatment for this tumor type. Based on this context, we investigated the molecular profile of this disease by using well-established methodologies (high-resolution microarray platform, targeted next-generation sequencing, and immunohistochemistry) that have proven potential to unveil cancer biomarkers. We found alterations related to IBC aggressiveness and metastasis (gains of MDM4, losses of CHL1, and high homologous recombination deficiency scores), and worse overall survival (variants in HR and mismatch repair genes). We also compared the mutational profiling of our cases with literature data, which includes both non-IBC and IBC cases, validating our findings. Overall, we describe genetic alterations with the potential to be used as prognostic or predictive biomarkers and ultimately improve IBC patients’ care. Abstract Inflammatory breast cancer (IBC) is a rare and aggressive type of breast cancer whose molecular basis is poorly understood. We performed a comprehensive molecular analysis of 24 IBC biopsies naïve of treatment, using a high-resolution microarray platform and targeted next-generation sequencing (105 cancer-related genes). The genes more frequently affected by gains were MYC (75%) and MDM4 (71%), while frequent losses encompassed TP53 (71%) and RB1 (58%). Increased MYC and MDM4 protein expression levels were detected in 18 cases. These genes have been related to IBC aggressiveness, and MDM4 is a potential therapeutic target in IBC. Functional enrichment analysis revealed genes associated with inflammatory regulation and immune response. High homologous recombination (HR) deficiency scores were detected in triple-negative and metastatic IBC cases. A high telomeric allelic imbalance score was found in patients having worse overall survival (OS). The mutational profiling was compared with non-IBC (TCGA, n = 250) and IBC (n = 118) from four datasets, validating our findings. Higher frequency of TP53 and BRCA2 variants were detected compared to non-IBC, while PIKC3A showed similar frequency. Variants in mismatch repair and HR genes were associated with worse OS. Our study provided a framework for improved diagnosis and therapeutic alternatives for this aggressive tumor type.
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Affiliation(s)
- Flávia L. C. Faldoni
- International Research Center, A.C.Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.L.C.F.); (F.A.M.)
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
| | - Rolando A. R. Villacis
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília-UnB, Brasília 70910-900, Brazil;
| | - Luisa M. Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
| | - Carlos E. Fonseca-Alves
- Department of Veterinary Surgery and Anesthesiology, School of Veterinary Medicine and Animal Science, São Paulo State University-UNESP, Botucatu 18618-681, Brazil;
| | - Sarah S. Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University-UNESP, Botucatu 18618-689, Brazil;
| | - Simon J. Larsen
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; (S.J.L.); (J.B.)
| | - Mads M. Aagaard
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
| | - Cristiano P. Souza
- Department of Breast and Gynecologic Oncology, Barretos Cancer Hospital, Pio XII Foundation, Barretos 14784-390, Brazil;
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos SP 14784-400, Brazil;
- Diagnósticos da América (DASA), Barueri 01525-001, Brazil
| | | | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark; (S.J.L.); (J.B.)
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Fabio A. Marchi
- International Research Center, A.C.Camargo Cancer Center, São Paulo 01508-010, Brazil; (F.L.C.F.); (F.A.M.)
| | - Silvia R. Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (L.M.C.); (M.M.A.)
- Institute of Regional Health Research, University of Southern Denmark, 500 Odense, Denmark
- Correspondence:
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16
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Bertucci F, Van Laere S, Birnbaum D. Genomic landscape of inflammatory breast cancer identifies potential actionable genetic alterations. Oncoscience 2020; 7:57-59. [PMID: 32923518 PMCID: PMC7458333 DOI: 10.18632/oncoscience.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/26/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille F-13009, France.,Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Steven Van Laere
- Department of Oncological Research, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille F-13009, France
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17
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Epigenetics in Inflammatory Breast Cancer: Biological Features and Therapeutic Perspectives. Cells 2020; 9:cells9051164. [PMID: 32397183 PMCID: PMC7291154 DOI: 10.3390/cells9051164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/25/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Evidence has emerged implicating epigenetic alterations in inflammatory breast cancer (IBC) origin and progression. IBC is a rare and rapidly progressing disease, considered the most aggressive type of breast cancer (BC). At clinical presentation, IBC is characterized by diffuse erythema, skin ridging, dermal lymphatic invasion, and peau d'orange aspect. The widespread distribution of the tumor as emboli throughout the breast and intra- and intertumor heterogeneity is associated with its poor prognosis. In this review, we highlighted studies documenting the essential roles of epigenetic mechanisms in remodeling chromatin and modulating gene expression during mammary gland differentiation and the development of IBC. Compiling evidence has emerged implicating epigenetic changes as a common denominator linking the main risk factors (socioeconomic status, environmental exposure to endocrine disruptors, racial disparities, and obesity) with IBC development. DNA methylation changes and their impact on the diagnosis, prognosis, and treatment of IBC are also described. Recent studies are focusing on the use of histone deacetylase inhibitors as promising epigenetic drugs for treating IBC. All efforts must be undertaken to unravel the epigenetic marks that drive this disease and how this knowledge could impact strategies to reduce the risk of IBC development and progression.
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18
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Testa U, Castelli G, Pelosi E. Breast Cancer: A Molecularly Heterogenous Disease Needing Subtype-Specific Treatments. Med Sci (Basel) 2020; 8:E18. [PMID: 32210163 PMCID: PMC7151639 DOI: 10.3390/medsci8010018] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly occurring cancer in women. There were over two-million new cases in world in 2018. It is the second leading cause of death from cancer in western countries. At the molecular level, breast cancer is a heterogeneous disease, which is characterized by high genomic instability evidenced by somatic gene mutations, copy number alterations, and chromosome structural rearrangements. The genomic instability is caused by defects in DNA damage repair, transcription, DNA replication, telomere maintenance and mitotic chromosome segregation. According to molecular features, breast cancers are subdivided in subtypes, according to activation of hormone receptors (estrogen receptor and progesterone receptor), of human epidermal growth factors receptor 2 (HER2), and or BRCA mutations. In-depth analyses of the molecular features of primary and metastatic breast cancer have shown the great heterogeneity of genetic alterations and their clonal evolution during disease development. These studies have contributed to identify a repertoire of numerous disease-causing genes that are altered through different mutational processes. While early-stage breast cancer is a curable disease in about 70% of patients, advanced breast cancer is largely incurable. However, molecular studies have contributed to develop new therapeutic approaches targeting HER2, CDK4/6, PI3K, or involving poly(ADP-ribose) polymerase inhibitors for BRCA mutation carriers and immunotherapy.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Regina Elena 299, 00161 Rome, Italy; (G.C.); (E.P.)
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19
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Genetic Variants Detected Using Cell-Free DNA from Blood and Tumor Samples in Patients with Inflammatory Breast Cancer. Int J Mol Sci 2020; 21:ijms21041290. [PMID: 32075053 PMCID: PMC7072950 DOI: 10.3390/ijms21041290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
We studied genomic alterations in 19 inflammatory breast cancer (IBC) patients with advanced disease using samples of tissue and paired blood serum or plasma (cell-free DNA, cfDNA) by targeted next generation sequencing (NGS). At diagnosis, the disease was triple negative (TN) in eleven patients (57.8%), ER+ Her2- IBC in six patients (31.6%), ER+ Her2+ IBC in one patient (5.3%), and ER- Her2+ IBC in one other patient (5.3%). Pathogenic or likely pathogenic variants were frequently detected in TP53 (47.3%), PMS2 (26.3%), MRE11 (26.3%), RB1 (10.5%), BRCA1 (10.5%), PTEN (10.5%) and AR (10.5%); other affected genes included PMS1, KMT2C, BRCA2, PALB2, MUTYH, MEN1, MSH2, CHEK2, NCOR1, PIK3CA, ESR1 and MAP2K4. In 15 of the 19 patients in which tissue and paired blood were collected at the same time point, 80% of the variants detected in tissue were also detected in the paired cfDNA. Higher concordance between tissue and cfDNA was found for variants with higher allele fraction in tissue (AFtissue ≥ 5%). Furthermore, 86% of the variants detected in cfDNA were also detected in paired tissue. Our study suggests that the genetic profile measured in blood cfDNA is complementary to that of tumor tissue in IBC patients.
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20
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Bertucci F, Rypens C, Finetti P, Guille A, Adélaïde J, Monneur A, Carbuccia N, Garnier S, Dirix P, Gonçalves A, Vermeulen P, Debeb BG, Wang X, Dirix L, Ueno NT, Viens P, Cristofanilli M, Chaffanet M, Birnbaum D, Van Laere S. NOTCH and DNA repair pathways are more frequently targeted by genomic alterations in inflammatory than in non-inflammatory breast cancers. Mol Oncol 2020; 14:504-519. [PMID: 31854063 PMCID: PMC7053236 DOI: 10.1002/1878-0261.12621] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/06/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
Inflammatory breast cancer (IBC) is the most pro‐metastatic form of breast cancer. Better understanding of its pathophysiology and identification of actionable genetic alterations (AGAs) are crucial to improve systemic treatment. We aimed to define the DNA profiles of IBC vs noninflammatory breast cancer (non‐IBC) clinical samples in terms of copy number alterations (CNAs), mutations, and AGAs. We applied targeted next‐generation sequencing (tNGS) and array‐comparative genomic hybridization (aCGH) to 57 IBC and 50 non‐IBC samples and pooled these data with four public datasets profiled using NGS and aCGH, leading to a total of 101 IBC and 2351 non‐IBC untreated primary tumors. The respective percentages of each molecular subtype [hormone receptor‐positive (HR+)/HER2−, HER2+, and triple‐negative] were 68%, 15%, and 17% in non‐IBC vs 25%, 35%, and 40% in IBC. The comparisons were adjusted for both the molecular subtypes and the American Joint Committee on Cancer (AJCC) stage. The 10 most frequently altered genes in IBCs were TP53 (63%), HER2/ERBB2 (30%), MYC (27%), PIK3CA (21%), BRCA2 (14%), CCND1 (13%), GATA3 (13%), NOTCH1 (12%), FGFR1 (11%), and ARID1A (10%). The tumor mutational burden was higher in IBC than in non‐IBC. We identified 96 genes with an alteration frequency (p < 5% and q < 20%) different between IBC and non‐IBC, independently from the molecular subtypes and AJCC stage; 95 were more frequently altered in IBC, including TP53, genes involved in the DNA repair (BRCA2) and NOTCH pathways, and one (PIK3CA) was more frequently altered in non‐IBC. Ninety‐seven percent of IBCs displayed at least one AGA. This percentage was higher than in non‐IBC (87%), notably for drugs targeting DNA repair, NOTCH signaling, and CDK4/6, whose pathways were more frequently altered (DNA repair) or activated (NOTCH and CDK4/6) in IBC than in non‐IBC. The genomic landscape of IBC is different from that of non‐IBC. Enriched AGAs in IBC may explain its aggressiveness and provide clinically relevant targets.
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Affiliation(s)
- François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France.,Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Charlotte Rypens
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Pascal Finetti
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - José Adélaïde
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Audrey Monneur
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Nadine Carbuccia
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Séverine Garnier
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Piet Dirix
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Anthony Gonçalves
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France.,Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Peter Vermeulen
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Bisrat G Debeb
- MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoping Wang
- MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Dirix
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
| | - Naoto T Ueno
- MD Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrice Viens
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Max Chaffanet
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Institut Paoli-Calmettes, Aix-Marseille Université, France
| | - Steven Van Laere
- Translational Cancer Research Unit and Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, GZA Hospitals Sint-Augustinus and University of Antwerp Wilrijk, Antwerp, Belgium
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21
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HER2 somatic mutation analysis in breast cancer: correlation with clinicopathological features. Hum Pathol 2019; 92:32-38. [DOI: 10.1016/j.humpath.2019.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/13/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022]
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22
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Liang X, Vacher S, Boulai A, Bernard V, Baulande S, Bohec M, Bièche I, Lerebours F, Callens C. Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer. Breast Cancer Res 2018; 20:88. [PMID: 30086764 PMCID: PMC6081877 DOI: 10.1186/s13058-018-1007-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background Inflammatory breast cancer (IBC) is the most aggressive form of primary breast cancer. Using a custom-made breast cancer gene sequencing panel, we investigated somatic mutations in IBC to better understand the genomic differences compared with non-IBC and to consider new targeted therapy in IBC patients. Methods Targeted next-generation sequencing (NGS) of 91 candidate breast cancer-associated genes was performed on 156 fresh-frozen breast tumor tissues from IBC patients. Mutational profiles from 197 primary breast tumors from The Cancer Genome Atlas (TCGA) were used as non-IBC controls for comparison analysis. The mutational landscape of IBC was correlated with clinicopathological data and outcomes. Results After genotype calling and algorithmic annotations, we identified 392 deleterious variants in IBC and 320 variants in non-IBC cohorts, respectively. IBC tumors harbored more mutations than non-IBC (2.5 per sample vs. 1.6 per sample, p < 0.0001). Eighteen mutated genes were significantly different between the two cohorts, namely TP53, CDH1, NOTCH2, MYH9, BRCA2, ERBB4, POLE, FGFR3, ROS1, NOTCH4, LAMA2, EGFR, BRCA1, TP53BP1, ESR1, THBS1, CASP8, and NOTCH1. In IBC, the most frequently mutated genes were TP53 (43.0%), PIK3CA (29.5%), MYH9 (8.3%), NOTCH2 (8.3%), BRCA2 (7.7%), ERBB4 (7.1%), FGFR3 (6.4%), POLE (6.4%), LAMA2 (5.8%), ARID1A (5.1%), NOTCH4 (5.1%), and ROS1 (5.1%). After grouping 91 genes on 10 signaling pathways, we found that the DNA repair pathway for the triple-negative breast cancer (TNBC) subgroup, the RTK/RAS/MAPK and cell cycle pathways for the HR–/HER2+ subgroup, the DNA repair, RTK/RAS/MAPK, and NOTCH pathways for the HR+/HER2– subgroup, and the DNA repair, epigenome, and diverse pathways for the HR+/HER2+ subgroup were all significantly differently altered between IBC and non-IBC. PIK3CA mutation was independently associated with worse metastasis-free survival (MFS) in IBC since the median MFS for the PIK3CA mutant type was 26.0 months and for the PIK3CA wild type was 101.1 months (p = 0.002). This association was observed in TNBC (p = 0.04) and the HR–/HER2+ subgroups (p = 0.0003), but not in the HR+/HER2– subgroup of IBC. Conclusions Breast cancer-specific targeted NGS uncovered a high frequency of deleterious somatic mutations in IBC, some of which may be relevant for clinical management. Electronic supplementary material The online version of this article (10.1186/s13058-018-1007-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu Liang
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.,Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Sophie Vacher
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Anais Boulai
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Virginie Bernard
- Clinic bioinformatic Unit, Department of Biopathology, Curie Institute, PSL Research University, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Curie Institute, PSL Research University, Paris, France
| | - Mylene Bohec
- Institut Curie Genomics of Excellence (ICGex) Platform, Curie Institute, PSL Research University, Paris, France
| | - Ivan Bièche
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.,EA7331, Paris Descartes University, Sorbonne Paris Cité, Faculty of Pharmaceutical and Biological Sciences, Paris, France
| | - Florence Lerebours
- Department of Medical Oncology, Curie Institute, René Huguenin Hospital, Saint-Cloud, France
| | - Céline Callens
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
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Lim B, Woodward WA, Wang X, Reuben JM, Ueno NT. Inflammatory breast cancer biology: the tumour microenvironment is key. Nat Rev Cancer 2018; 18:485-499. [PMID: 29703913 DOI: 10.1038/s41568-018-0010-y] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Inflammatory breast cancer (IBC) is a rare and aggressive disease that accounts for ~2-4% of all breast cancers. However, despite its low incidence rate, IBC is responsible for 7-10% of breast cancer-related mortality in Western countries. Thus, the discovery of robust biological targets and the development of more effective therapeutics in IBC are crucial. Despite major international efforts to understand IBC biology, genomic studies have not led to the discovery of distinct biological mechanisms in IBC that can be translated into novel therapeutic strategies. In this Review, we discuss these molecular profiling efforts and highlight other important aspects of IBC biology. We present the intrinsic characteristics of IBC, including stemness, metastatic potential and hormone receptor positivity; the extrinsic features of the IBC tumour microenvironment (TME), including various constituent cell types; and lastly, the communication between these intrinsic and extrinsic components. We summarize the latest perspectives on the key biological features of IBC, with particular emphasis on the TME as an important contributor to the aggressive nature of IBC. On the basis of the current understanding of IBC, we hope to develop the next generation of translational studies, which will lead to much-needed survival improvements in patients with this deadly disease.
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Affiliation(s)
- Bora Lim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Wendy A Woodward
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoping Wang
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James M Reuben
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Philley JV, Hertweck KL, Kannan A, Brown-Elliott BA, Wallace RJ, Kurdowska A, Ndetan H, Singh KP, Miller EJ, Griffith DE, Dasgupta S. Sputum Detection of Predisposing Genetic Mutations in Women with Pulmonary Nontuberculous Mycobacterial Disease. Sci Rep 2018; 8:11336. [PMID: 30054559 PMCID: PMC6063893 DOI: 10.1038/s41598-018-29471-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/26/2018] [Indexed: 01/08/2023] Open
Abstract
Nontuberculous mycobacterial lung disease (NTM), including Mycobacterium avium complex (MAC), is a growing health problem in North America and worldwide. Little is known about the molecular alterations occurring in the tissue microenvironment during NTM pathogenesis. Utilizing next generation sequencing, we sequenced sputum and matched lymphocyte DNA in 15 MAC patients for a panel of 19 genes known to harbor cancer susceptibility associated mutations. Thirteen of 15 NTM subjects had a diagnosis of breast cancer (BCa) before or after NTM infection. Thirty three percent (4/12) of these NTM-BCa cases exhibited at least 3 somatic mutations in sputa compared to matched lymphocytes. Twenty four somatic mutations were detected with at least one mutation in ATM, ERBB2, BARD1, BRCA1, BRCA2, AR, TP53, PALB2, CASP8, BRIP1, NBN and TGFB1 genes. All four NTM-BCa patients harboring somatic mutations also exhibited 15 germ line BRCA1 and BRCA2 mutations. The two NTM subjects without BCa exhibited twenty somatic mutations spanning BRCA1, BRCA1, BARD1, BRIP1, CHEK2, ERBB2, TP53, ATM, PALB2, TGFB1 and 3 germ line mutations in BRCA1 and BRCA2 genes. A single copy loss of STK11 and AR gene was noted in NTM-BCa subjects. Periodic screening of sputa may aid to develop risk assessment biomarkers for neoplastic diseases in NTM patients.
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Affiliation(s)
- Julie V Philley
- Department of Medicine, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Kate L Hertweck
- Department of Biology, The University of Texas at Tyler, Tyler, Texas, USA
| | - Anbarasu Kannan
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Barbara A Brown-Elliott
- Department of The Mycobacteria/Nocardia Research Laboratory Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Richard J Wallace
- Department of The Mycobacteria/Nocardia Research Laboratory Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Anna Kurdowska
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Harrison Ndetan
- Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Karan P Singh
- Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Edmund J Miller
- Department of The Center for Heart and Lung Research, The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - David E Griffith
- Department of Medicine, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA.
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25
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Heeke AL, Pishvaian MJ, Lynce F, Xiu J, Brody JR, Chen WJ, Baker TM, Marshall JL, Isaacs C. Prevalence of Homologous Recombination-Related Gene Mutations Across Multiple Cancer Types. JCO Precis Oncol 2018; 2018. [PMID: 30234181 DOI: 10.1200/po.17.00286] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose The prevalence of homologous recombination DNA damage repair (HR-DDR) deficiencies among all tumor lineages is not well characterized. Therapy directed toward homologous recombination DDR deficiency (HRD) is now approved in ovarian and breast cancer, and there may be additional opportunities for benefit for patients with other cancers. Comprehensive evaluations for HRD are limited in part by the lack of a uniform, cost-effective method for testing and defining HRD. Methods Molecular profiles of 52,426 tumors were reviewed to identify pathogenic mutations in the HR-DDR genes ARID1A, ATM, ATRX, BAP1, BARD1, BLM, BRCA1/2, BRIP1, CHEK1/2, FANCA/C/D2/E/F/G/L, MRE11A, NBN, PALB2, RAD50, RAD51, RAD51B, or WRN. From solid tumors submitted to Caris Life Sciences, molecular profiles were generated using next-generation sequencing (NGS; average read depth, 500×). A total of 17,566 tumors were sequenced with NGS600 (n = 592 genes), and 34,860 tumors underwent hotspot Illumina MiSeq platform testing (n = 47 genes). Results Of the tumors that underwent NGS600 testing, the overall frequency of HRDDR mutations detected was 17.4%, and the most commonly mutated lineages were endometrial (34.4%; n = 1,475), biliary tract (28.9%; n = 343), bladder (23.9%; n = 201), hepatocellular (20.9%; n = 115), gastroesophageal (20.8%; n = 619), and ovarian (20.0%; n = 2,489). Least commonly mutated lineages included GI stromal (3.7%; n = 108), head and neck (6.8%; n = 206), and sarcoma (9.3%; n = 592). ARID1A was the most commonly mutated gene (7.2%), followed by BRCA2 (3.0%), BRCA1 (2.8%), ATM (1.3%), ATRX (1.3%), and CHEK2 (1.3%). Conclusions HR-DDR mutations were seen in 17.4% of tumors across 21 cancer lineages, providing a path to explore the role of HRD-directed therapies, including poly-ADP ribose polymerase inhibitors, DNA-damaging chemotherapies, and newer agents such as ATR inhibitors.
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Affiliation(s)
- Arielle L Heeke
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Michael J Pishvaian
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Filipa Lynce
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Joanne Xiu
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Jonathan R Brody
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Wang-Juh Chen
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Tabari M Baker
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - John L Marshall
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
| | - Claudine Isaacs
- Arielle L. Heeke, Michael J. Pishvaian, Filipa Lynce, John L. Marshall, Claudine Isaacs, Georgetown University, Washington, DC, Joanne Xiu, Wang-Juh Chen, Tabari M. Baker, Caris Life Sciences, Inc., Phoenix, AZ; and Jonathan R. Brody, Thomas Jefferson University, Philadelphia, PA
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26
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Bieg-Bourne CC, Millis SZ, Piccioni DE, Fanta PT, Goldberg ME, Chmielecki J, Parker BA, Kurzrock R. Next-Generation Sequencing in the Clinical Setting Clarifies Patient Characteristics and Potential Actionability. Cancer Res 2017; 77:6313-6320. [PMID: 28939679 PMCID: PMC5690871 DOI: 10.1158/0008-5472.can-17-1569] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/22/2017] [Accepted: 09/11/2017] [Indexed: 12/17/2022]
Abstract
Enhancements in clinical-grade next-generation sequencing (NGS) have fueled the advancement of precision medicine in the clinical oncology field. Here, we survey the molecular profiles of 1,113 patients with diverse malignancies who successfully underwent clinical-grade NGS (236-404 genes) in an academic tertiary cancer center. Among the individual tumors examined, the majority showed at least one detectable alteration (97.2%). Among 2,045 molecular aberrations was the involvement of 302 distinct genes. The most commonly altered genes were TP53 (47.0%), CDKN2A (18.0%), TERT (17.0%), and KRAS (16.0%), and the majority of patients had tumors that harbored multiple alterations. Tumors displayed a median of four alterations (range, 0-29). Most individuals had at least one potentially actionable alteration (94.7%), with the median number of potentially actionable alterations per patient being 2 (range, 0-13). A total of 1,048 (94.2%) patients exhibited a unique molecular profile, with either genes altered or loci within the gene(s) altered being distinct. Approximately 13% of patients displayed a genomic profile identical to at least one other patient; although genes altered were the same, the affected loci may have differed. Overall, our results underscore the complex heterogeneity of malignancies and argue that customized combination therapies will be essential to optimize cancer treatment regimens. Cancer Res; 77(22); 6313-20. ©2017 AACR.
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Affiliation(s)
- Cheyennedra C Bieg-Bourne
- San Diego State University, San Diego, California.
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, California
| | | | - David E Piccioni
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, California
| | - Paul T Fanta
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, California
| | | | | | - Barbara A Parker
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UC San Diego Moores Cancer Center, La Jolla, California
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