1
|
Sun Y, Zhang X, Yang X, Ma J. Clinical Utility of Circulating Tumor DNA for Detecting Lung Cancer Mutations by Targeted Next-Generation Sequencing With Insufficient Tumor Samples. J Clin Lab Anal 2024:e25099. [PMID: 39315762 DOI: 10.1002/jcla.25099] [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: 02/14/2024] [Revised: 08/07/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Circulating tumor deoxyribonucleic acid (ctDNA) is increasingly applied in clinical practice. This study aimed to explore clinical utility of a minimal invasive and sensitive way of ctDNA for next-generation sequencing in non-small cell lung cancer (NSCLC) with inadequate tumor samples. METHODS Targeted DNA sequencing was performed on tissue biopsies and matched plasma samples from 60 patients with NSCLC. RESULTS A total of 13 driving genes were detected in 60 matched tissue DNA (tDNA) and ctDNA samples. Overall concordance rate was 75.47%, with 77.55% sensitivity and 50% specificity. Epidermal growth factor receptor (EGFR) mutations were the most common in both tDNA and ctDNA samples. Among other mutated genes were tumor protein p53 (TP53), erb-b2 receptor tyrosine kinase 2 (ERBB2), anaplastic lymphoma kinase (ALK), cyclin-dependent kinase inhibitor 2A (CDKN2A), ros proto-oncogene 1, and receptor tyrosine kinase (ROS1). Mutations in b-raf proto-oncogene, serine/threonine kinase (BRAF), cluster of differentiation 274 (CD274), neurotrophin receptor tyrosine kinase 1 (NTRK1), and rearranged during transfection (RET) occurred only in plasma. The majority of mutations in both samples were single-nucleotide variants. Deletions were found in EGFR, BRAF, and TP53 in ctDNA, whereas in tDNA, deletions were only found in EGFR. In ALK, single nucleic acid-site amplification occurred simultaneously in tissue and plasma, but insertions and copy number variations were detected only in plasma. CONCLUSIONS Identifying ctDNA mutations by targeted sequencing in plasma is feasible, showing the clinical value of ctDNA-targeted sequencing in NSCLC patients when tumor tissue sampling is insufficient or even impossible.
Collapse
Affiliation(s)
- Yi Sun
- Pediatric, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Xu Zhang
- Department of Molecular Diagnostics, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
| | - Xinhua Yang
- Department of Molecular Diagnostics, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
| | - Jiangjun Ma
- Department of Molecular Diagnostics, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
| |
Collapse
|
2
|
Lai J, Deng S, Cao J, Ren Y, Xu Z, Qi X, Xu M, Liao N. Identification of biomarker associated with Trop2 in breast cancer: implication for targeted therapy. Discov Oncol 2024; 15:413. [PMID: 39240479 PMCID: PMC11379678 DOI: 10.1007/s12672-024-01261-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 08/22/2024] [Indexed: 09/07/2024] Open
Abstract
PURPOSE Trop2, a cell membrane glycoprotein, is overexpressed in almost all epithelial cancers. This study aimed to explore the mutational characteristics and significance of Trop2 in breast cancer (BC). METHODS Patients diagnosed with BC (n = 77) were enrolled to investigate expression level and clinical characteristics of Trop2. Database of cBioPortal and Kaplan-Meier Plotter were used to evaluate the effects of Trop2 (TACSTD2) genomic ateration and mRNA expression levels on disease-free survival (DFS) and relapse-free survival (RFS), respectively. Based on next generation sequencing analysis, the Trop2 mutation characteristics of BC patients were deeply depicted. In addition, Trop2 expression, mutation and methylation signature associated with Trop2 mutations were analyzed. RESULTS Trop2 mutation and high expression of Trop2 were predictive biomarker for shorter DFS and RFS in BC. The positive rate of Trop2 expression in these 77 BC patients was 96.1% (74/77). Based on the Trop2 expression level, the patients were classified into Trop2 negative group, medium expression group and high expression group. The mutation frequencies of MAP3K1, NOTCH2, PTEN and MAGI2 were significantly higher in Trop2 medium expression group than high expression group. Moreover, we investigated the effect of the Trop2 mutations on other genes, including co-expressed genes, differentially mutated genes, differentially expressed genes, gene methylation and phosphorylation. We found that MED8, DPH2, KDM4A, EBNA1BP2, USP1, IPO13, CGAS, PRKAA2, NCOA7, ASCC3 and ABRACL were differentially expressed, mutated and methylated between Trop2 mutation group and wild group. CONCLUSION MAP3K1, NOTCH2, PTEN and MAGI2 mutations were significantly different between Trop2 medium expression and Trop2 high expression BC patients. The effects of Trop2 mutation on the expression, variation, methylation, and phosphorylation of other genes were comprehensively revealed. High expression level of Trop2 and Trop2 mutation were predictive biomarker for poor prognosis and targeted therapy in BC.
Collapse
Affiliation(s)
- Jianguo Lai
- Department of Breast Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Shuxuan Deng
- Department of Breast Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Jiyuan Cao
- Department of Breast Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yongqi Ren
- Department of Breast Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zanmei Xu
- Medical Department, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Xiaofang Qi
- Medical Department, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Mian Xu
- Medical Department, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Ning Liao
- Department of Breast Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China.
| |
Collapse
|
3
|
Raei M, Heydari K, Tabarestani M, Razavi A, Mirshafiei F, Esmaeily F, Taheri M, Hoseini A, Nazari H, Shamshirian D, Alizadeh-Navaei R. Diagnostic accuracy of ESR1 mutation detection by cell-free DNA in breast cancer: a systematic review and meta-analysis of diagnostic test accuracy. BMC Cancer 2024; 24:908. [PMID: 39069608 DOI: 10.1186/s12885-024-12674-z] [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: 02/20/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Estrogen receptors express in nearly 70% of breast cancers (ER-positive). Estrogen receptor alpha plays a fundamental role as a significant factor in breast cancer progression for the early selection of therapeutic approaches. Accordingly, there has been a surge of attention to non-invasive techniques, including circulating Cell-free DNA (ccfDNA) or Cell-Free DNA (cfDNA), to detect and track ESR1 genotype. Therefore, this study aimed to examine the diagnosis accuracy of ESR1 mutation detection by cell-free DNA in breast cancer patientsthrough a systematic review and comprehensive meta-analysis. METHODS PubMed, Embase, and Web of Science databases were searched up to 6 April 2022. Diagnostic studies on ESR1 measurement by cfDNA, which was confirmed using the tumour tissue biopsy, have been included in the study. The sensitivity, specificity, accuracy, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR) and negative likelihood ratio (NLR) were considered to analyse the data. RESULTS Out of 649 papers, 13 papers with 15 cohorts, including 389 participants, entered the meta-analyses. The comprehensive meta-analysis indicated a high sensitivity (75.52, 95% CI 60.19-90.85), specificity (88.20, 95% CI 80.99-95.40), and high accuracy of 88.96 (95% CI 83.23-94.69) for plasma ESR1. We also found a moderate PPV of 56.94 (95% CI 41.70-72.18) but a high NPV of 88.53 (95% CI 82.61-94.44). We also found an NLR of 0.443 (95% CI 0.09-0.79) and PLR of 1.60 (95% CI 1.20-1.99). CONCLUSION This systematic review and comprehensive meta-analysis reveal that plasma cfDNA testing exhibits high sensitivity and specificity in detecting ESR1 mutations in breast cancer patients. This suggests that the test could be a valuable diagnostic tool. It may serve as a dependable and non-invasive technique for identifying ESR1 mutations in breast cancer patients. However, more extensive research is needed to confirm its prognostic value.
Collapse
Affiliation(s)
- Maedeh Raei
- Gastrointestinal Cancer Research Center, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Moallem Sq, Sari, Sari, 44817844718, Iran
| | - Keyvan Heydari
- Gastrointestinal Cancer Research Center, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Moallem Sq, Sari, Sari, 44817844718, Iran
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Tabarestani
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Razavi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Mirshafiei
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Esmaeily
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahsa Taheri
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Aref Hoseini
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Danial Shamshirian
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Center, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Moallem Sq, Sari, Sari, 44817844718, Iran.
| |
Collapse
|
4
|
Li T, Ma W, Al-Obeidi E. Evolving Precision First-Line Systemic Treatment for Patients with Unresectable Non-Small Cell Lung Cancer. Cancers (Basel) 2024; 16:2350. [PMID: 39001412 PMCID: PMC11240640 DOI: 10.3390/cancers16132350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
First-line systemic therapy for patients with advanced or metastatic non-small cell lung cancer (NSCLC) has rapidly evolved over the past two decades. First, molecularly targeted therapy for a growing number of gain-of-function molecular targets has been shown to improve progression-free survival (PFS) and overall survival (OS) with favorable toxicity profiles compared to platinum-containing chemotherapy and can be given as first-line systemic therapy in ~25% of patients with NSCLC. Actionable genetic alterations include EGFR, BRAF V600E, and MET exon 14 splicing site-sensitizing mutations, as well as ALK-, ROS1-, RET-, and NTRK-gene fusions. Secondly, inhibitors of programmed cell death protein 1 or its ligand 1 (PD-1/L1) such as pembrolizumab, atezolizumab, or cemiplimab monotherapy have become a standard of care for ~25% of patients with NSCLC whose tumors have high PD-L1 expression (total proportion score (TPS) ≥50%) and no sensitizing EGFR/ALK alterations. Lastly, for the remaining ~50% of patients who are fit and whose tumors have no or low PD-L1 expression (TPS of 0-49%) and no sensitizing EGFR/ALK aberrations, platinum-containing chemotherapy with the addition of a PD-1/L1 inhibitor alone or in combination of a cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) inhibitor improves PFS and OS compared to chemotherapy alone. The objectives of this review are to summarize the current data and perspectives on first-line systemic treatment in patients with unresectable NSCLC and propose a practical algorithm for implementing precision biomarker testing at diagnosis.
Collapse
Affiliation(s)
- Tianhong Li
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis School of Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; (W.M.)
- Medical Service, Hematology/Oncology, Veterans Affairs Northern California Health Care System, 10535 Hospital Way, Mather, CA 95655, USA
| | - Weijie Ma
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis School of Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; (W.M.)
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Ebaa Al-Obeidi
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis School of Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; (W.M.)
| |
Collapse
|
5
|
Hancock GR, Gertz J, Jeselsohn R, Fanning SW. Estrogen Receptor Alpha Mutations, Truncations, Heterodimers, and Therapies. Endocrinology 2024; 165:bqae051. [PMID: 38643482 PMCID: PMC11075793 DOI: 10.1210/endocr/bqae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024]
Abstract
Annual breast cancer (BCa) deaths have declined since its apex in 1989 concomitant with widespread adoption of hormone therapies that target estrogen receptor alpha (ERα), the prominent nuclear receptor expressed in ∼80% of BCa. However, up to ∼50% of patients who are ER+ with high-risk disease experience post endocrine therapy relapse and metastasis to distant organs. The vast majority of BCa mortality occurs in this setting, highlighting the inadequacy of current therapies. Genomic abnormalities to ESR1, the gene encoding ERα, emerge under prolonged selective pressure to enable endocrine therapy resistance. These genetic lesions include focal gene amplifications, hotspot missense mutations in the ligand binding domain, truncations, fusions, and complex interactions with other nuclear receptors. Tumor cells utilize aberrant ERα activity to proliferate, spread, and evade therapy in BCa as well as other cancers. Cutting edge studies on ERα structural and transcriptional relationships are being harnessed to produce new therapies that have shown benefits in patients with ESR1 hotspot mutations. In this review we discuss the history of ERα, current research unlocking unknown aspects of ERα signaling including the structural basis for receptor antagonism, and future directions of ESR1 investigation. In addition, we discuss the development of endocrine therapies from their inception to present day and survey new avenues of drug development to improve pharmaceutical profiles, targeting, and efficacy.
Collapse
Affiliation(s)
- Govinda R Hancock
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60513, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Center, University of Utah, Salt Lake City, UT 84112, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sean W Fanning
- Department of Cancer Biology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60513, USA
| |
Collapse
|
6
|
Hattori M, Serelli-Lee V, Naito Y, Yamanaka T, Yasojima H, Nakamura R, Fujisawa T, Imai M, Nakamura Y, Bando H, Kawaguchi T, Yoshino T, Iwata H. Genomic Landscape of Circulating Tumor DNA in Patients With Hormone Receptor-Positive/Human Epidermal Growth Factor Receptor-2-Negative Metastatic Breast Cancer Treated With Abemaciclib: Data From the SCRUM-Japan Cancer Genome Screening Project. JCO Precis Oncol 2024; 8:e2300647. [PMID: 38635933 PMCID: PMC11161242 DOI: 10.1200/po.23.00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/13/2024] [Accepted: 03/05/2024] [Indexed: 04/20/2024] Open
Abstract
PURPOSE To understand the mutational landscape of circulating tumor DNA (ctDNA) and tumor tissue of patients with hormone receptor-positive (HR+), human epidermal growth factor receptor-2-negative (HER2-) metastatic breast cancer (MBC) treated with abemaciclib + endocrine therapy (ET). METHODS Blood samples for ctDNA and/or tissue samples were collected from abemaciclib-treated patients with HR+/HER2- MBC enrolled in the SCRUM-Japan MONSTAR-SCREEN project. Blood samples were collected before abemaciclib initiation (baseline) and at disease progression/abemaciclib discontinuation (post abemaciclib treatment). Clinical and genomic characteristics including neoplastic burden (measured by shedding rate and maximum variant allele frequency [VAF]) were assessed at baseline. Genomic alterations in ctDNA were compared in paired baseline and post abemaciclib treatment samples. RESULTS All patients (N = 97) were female (median age, 57 years [IQR, 50-67]). In baseline ctDNA (n = 77), PIK3CA (37%), TP53 (28%), ESR1 (16%), and GATA3 (11%) were the most frequently mutated genes. Baseline tissue samples (n = 79) showed similar alteration frequencies. Among patients with baseline ctDNA data, 30% had received previous ET. ESR1 alteration frequency (35% v 8%; P < .01), median shedding rate (3 v 2), and maximum somatic VAF (4 v 0.8; both P < .05) were significantly higher in ctDNA from patients with previous ET than those without previous ET. In paired ctDNA samples (n = 33), PIK3CA and ESR1 alteration frequencies were higher after abemaciclib treatment than at baseline, though not statistically significant. Among the post-treatment alterations, those newly acquired were detected most frequently in FGF3/4/19 (18%); PIK3CA, TP53, CCND1, and RB1 (all 15%); and ESR1 (12%). CONCLUSION We summarized the ctDNA and cancer tissue mutational landscape, including overall neoplastic burden and PIK3CA and ESR1 hotspot mutations in abemaciclib-treated patients with HR+/HER2- MBC. The data provide insights that could help optimize treatment strategies in this population.
Collapse
Affiliation(s)
| | | | - Yoichi Naito
- National Cancer Center Hospital East, Chiba, Japan
| | | | - Hiroyuki Yasojima
- National Hospital Organization Osaka National Hospital, Osaka, Japan
| | | | | | - Mitsuho Imai
- National Cancer Center Hospital East, Chiba, Japan
| | | | | | | | | | | |
Collapse
|
7
|
Stenzinger A, Vogel A, Lehmann U, Lamarca A, Hofman P, Terracciano L, Normanno N. Molecular profiling in cholangiocarcinoma: A practical guide to next-generation sequencing. Cancer Treat Rev 2024; 122:102649. [PMID: 37984132 DOI: 10.1016/j.ctrv.2023.102649] [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: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Cholangiocarcinomas (CCA) are a heterogeneous group of tumors that are classified as intrahepatic, perihilar, or distal according to the anatomic location within the biliary tract. Each CCA subtype is associated with distinct genomic alterations, including single nucleotide variants, copy number variants, and chromosomal rearrangements or gene fusions, each of which can influence disease prognosis and/or treatment outcomes. Molecular profiling using next-generation sequencing (NGS) is a powerful technique for identifying unique gene variants carried by an individual tumor, which can facilitate their accurate diagnosis as well as promote the optimal selection of gene variant-matched targeted treatments. NGS is particularly useful in patients with CCA because between one-third and one-half of these patients have genomic alterations that can be targeted by drugs that are either approved or in clinical development. NGS can also provide information about disease evolution and secondary resistance alterations that can develop during targeted therapy, and thus facilitate assessment of prognosis and choice of alternative targeted treatments. Pathologists play a critical role in assessing the viability of biopsy samples for NGS, and advising treating clinicians whether NGS can be performed and which of the available platforms should be used to optimize testing outcomes. This review aims to provide clinical pathologists and other healthcare professionals with practical step-by-step guidance on the use of NGS for molecular profiling of patients with CCA, with respect to tumor biopsy techniques, pre-analytic sample preparation, selecting the appropriate NGS panel, and understanding and interpreting results of the NGS test.
Collapse
Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology Heidelberg (IPH), Center for Molecular Pathology, University Hospital Heidelberg, In Neuenheimer Feld 224, 69120 Heidelberg, Building 6224, Germany.
| | - Arndt Vogel
- Division of Gastroenterology and Hepatology, Toronto General Hospital Medical Oncology, Princess Margaret Cancer Centre, Schwartz Reisman Liver Research Centre, 200 Elizabeth Street, Office: 9 EB 236 Toronto, ON, M5G 2C4, Canada.
| | - Ulrich Lehmann
- Institute for Pathology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Angela Lamarca
- Department of Medical Oncology, Oncohealth Institute, Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Fundación Jiménez Díaz University Hospital, Av. de los Reyes Católicos, 2, 28040 Madrid, Spain; Department of Medical Oncology, The Christie NHS Foundation Trust, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, IHU RespirERA, Siège de l'Université: Grand Château, 28 Avenue de Valrose, 06103 Nice CEDEX 2, France.
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 4, 20072 Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
| |
Collapse
|
8
|
Betz M, Massard V, Gilson P, Witz A, Dardare J, Harlé A, Merlin JL. ESR1 Gene Mutations and Liquid Biopsy in ER-Positive Breast Cancers: A Small Step Forward, a Giant Leap for Personalization of Endocrine Therapy? Cancers (Basel) 2023; 15:5169. [PMID: 37958343 PMCID: PMC10649433 DOI: 10.3390/cancers15215169] [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: 10/03/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The predominant forms of breast cancer (BC) are hormone receptor-positive (HR+) tumors characterized by the expression of estrogen receptors (ERs) and/or progesterone receptors (PRs). Patients with HR+ tumors can benefit from endocrine therapy (ET). Three types of ET are approved for the treatment of HR+ BCs and include selective ER modulators, aromatase inhibitors, and selective ER downregulators. ET is the mainstay of adjuvant treatment in the early setting and the backbone of the first-line treatment in an advanced setting; however, the emergence of acquired resistance can lead to cancer recurrence or progression. The mechanisms of ET resistance are often related to the occurrence of mutations in the ESR1 gene, which encodes the ER-alpha protein. As ESR1 mutations are hardly detectable at diagnosis but are present in 30% to 40% of advanced BC (ABC) after treatment, the timeline of testing is crucial. To manage this resistance, ESR1 testing has recently been recommended; in ER+ HER2- ABC and circulating cell-free DNA, so-called liquid biopsy appears to be the most convenient way to detect the emergence of ESR1 mutations. Technically, several options exist, including Next Generation Sequencing and ultra-sensitive PCR-based techniques. In this context, personalization of ET through the surveillance of ESR1 mutations in the plasma of HR+ BC patients throughout the disease course represents an innovative way to improve the standard of care.
Collapse
Affiliation(s)
- Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Vincent Massard
- Département d’Oncologie Médicale, Institut de Cancérologie de Lorraine, 54519 Vandœuvre-lès-Nancy, France;
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN, Université de Lorraine, 54519 Vandœuvre-lès-Nancy, France
| |
Collapse
|
9
|
Hashimoto Y, Masunaga N, Kagara N, Abe K, Yoshinami T, Tsukabe M, Sota Y, Miyake T, Tanei T, Shimoda M, Shimazu K. Detection of Ultra-Rare ESR1 Mutations in Primary Breast Cancer Using LNA-Clamp ddPCR. Cancers (Basel) 2023; 15:cancers15092632. [PMID: 37174098 PMCID: PMC10177270 DOI: 10.3390/cancers15092632] [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: 03/29/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
ESR1 mutations in breast cancer are one of the mechanisms of resistance to aromatase inhibitors. These mutations are common in metastatic breast cancer; however, these are rare in primary breast cancer. However, these data have been analyzed mainly in formalin-fixed, paraffin-embedded tissue; thus, rare mutations that may be present in primary breast cancer may be overlooked. In this study, we developed a highly sensitive mutation detection method called locked nucleic acid (LNA)-clamp droplet digital PCR (ddPCR) and validated it. The mutation detection sensitivity was substantiated to 0.003%. Then, we used this method to analyze ESR1 mutations in fresh-frozen (FF) tissues of primary breast cancer. cDNA extracted from the FF tissues of 212 patients with primary breast cancers were measured. Twenty-eight ESR1 mutations were found in twenty-seven (12.7%) patients. Sixteen (7.5%) patients had Y537S mutations and twelve (5.7%) had D538G mutations. Two mutations with a variant allele frequency (VAF) of ≥0.1% and twenty-six mutations with a VAF of <0.1% were found. By using this LNA-clamp ddPCR, this study demonstrated the presence of minor clones with a VAF of <0.1% in primary breast cancer.
Collapse
Affiliation(s)
- Yoko Hashimoto
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Nanae Masunaga
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Naofumi Kagara
- Department of Breast Surgery, Osaka General Medical Center, 3-1-56, Bandai-Higashi, Sumiyoshi-ku, Osaka 558-8558, Osaka, Japan
| | - Kaori Abe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Tetsuhiro Yoshinami
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Masami Tsukabe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Yoshiaki Sota
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Tomohiro Miyake
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Tomonori Tanei
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, Osaka University, 2-2-E10 Yamadaoka, Suita 565-0871, Osaka, Japan
| |
Collapse
|
10
|
Hu S, Liu Y, Yang Q, Chen L, Chai H, Xiao M, Qi C, Qiu W. Liquid biopsy using cell-free DNA in the early diagnosis of hepatocellular carcinoma. Invest New Drugs 2023:10.1007/s10637-023-01363-6. [PMID: 37099161 DOI: 10.1007/s10637-023-01363-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 04/27/2023]
Abstract
Hepatocellular carcinoma ranks fourth in cancer-related causes of death worldwide and second in China. Patients with hepatocellular carcinoma (HCC) at the early stage have a better prognosis compared to HCC patients at the late stage. Therefore, early screening for HCC is critical for clinical treatment decisions and improving the prognosis of patients. Ultrasound (US), computed tomography (CT), and serum alpha fetoprotein (AFP) have been used to screen HCC, but HCC is still difficult to be diagnosed in the early stage due to the low sensitivity of the above methods. It is urgent to find a method with high sensitivity and specificity for the early diagnosis of HCC. Liquid biopsy is a noninvasive detection method using blood or other bodily fluids. Cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) are important biomarkers for liquid biopsy. Recently, HCC screening methods using the application of cfDNA and ctDNA have become the hot spot of early HCC diagnostics. In this mini review, we summarize the latest research progress of liquid biopsy based on blood cfDNA in early screening of HCC.
Collapse
Affiliation(s)
- Shiqi Hu
- The oncology department, Xiangtan Central Hospital, Hunan, China
| | - Yaqin Liu
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210002, China
| | - Qidong Yang
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210002, China
| | - Lin Chen
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210002, China
| | - Huizi Chai
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210002, China
| | - Mingzhe Xiao
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210002, China
| | - Chuang Qi
- The Medical Department, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, Nanjing, 210002, China
| | - Wei Qiu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, 71 Xinmin Street, Chaoyang District, Changchun, 130000, Jilin, China.
| |
Collapse
|
11
|
Dabbs DJ, Huang RS, Ross JS. Novel markers in breast pathology. Histopathology 2023; 82:119-139. [PMID: 36468266 DOI: 10.1111/his.14770] [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: 06/27/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 12/12/2022]
Abstract
Breast pathology is an ever-expanding database of information which includes markers, or biomarkers, that detect or help treat the disease as prognostic or predictive information. This review focuses on these aspects of biomarkers which are grounded in immunohistochemistry, liquid biopsies and next-generation sequencing.
Collapse
Affiliation(s)
- David J Dabbs
- PreludeDx, Laguna Hills, CA, USA.,Department of Pathology, University of Pittsburgh, Board Member, CASI (Consortium for Analytical Standardization in Immunohistochemistry), Pittsburgh, PA, USA
| | - Richard S Huang
- Clinical Development, Foundation Medicine, Cambridge, MA, USA
| | | |
Collapse
|
12
|
Husain H, Pavlick DC, Fendler BJ, Madison RW, Decker B, Gjoerup O, Parachoniak CA, McLaughlin-Drubin M, Erlich RL, Schrock AB, Frampton GM, Das Thakur M, Oxnard GR, Tukachinsky H. Tumor Fraction Correlates With Detection of Actionable Variants Across > 23,000 Circulating Tumor DNA Samples. JCO Precis Oncol 2022; 6:e2200261. [PMID: 36265119 PMCID: PMC9616642 DOI: 10.1200/po.22.00261] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Profiling of circulating tumor DNA (ctDNA) is increasingly adopted in the management of solid tumors, concurrent with increased availability of more comprehensive ctDNA panels. However, variable ctDNA shed can result in variable assay sensitivity. We studied the relationship between ctDNA tumor fraction (TF) and detection of actionable alterations across cancer types. METHODS A total of 23,482 liquid biopsies (LBx) submitted between September 2020 and October 2021 were sequenced using a hybrid capture panel that reports genomic alterations (GAs) and genomic biomarkers across 324 cancer-related genes. The primary end points were the prevalence of targetable GAs by cancer type and detection in relationship to ctDNA TF. Sensitivity of detection in LBx was assessed in 1,289 patients with available tissue results. RESULTS 94% (n = 22,130) of LBx had detectable ctDNA, with a median TF of 2.2%. LBx profiling detected GAs in National Comprehensive Cancer Network category 1 genes in 37% of lung, 30% of prostate, 36% of breast, and 51% of colon cancer cases. Potential germline GAs flagged on clinical reports were detected in genes including <i>BRCA1/2</i>, <i>PALB2</i>, <i>CHEK2</i>, and <i>ATM.</i> Polyclonal mutations in genes associated with resistance such as <i>AR</i>, <i>ESR1</i>, <i>RB1</i>, and <i>NF1</i> were detected. The sensitivity of LBx to detect driver alterations identified in tissue biopsy from the same patient ranged from 58% to 86% but was consistently at or near 100% in cases with TF ≥ 10%. CONCLUSION Elevated ctDNA shed is associated with both high sensitivity and negative predictive value for detection of actionable GAs. The presence of elevated TF suggests adequate tumor profiling and may reduce the value of subsequent reflex to confirmatory tissue testing in patients with negative LBx results.
Collapse
Affiliation(s)
- Hatim Husain
- University of California, San Diego, La Jolla, CA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hanna Tukachinsky
- Foundation Medicine, Cambridge, MA,Hanna Tukachinsky, PhD, Foundation Medicine, 150 Second St, Cambridge, MA 02141; e-mail:
| |
Collapse
|
13
|
Galvano A, Castellana L, Gristina V, La Mantia M, Insalaco L, Barraco N, Perez A, Cutaia S, Calò V, Bazan Russo TD, Francini E, Incorvaia L, Mirisola MG, Vieni S, Rolfo C, Bazan V, Russo A. The diagnostic accuracy of PIK3CA mutations by circulating tumor DNA in breast cancer: an individual patient data meta-analysis. Ther Adv Med Oncol 2022; 14:17588359221110162. [PMID: 36188485 PMCID: PMC9516428 DOI: 10.1177/17588359221110162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Background The circulating tumor DNA (ctDNA) diagnostic accuracy for detecting phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutations in breast cancer (BC) is under discussion. We aimed to compare plasma and tissue PIK3CA alterations, encompassing factors that could affect the results. Methods Two reviewers selected studies from different databases until December 2020. We considered BC patients with matched tumor tissue and plasma ctDNA. We performed meta-regression and subgroup analyses to explore sources of heterogeneity concerning tumor burden, diagnostic technique, sample size, sampling time, biological subtype, and hotspot mutation. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the related area under the curve (AUC) were elaborated for the overall population and each subgroup. Results The pooled analysis was carried out on 25 cohorts for a total of 1966 patients. The overall ctDNA sensitivity and specificity were 0.73 (95% CI: 0.70-0.77) and 0.87 (95% CI: 0.85-0.89). The AUC was 0.93. Pooled concordance, negative predictive value and positive predictive value values were 0.87 (95% CI: 0.82-0.92), 0.86 (95% CI: 0.81-0.90), and 0.89 (95% CI: 0.81-0.95) with pooled PLR, NLR, and DOR of 7.94 (95% CI: 4.90-12.86), 0.33 (95% CI: 0.25-0.45), and 33.41 (95% CI: 17.23-64.79), respectively. The pooled results consistently favored next-generation sequencing (NGS)- over polymerase chain reaction-based methodologies. The best ctDNA performance in terms of sensitivity, specificity, and AUC (0.85, 0.99, and 0.94, respectively) was observed in the low-time sampling subgroup (⩽18 days between tissue and plasma collection). Meta-regression and subgroup analyses highlighted sampling time as a possible major cause of heterogeneity. Conclusions These findings reliably estimate the high ctDNA accuracy for the detection of PIK3CA mutations. A ctDNA-first approach for the assessment of PIK3CA mutational status by NGS may accurately replace tissue tumor sampling, representing the preferable strategy at diagnosis of metastatic BC in patients who present with visceral involvement and at least two metastatic lesions, primarily given low clinical compliance or inaccessible metastatic sites.
Collapse
Affiliation(s)
- Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Luisa Castellana
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Maria La Mantia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Lavinia Insalaco
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Nadia Barraco
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Alessandro Perez
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Sofia Cutaia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valentina Calò
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Edoardo Francini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lorena Incorvaia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Mario Giuseppe Mirisola
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Salvatore Vieni
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viviana Bazan
- Department of Experimental Biomedicine and Clinical Neurosciences, School of Medicine, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Via del Vespro 129, Palermo 90127, Italy
| |
Collapse
|
14
|
Herzog H, Dogan S, Aktas B, Nel I. Targeted Sequencing of Plasma-Derived vs. Urinary cfDNA from Patients with Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:4101. [PMID: 36077638 PMCID: PMC9454533 DOI: 10.3390/cancers14174101] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
In breast cancer, the genetic profiling of circulating cell-free DNA (cfDNA) from blood plasma was shown to have good potential for clinical use. In contrast, only a few studies were performed investigating urinary cfDNA. In this pilot study, we analyzed plasma-derived and matching urinary cfDNA samples obtained from 15 presurgical triple-negative breast cancer patients. We used a targeted next-generation sequencing approach to identify and compare genetic alterations in both body fluids. The cfDNA concentration was higher in urine compared to plasma, but there was no significant correlation between matched samples. Bioinformatical analysis revealed a total of 3339 somatic breast-cancer-related variants (VAF ≥ 3%), whereof 1222 vs. 2117 variants were found in plasma-derived vs. urinary cfDNA, respectively. Further, 431 shared variants were found in both body fluids. Throughout the cohort, the recovery rate of plasma-derived mutations in matching urinary cfDNA was 47% and even 63% for pathogenic variants only. The most frequently occurring pathogenic and likely pathogenic mutated genes were NF1, CHEK2, KMT2C and PTEN in both body fluids. Notably, a pathogenic CHEK2 (T519M) variant was found in all 30 samples. Taken together, our results indicated that body fluids appear to be valuable sources bearing complementary information regarding the genetic tumor profile.
Collapse
Affiliation(s)
- Henrike Herzog
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Senol Dogan
- Soft Matter Physics Division, Peter-Debye-Institute, University of Leipzig, 04103 Leipzig, Germany
| | - Bahriye Aktas
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Ivonne Nel
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| |
Collapse
|
15
|
Furman C, Puyang X, Zhang Z, Wu ZJ, Banka D, Aithal KB, Albacker LA, Hao MH, Irwin S, Kim A, Montesion M, Moriarty AD, Murugesan K, Nguyen TV, Rimkunas V, Sahmoud T, Wick MJ, Yao S, Zhang X, Zeng H, Vaillancourt FH, Bolduc DM, Larsen N, Zheng GZ, Prajapati S, Zhu P, Korpal M. Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer. Mol Cancer Ther 2022; 21:890-902. [PMID: 35642432 PMCID: PMC9381127 DOI: 10.1158/1535-7163.mct-21-0378] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/19/2021] [Accepted: 03/18/2022] [Indexed: 01/07/2023]
Abstract
Nearly 30% of patients with relapsed breast cancer present activating mutations in estrogen receptor alpha (ERα) that confer partial resistance to existing endocrine-based therapies. We previously reported the development of H3B-5942, a covalent ERα antagonist that engages cysteine-530 (C530) to achieve potency against both wild-type (ERαWT) and mutant ERα (ERαMUT). Anticipating that the emergence of C530 mutations could promote resistance to H3B-5942, we applied structure-based drug design to improve the potency of the core scaffold to further enhance the antagonistic activity in addition to covalent engagement. This effort led to the development of the clinical candidate H3B-6545, a covalent antagonist that is potent against both ERαWT/MUT, and maintains potency even in the context of ERα C530 mutations. H3B-6545 demonstrates significant activity and superiority over standard-of-care fulvestrant across a panel of ERαWT and ERαMUT palbociclib sensitive and resistant models. In summary, the compelling preclinical activity of H3B-6545 supports its further development for the potential treatment of endocrine therapy-resistant ERα+ breast cancer harboring wild-type or mutant ESR1, as demonstrated by the ongoing clinical trials (NCT03250676, NCT04568902, NCT04288089). SUMMARY H3B-6545 is an ERα covalent antagonist that exhibits encouraging preclinical activity against CDK4/6i naïve and resistant ERαWT and ERαMUT tumors.
Collapse
Affiliation(s)
- Craig Furman
- H3 Biomedicine Inc., Cambridge, Massachusetts.,Corresponding Authors: Craig Furman, H3 Biomedicine, 300 Technology Square, Cambridge, MA 02139. E-mail: ; Manav Korpal, ; and Ping Zhu,
| | | | | | | | | | - Kiran B. Aithal
- Aurigene Discovery Technologies Ltd, Bangalore, Karnataka, India
| | | | | | - Sean Irwin
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | - Amy Kim
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | | | | | | | | | | | | | | | - Shihua Yao
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | - Xun Zhang
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | - Hao Zeng
- H3 Biomedicine Inc., Cambridge, Massachusetts
| | | | | | | | | | | | - Ping Zhu
- H3 Biomedicine Inc., Cambridge, Massachusetts.,Corresponding Authors: Craig Furman, H3 Biomedicine, 300 Technology Square, Cambridge, MA 02139. E-mail: ; Manav Korpal, ; and Ping Zhu,
| | - Manav Korpal
- H3 Biomedicine Inc., Cambridge, Massachusetts.,Corresponding Authors: Craig Furman, H3 Biomedicine, 300 Technology Square, Cambridge, MA 02139. E-mail: ; Manav Korpal, ; and Ping Zhu,
| |
Collapse
|
16
|
Liao H, Zhang J, Zheng T, Liu X, Zhong J, Shao B, Dong X, Wang X, Du P, King BL, Jia S, Yu J, Li H. Identification of mutation patterns and circulating tumour DNA-derived prognostic markers in advanced breast cancer patients. J Transl Med 2022; 20:211. [PMID: 35562750 PMCID: PMC9101837 DOI: 10.1186/s12967-022-03421-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/02/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The correlations between circulating tumour DNA (ctDNA)-derived genomic markers and treatment response and survival outcome in Chinese patients with advanced breast cancer (ABC) have not been extensively characterized. METHODS Blood samples from 141 ABC patients who underwent first-line standard treatment in Peking University Cancer Hospital were collected. A next-generation sequencing based liquid biopsy assay (PredicineCARE) was used to detect somatic mutations and copy number variations (CNVs) in ctDNA. A subset of matched blood samples and tumour tissue biopsies were compared to evaluate the concordance. RESULTS Overall, TP53 (44.0%) and PIK3CA (28.4%) were the top two altered genes. Frequent CNVs included amplifications of ERBB2 (24.8%) and FGFR1 (8.5%) and deletions of CDKN2A (3.5%). PIK3CA/TP53 and FGFR1/2/3 variants were associated with drug resistance in hormone receptor-positive (HR +) and human epidermal growth factor receptor 2-positive (HER2 +) patients. The comparison of genomic variants across matched tumour tissue and ctDNA samples revealed a moderate to high concordance that was gene dependent. Triple-negative breast cancer (TNBC) patients harbouring TP53 or PIK3CA alterations had a shorter overall survival than those without corresponding mutations (P = 0.03 and 0.008). A high ctDNA fraction was correlated with a shorter progression-free survival (PFS) (P = 0.005) in TNBC patients. High blood-based tumor mutation burden (bTMB) was associated with a shorter PFS for HER2 + and TNBC patients (P = 0.009 and 0.05). Moreover, disease monitoring revealed several acquired genomic variants such as ESR1 mutations, CDKN2A deletions, and FGFR1 amplifications. CONCLUSIONS This study revealed the molecular profiles of Chinese patients with ABC and the clinical validity of ctDNA-derived markers, including the ctDNA fraction and bTMB, for predicting treatment response, prognosis, and disease progression. TRIAL REGISTRATION ClinicalTrials.gov ID: NCT03792529. Registered January 3rd 2019, https://clinicaltrials.gov/ct2/show/NCT03792529 .
Collapse
Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Jiayang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Tiantian Zheng
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Jianxin Zhong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Bin Shao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Xiaoxi Dong
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Xiaohong Wang
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Pan Du
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Bonnie L King
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Shidong Jia
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Jianjun Yu
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China.
| |
Collapse
|
17
|
Callens C, Bidard FC, Curto-Taribo A, Trabelsi-Grati O, Melaabi S, Delaloge S, Hardy-Bessard AC, Bachelot T, Clatot F, De La Motte Rouge T, Canon JL, Arnould L, Andre F, Marques S, Stern MH, Pierga JY, Vincent-Salomon A, Benoist C, Jeannot E, Berger F, Bieche I, Pradines A. Real-Time Detection of ESR1 Mutation in Blood by Droplet Digital PCR in the PADA-1 Trial: Feasibility and Cross-Validation with NGS. Anal Chem 2022; 94:6297-6303. [PMID: 35416669 DOI: 10.1021/acs.analchem.2c00446] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The clinical actionability of circulating tumor DNA requires sensitive detection methods with a short turnaround time. In the PADA-1 phase 3 trial (NCT03079011), metastatic breast cancer patients treated with an aromatase inhibitor and palbociclib were screened every 2 months for activating ESR1 mutations in blood (bESR1mut). We report the feasibility of the droplet digital polymerase chain reaction (ddPCR) and cross-validation with next-generation sequencing (NGS). bESR1mut testing was centralized in two platforms using the same ddPCR assay. Results were reported as copies/mL of plasma and mutant allele frequency (MAF). We analyzed 200 positive ddPCR samples with an NGS assay (0.5-1% sensitivity). Overall, 12,552 blood samples were collected from 1017 patients from 83 centers. Among the 12,525 available samples with ddPCR results, 11,533 (92%) were bESR1mut-negative. A total of 267 patients newly displayed bESR1mut (26% patients/2% samples) with a median copy number of 14/mL (range: 4-1225) and a median MAF of 0.83% (0.11-35), 648 samples (20% patients/5% samples) displayed persistent bESR1mut, and 77 (<1%) samples encountered a technical failure. The median turnaround time from blood drawing to result notification was 13 days (Q1:9; Q3:21 days). Among 200 ddPCR-positive samples tested, NGS detected bESR1mut in 168 (84%); 25 of the 32 cases missed by NGS had low MAF and/or low coverage. In these 200 samples, bESR1mut MAF by both techniques had an excellent intraclass correlation coefficient (ICC = 0.93; 95% CI [0.85; 0.97]). These results from a large-scale trial support the feasibility and accuracy of real-time bESR1mut tracking by ddPCR, opening new opportunities for therapeutic interventions.
Collapse
Affiliation(s)
- Celine Callens
- Pharmacogenomic Unit, Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Francois-Clement Bidard
- Department of Medical Oncology, Institut Curie, UVSQ/Paris Saclay University, 92210 Saint Cloud, France.,Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, 75005 Paris, France
| | - Anaïs Curto-Taribo
- Pharmacogenomic Unit, Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Olfa Trabelsi-Grati
- Pharmacogenomic Unit, Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Samia Melaabi
- Pharmacogenomic Unit, Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Suzette Delaloge
- Department of Medical Oncology, Gustave Roussy, 94800 Villejuif, France
| | | | - Thomas Bachelot
- Department of Medical Oncology, Centre Léon Bérard, 69000 Lyon, France
| | - Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 76000 Rouen, France
| | | | - Jean-Luc Canon
- Department of Medical Oncology, Grand Hôpital de Charleroi, 6000 Charleroi, Belgique
| | - Laurent Arnould
- Department of Pathology, Centre Georges François Leclerc, 21000 Dijon, France
| | - Fabrice Andre
- Department of Medical Oncology, Gustave Roussy, 94800 Villejuif, France
| | - Sandrine Marques
- Research and Development Department, UNICANCER, 75013 Paris, France
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie, PSL Research University, 75005 Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, 75005 Paris, France.,Department of Medical Oncology, Institut Curie & Université de Paris, 75005 Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75005 Paris, France
| | - Camille Benoist
- Bio-informatic Clinical Unit, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Emmanuelle Jeannot
- Pharmacogenomic Unit, Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Frederique Berger
- Biometry Unit, Institut Curie and PSL Research University, 75005 Paris and 92210 Saint-Cloud, France
| | - Ivan Bieche
- Pharmacogenomic Unit, Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and PSL University, 75005 Paris, France
| | - Anne Pradines
- INSERM U1037 CNRS ERL5294 UPS, Cancer Research Center of Toulouse, 31000 Toulouse, France.,Prospective Biology Unit, Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31000 Toulouse, France
| |
Collapse
|
18
|
Plichta JK, Thomas SM, Sergesketter AR, Greenup RA, Rosenberger LH, Fayanju OM, Kimmick G, Force J, Hyslop T, Hwang ES. A Novel Staging System for De Novo Metastatic Breast Cancer Refines Prognostic Estimates. Ann Surg 2022; 275:784-792. [PMID: 32657941 PMCID: PMC7794098 DOI: 10.1097/sla.0000000000004231] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE We aim to identify prognostic groups within a de novo metastatic cohort, incorporating both anatomic and biologic factors. BACKGROUND Staging for breast cancer now includes anatomic and biologic factors, although the guidelines for stage IV disease do not account for how these factors may influence outcomes. METHODS Adults with de novo metastatic breast cancer were selected from the National Cancer DataBase (2010-2013). Recursive partitioning analysis was used to group patients with similar overall survival (OS) based on clinical T/N stage, tumor grade, ER, PR, HER2, number of metastatic sites, and presence of bone-only metastases. Categories were created by amalgamating homogeneous groups based on 3-year OS rates (stage IVA: >50%, stage IVB: 30%-50%, stage IVC: <30%). RESULTS 16,187 patients were identified; median follow-up was 32 months. 65.2% had 1 site of distant metastasis, and 42.9% had bone-only metastases. Recursive partitioning analysis identified the number of metastatic sites (1 vs >1) as the first stratification point, and ER status as the second stratification point for both resulting groups. Additional divisions were made based on HER2 status, PR status, cT stage, tumor grade, and presence of bone-only metastases. After bootstrapping, significant differences in 3-year OS were noted between the 3 groups [stage IVB vs IVA: HR 1.58 (95% confidence interval 1.50-1.67), stage IVC vs IVA: HR 3.54 (95% confidence interval 3.33-3.77)]. CONCLUSIONS Both anatomic and biologic factors yielded reliable and reproducible prognostic estimates among patients with metastatic disease. These findings support formal stratification of de novo stage IV breast cancer into 3 distinct prognosis groups.
Collapse
Affiliation(s)
- Jennifer K. Plichta
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Durham, North Carolina
| | - Samantha M. Thomas
- Duke Cancer Institute, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University, Durham, North Carolina
| | | | - Rachel A. Greenup
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Durham, North Carolina
| | - Laura H. Rosenberger
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Durham, North Carolina
| | - Oluwadamilola M. Fayanju
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Durham, North Carolina
- Durham VA Medical Center, Durham, North Carolina
| | - Gretchen Kimmick
- Duke Cancer Institute, Durham, North Carolina
- Department of Medical Oncology, Duke University Medical Center, Durham, North Carolina
| | - Jeremy Force
- Duke Cancer Institute, Durham, North Carolina
- Department of Medical Oncology, Duke University Medical Center, Durham, North Carolina
| | - Terry Hyslop
- Duke Cancer Institute, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University, Durham, North Carolina
| | - E. Shelley Hwang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Durham, North Carolina
| |
Collapse
|
19
|
Makarem M, García-Pardo M, Leighl NB. Plasma-Based Genotyping in Advanced Solid Tumors: A Comprehensive Review. Cancers (Basel) 2021; 13:5299. [PMID: 34771462 PMCID: PMC8582457 DOI: 10.3390/cancers13215299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/25/2022] Open
Abstract
Molecular genotyping for advanced solid malignancies has transformed the clinical management of patients with metastatic disease. Treatment decisions in a growing number of tumors require knowledge of molecularly driven alterations in order to select optimal targeted therapy. Although genomic testing of tumor tissue is the gold standard for identifying targetable genomic alterations, biopsy samples are often limited or difficult to access. This has paved the way for the development of plasma-based approaches for genomic profiling. Recent advances in the detection of plasma-circulating tumor DNA (ctDNA) have enabled the integration of plasma-based molecular profiling into clinical practice as an alternative or complementary tool for genomic testing in the setting of advanced cancer, to facilitate the identification of driver mutations to guide initial treatment and diagnose resistance. Several guidelines now recommend the use of plasma where tumor tissue is limited to identify a targetable genomic alteration. Current plasma-based assays can evaluate multiple genes in comprehensive panels, and their application in advanced disease will be increasingly incorporated into standard practice. This review focuses on current and future applications of plasma ctDNA-based assays in advanced solid malignancies, while highlighting some limitations in implementing this technology into clinical practice.
Collapse
Affiliation(s)
| | | | - Natasha B. Leighl
- Princess Margaret Cancer Center, Department of Medical Oncology, Toronto, ON M5G 2C1, Canada; (M.M.); (M.G.-P.)
| |
Collapse
|
20
|
Liu X, Davis AA, Xie F, Gui X, Chen Y, Zhang Q, Gerratana L, Zhang Y, Shah AN, Behdad A, Wehbe F, Huang Y, Yu J, Du P, Jia S, Li H, Cristofanilli M. Cell-free DNA comparative analysis of the genomic landscape of first-line hormone receptor-positive metastatic breast cancer from the US and China. Breast Cancer Res Treat 2021; 190:213-226. [PMID: 34471951 PMCID: PMC8558197 DOI: 10.1007/s10549-021-06370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/20/2021] [Indexed: 12/01/2022]
Abstract
PURPOSE Meaningful comparison of mutational landscapes across ethnic groups requires the use of standardized platform technology. We have used a harmonized NGS-based liquid biopsy assay to explore the differential genomic landscape of patients with initially hormone receptor-positive (HR+), HER2-negative MBC of first line metastasis or primary Stage IV at diagnosis from the United States (US) and China (CN). METHODS Plasma circulating tumor DNA (ctDNA) from 27 US patients and 65 CN patients was sequenced using the harmonized CLIA-certified, 152-gene PredicineCare™ liquid biopsy assay. Kaplan-Meier survival analysis was performed to analyze the correlation between genomic alterations and progression-free survival (PFS), and p-values were calculated using the log-rank test. RESULTS All patients in the CN cohort received chemotherapy and/or hormonal therapy, while 85.2% (23/27) patients in the US cohort received hormonal therapy plus CDK4/6 inhibitors. Mutations were detected in 23 of 27 (85%) US patients and 54 of 65 (83%) CN patients. The prevalence of AKT1 (P = 0.008) and CDH1 (P = 0.021) alterations were both higher in the US vs. CN cohort. In addition, FGFR1 amplification were more frequent in the CN vs. US cohort (P = 0.048). PTEN deletions (P = 0.03) and ESR1 alterations (P = 0.02) were associated with shorter PFS in the CN cohort, neither of these associations were observed in the US cohort. Interestingly, a reduced association between PTEN deletion and PFS was observed in patients receiving CDK4/6 inhibitor treatment. CONCLUSION The differential prevalence of ctDNA-based alterations such as FGFR1, AKT1, and CDH1 was observed in initially HR+/HER2- MBC patients in the US vs. CN. In addition, the association of PTEN deletions with shorter PFS was found in the CN but not the US cohort. The differential genomic landscapes across the two ethnic groups may reflect biologic differences and clinical implications.
Collapse
Affiliation(s)
- Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Fu-Cheng road No. 52, Hai-Dian District, Beijing, 100142, China
| | - Andrew A Davis
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Department of Medicine, Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Feng Xie
- Huidu (Shanghai) Medical Sciences, Ltd., Shanghai, China
| | - Xinyu Gui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Fu-Cheng road No. 52, Hai-Dian District, Beijing, 100142, China
| | - Yifei Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Fu-Cheng road No. 52, Hai-Dian District, Beijing, 100142, China
| | - Qiang Zhang
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lorenzo Gerratana
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Youbin Zhang
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ami N Shah
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Amir Behdad
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Firas Wehbe
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yong Huang
- Huidu (Shanghai) Medical Sciences, Ltd., Shanghai, China
| | - Jianjun Yu
- Huidu (Shanghai) Medical Sciences, Ltd., Shanghai, China
| | - Pan Du
- Predicine, Inc., Hayward, CA, USA
| | - Shidong Jia
- Huidu (Shanghai) Medical Sciences, Ltd., Shanghai, China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Fu-Cheng road No. 52, Hai-Dian District, Beijing, 100142, China.
| | - Massimo Cristofanilli
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| |
Collapse
|
21
|
Rasha F, Sharma M, Pruitt K. Mechanisms of endocrine therapy resistance in breast cancer. Mol Cell Endocrinol 2021; 532:111322. [PMID: 34000350 DOI: 10.1016/j.mce.2021.111322] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/29/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023]
Abstract
The most commonly diagnosed breast cancer (BC) subtype is characterized by estrogen receptor (ER) expression. Treatment of this BC subtype typically involves modalities that either suppress the production of estrogen or impede the binding of estrgen to its receptors, constituting the basis for endocrine therapy. While many patients have benefitted from endocrine therapy with clear reduction in mortality and cancer recurrence, one of the clinical hurdles that remain involves overcoming intrinsic (de novo) or acquired resistance to endocrine therapy driven by diverse and complex changes occurring in the tumor microenvironment. Moreover, such resistance may persist even after progression through additional antiestrogen therapies thus demonstrating the importance of further investigation of mechanisms of ER modulation. Here, we discuss a number of advances that provide a better understanding of the complex mechanistic basis for resistance to endocrine therapy as well as future therapeutic maneuvers that may break this resistance.
Collapse
Affiliation(s)
- Fahmida Rasha
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA
| | - Monica Sharma
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA
| | - Kevin Pruitt
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX, 79430, USA.
| |
Collapse
|
22
|
Puglisi F, Gerratana L, Lambertini M, Ceppi M, Boni L, Montemurro F, Russo S, Bighin C, De Laurentiis M, Giuliano M, Bisagni G, Durando A, Turletti A, Garrone O, Ardizzoni A, Gamucci T, Colantuoni G, Gravina A, De Placido S, Cognetti F, Del Mastro L. Composite risk and benefit from adjuvant dose-dense chemotherapy in hormone receptor-positive breast cancer. NPJ Breast Cancer 2021; 7:82. [PMID: 34183674 PMCID: PMC8238951 DOI: 10.1038/s41523-021-00286-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 05/27/2021] [Indexed: 11/09/2022] Open
Abstract
The GIM2 phase III trial demonstrated the benefit of dose-dense chemotherapy in node-positive early breast cancer (eBC). To better define the dose-dense effect in the hormone receptor-positive subgroup, we evaluated its benefit through a composite measure of recurrence risk. We conducted an ancillary analysis of the GIM2 trial evaluating the absolute treatment effect through a composite measure of recurrence risk (CPRS) in patients with hormone receptor-positive HER2-negative eBC. CPRS was estimated through Cox proportional hazards models applied to the different clinicopathological features. The treatment effect was compared to the values of CPRS by using the Sub-population Treatment Effect Pattern Plot (STEPP) process. The Disease-Free Survival (DFS)-oriented STEPP analysis showed distinct patterns of relative treatment effect with respect to CPRS. Overall, 5-year DFS differed across CPRS quartiles ranging from 95.2 to 66.4%. Each CPRS quartile was characterized by a different patients' composition, especially for age, lymph node involvement, tumor size, estrogen and progesterone receptor expression, and Ki-67. A number needed to treat of 154 and 6 was associated with the lowest and the highest CPRS quartile, respectively. Dose-dense adjuvant chemotherapy showed a consistent benefit in node-positive eBC patients with hormone receptor-positive HER2-negative disease, but its effect varied according to CPRS.
Collapse
Affiliation(s)
- Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Udine, Italy.
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano (PN), Italy.
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano (PN), Italy
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genoa, Genova, Italy
- Department of Medical Oncology, U.O.C. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marcello Ceppi
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Luca Boni
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Filippo Montemurro
- Day Hospital Oncologico Multidisciplinare, Istituto di Candiolo, FPO-IRCCS, Candiolo, Italy
| | - Stefania Russo
- Department of Oncology, ASU FC University Hospital, Udine, Italy
| | - Claudia Bighin
- Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Michelino De Laurentiis
- Department of Breast Oncology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Napoli, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | | | - Antonio Durando
- Breast Unit Ospedale S Anna, Citta' della Salute e della Scienza di Torino, Torino, Italy
| | | | - Ornella Garrone
- Breast Unit, Department of Medical Oncology AO S. Croce e Carle Ospedale di Insegnamento, Cuneo, Italy
| | | | - Teresa Gamucci
- Department of Medical Oncology, Sandro Pertini Hospital and S. Eugenio Hospital, ASL Roma2, Roma, Italy
| | | | - Adriano Gravina
- Clinical Trial Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Napoli, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Francesco Cognetti
- Department of Medical Oncology, Istituto Regina Elena per lo Studio e la Cura dei Tumori, Roma, Italy
| | - Lucia Del Mastro
- Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genoa, Genova, Italy
- UO Breast Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| |
Collapse
|
23
|
Sukumar J, Gast K, Quiroga D, Lustberg M, Williams N. Triple-negative breast cancer: promising prognostic biomarkers currently in development. Expert Rev Anticancer Ther 2021; 21:135-148. [PMID: 33198517 PMCID: PMC8174647 DOI: 10.1080/14737140.2021.1840984] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer associated with poor prognosis and limited treatment options. Validated prognostic and predictive biomarkers are needed to guide treatment decisions and prognostication.Areas covered: In this review, we discuss established and developing prognostic and predictive biomarkers in TNBC and associated emerging and approved therapies. Biomarkers reviewed include epidermal growth factor receptor (EGFR), vascular endothelial growth factors (VEGF), fibroblast growth factor receptor (FGFR), human epidermal growth factor receptor 2 (HER2), androgen receptor, NOTCH signaling, oxidative stress/redox signaling, microRNAs, TP53 mutation, breast cancer susceptibility gene 1 or 2 (BRCA1/2) mutation/homologous recombination deficiency (HRD), NTRK gene fusion, PI3K/AKT/mTOR, immune biomarkers (programmed death-ligand 1 (PDL1), tumor-infiltrating lymphocytes (TILs), tumor mutational burden (TMB), neoantigens, defects in DNA mismatch repair proteins (dMMR)/microsatellite instability-high (MSI-H)), circulating tumor cells/cell-free DNA, novel targets of antibody-drug conjugates, and residual disease.Expert opinion: Biomarker-driven care in the management of TNBC is increasing and has helped expand options for patients diagnosed with this subtype of breast cancer. Research efforts are ongoing to identify additional biomarkers and targeted treatment options with the ultimate goal of improving clinical outcomes and survivorship.
Collapse
Affiliation(s)
- Jasmine Sukumar
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH, USA
| | - Kelly Gast
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH, USA
| | - Dionisia Quiroga
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH, USA
| | - Maryam Lustberg
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH, USA
| | - Nicole Williams
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH, USA
| |
Collapse
|
24
|
Pellini B, Pejovic N, Feng W, Earland N, Harris PK, Usmani A, Szymanski JJ, Qaium F, Mudd J, Petty M, Jiang Y, Singh A, Maher CA, Henke LE, Park H, Ciorba MA, Kim H, Mutch MG, Pedersen KS, Tan BR, Hawkins WG, Fields RC, Chaudhuri AA. ctDNA MRD Detection and Personalized Oncogenomic Analysis in Oligometastatic Colorectal Cancer From Plasma and Urine. JCO Precis Oncol 2021; 5:PO.20.00276. [PMID: 34250420 PMCID: PMC8232837 DOI: 10.1200/po.20.00276] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/14/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
We hypothesized that circulating tumor DNA (ctDNA) molecular residual disease (MRD) analysis without prior mutational knowledge could be performed after neoadjuvant chemotherapy to assess oligometastatic colorectal cancer (CRC) treated surgically with curative intent. We also investigated urine as an alternative analyte for ctDNA MRD detection in this nongenitourinary setting. PATIENTS AND METHODS We applied AVENIO targeted next-generation sequencing to plasma, tumor, and urine samples acquired on the day of curative-intent surgery from 24 prospectively enrolled patients with oligometastatic CRC. Age-related clonal hematopoiesis was accounted for by removing variants also present in white blood cells. Plasma and urine ctDNA MRD were correlated with tumor cells detected in the surgical specimen, and adjuvant treatment strategies were proposed based on ctDNA-inferred tumor mutational burden (iTMB) and targetable alterations. RESULTS Seventy-one percent of patients were treated with neoadjuvant chemotherapy. Tumor-naive plasma ctDNA analysis detected MRD at a median level of 0.62% with 95% sensitivity and 100% specificity, and 94% and 77% sensitivity when only considering patients treated with neoadjuvant chemotherapy and putative driver mutations, respectively. In urine, ctDNA MRD detection specificity remained high at 100%, but sensitivity decreased to 64% with median levels being 11-fold lower than in plasma (P < .0001). Personalized ctDNA MRD oncogenomic analysis revealed 81% of patients might have been candidates for adjuvant immunotherapy based on high iTMB or targeted therapy based on actionable PIK3CA mutations. CONCLUSION Tumor-naive plasma ctDNA analysis can sensitively and specifically detect MRD in patients with oligometastatic CRC after neoadjuvant chemotherapy. Urine-based ctDNA MRD detection is also feasible; however, it is less sensitive than plasma because of significantly lower levels. Oligometastatic patients with detectable MRD may benefit from additional personalized treatment based on ctDNA-derived oncogenomic profiling.
Collapse
Affiliation(s)
- Bruna Pellini
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Nadja Pejovic
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Wenjia Feng
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Noah Earland
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Peter K. Harris
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Abul Usmani
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Jeffrey J. Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Faridi Qaium
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
| | - Jacqueline Mudd
- Section of Surgical Oncology, Department of Surgery, Washington University School of Medicine, St Louis, MO
| | - Marvin Petty
- Section of Surgical Oncology, Department of Surgery, Washington University School of Medicine, St Louis, MO
| | | | | | - Christopher A. Maher
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
- Department of Biomedical Engineering, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Lauren E. Henke
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
| | - Haeseong Park
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
| | - Matthew A. Ciorba
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Hyun Kim
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
| | - Matthew G. Mutch
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
- Section of Colon and Rectal Surgery, Department of Surgery, Washington University School of Medicine, St Louis, MO
| | - Katrina S. Pedersen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
| | - Benjamin R. Tan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
| | - William G. Hawkins
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
- Section of Hepatobiliary-Pancreatic and Gastrointestinal Surgery, Department of Surgery, Washington University School of Medicine, St Louis, MO
| | - Ryan C. Fields
- Section of Surgical Oncology, Department of Surgery, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO
- Department of Biomedical Engineering, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St Louis, MO
- Department of Genetics, Washington University School of Medicine, St Louis, MO
- Department of Computer Science and Engineering, Washington University in St Louis, St Louis, MO
| |
Collapse
|
25
|
Fiste O, Liontos M, Koutsoukos K, Terpos E, Dimopoulos MA, Zagouri F. Circulating tumor DNA-based predictive biomarkers in breast cancer clinical trials: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1603. [PMID: 33437802 PMCID: PMC7791253 DOI: 10.21037/atm-20-1175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 09/06/2020] [Indexed: 12/31/2022]
Abstract
Breast carcinoma is the most frequent and the second leading cause of cancer mortality in women worldwide. Current treatment decisions are based on tumor profiling of the initial tissue biopsy. Cancer though evolves both spatially and temporarily in a significant percentage of patients during treatment. However, sequential biopsies from the primary tumor or its metastatic sites are not either convenient or feasible in the majority of cases. In the era of precision medicine, analysis of circulating blood-based biomarkers in the field of liquid biopsies provides an insight into the dynamic molecular profiling of the primary tumor and its metastases, in a relatively non-invasive way. The latter permits not only patient stratification but also longitudinal evaluation of treatment response, when incorporated into clinical trials. This review summarizes the results from recent and ongoing circulating tumor DNA (ctDNA)-based biomarker-driven clinical trials, with respect to ctDNA analysis' predictive role, both in adjuvant, neo-adjuvant, and metastatic setting. Furthermore, current challenges in ctDNA analysis applications are critically discussed, including pre-analytical and analytical issues, and future perspectives in this field, through the conduct of well-designed, multicenter, randomized, large-scale, biomarker-stratified trials, with robust statistical methods. Despite in its infancy, ctDNA analysis holds great promise as a minimally invasive tool regarding tailored, personalized treatment guidance for breast cancer patients.
Collapse
Affiliation(s)
- Oraianthi Fiste
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Liontos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Koutsoukos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
26
|
Santolla MF, Maggiolini M. The FGF/FGFR System in Breast Cancer: Oncogenic Features and Therapeutic Perspectives. Cancers (Basel) 2020; 12:E3029. [PMID: 33081025 PMCID: PMC7603197 DOI: 10.3390/cancers12103029] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
One of the major challenges in the treatment of breast cancer is the heterogeneous nature of the disease. With multiple subtypes of breast cancer identified, there is an unmet clinical need for the development of therapies particularly for the less tractable subtypes. Several transduction mechanisms are involved in the progression of breast cancer, therefore making the assessment of the molecular landscape that characterizes each patient intricate. Over the last decade, numerous studies have focused on the development of tyrosine kinase inhibitors (TKIs) to target the main pathways dysregulated in breast cancer, however their effectiveness is often limited either by resistance to treatments or the appearance of adverse effects. In this context, the fibroblast growth factor/fibroblast growth factor receptor (FGF/FGFR) system represents an emerging transduction pathway and therapeutic target to be fully investigated among the diverse anti-cancer settings in breast cancer. Here, we have recapitulated previous studies dealing with FGFR molecular aberrations, such as the gene amplification, point mutations, and chromosomal translocations that occur in breast cancer. Furthermore, alterations in the FGF/FGFR signaling across the different subtypes of breast cancer have been described. Next, we discussed the functional interplay between the FGF/FGFR axis and important components of the breast tumor microenvironment. Lastly, we pointed out the therapeutic usefulness of FGF/FGFR inhibitors, as revealed by preclinical and clinical models of breast cancer.
Collapse
Affiliation(s)
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
| |
Collapse
|
27
|
Ferreira-Gonzalez A. Plasma PIK3CA Mutation Testing in Advanced Breast Cancer Patients for Personalized Medicine: A Value Proposition. J Appl Lab Med 2020; 5:1076-1089. [PMID: 32901282 DOI: 10.1093/jalm/jfaa117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Even though endocrine therapy is often initially successful in treating advanced breast cancer, most patients inevitably face disease progression. In advanced hormone receptor-positive (HR+) breast cancer, activation of the PI3K downstream pathway is a critical feature of the mechanism of endocrine resistance. A significant recent advance in treating HR+ advanced breast cancer has been the recent introduction of PI3K inhibitor (PI3Ki) for the treatment of patients with HR+, HER2-negative (HER2-) advanced or metastatic breast cancer that harbors PIK3CA mutations. A value proposition concept was applied to assess the potential benefits of cell-free tumor DNA (ctDNA) testing to identify patients who might respond to PI3Ki treatment. CONTENT By applying the framework of the value proposition to >35 publications, in addition to recommendations from professional organizations, it was evident that robust clinical evidence exists to support the role of ctDNA PIK3CA mutation evaluation in identifying patients with advanced breast cancer who could benefit from PI3Ki treatment. SUMMARY Detection of PIK3CA gene mutations in HR+HER2- advanced breast cancer patients allows for the identification of patients who might benefit from more effective personalized treatment with molecularly targeted drugs.
Collapse
|
28
|
Zelinova K, Jagelkova M, Laucekova Z, Bobrovska M, Dankova Z, Grendar M, Dokus K. Molecular analysis of circulating tumor DNA from breast cancer patients before and after surgery and following adjuvant chemotherapy. Mol Clin Oncol 2020; 13:26. [PMID: 32765873 PMCID: PMC7403808 DOI: 10.3892/mco.2020.2096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
The primary aim of the present study is to provide a complex molecular profile of tumors using liquid biopsy and to monitor profile changes over time in association with surgery and administered adjuvant therapy. Our secondary aim was to compare the liquid biopsy profile with the tissue biopsy and assess concordance. A total of 27 samples of circulating tumor DNA (ctDNA) collected from 9 breast cancer patients at three different time points and their matched formalin-fixed and paraffin-embedded (FFPE) samples of primary tumor were analyzed with targeted next-generation sequencing. Somatic pathogenic variants were detected before surgery in samples from 5 patients (55.6%). The most frequently mutated genes were phosphatase and tensin homolog (4/9, 44.4%) and tumor protein 53 (4/9, 44.4%). Serial sampling of ctDNA enabled the detection of more variants compared with single-time tissue primary tumor biopsy. There were 17 ctDNA variants across all samples, but only 6 FFPE variants across all patients. In addition, the concordance between ctDNA and FFPE DNA was determined in only 1 patient, and this was connected with higher variant allele frequency. The findings of the present study suggest that liquid biopsy and tissue biopsy may be used as complementary analyses to adequately capture all tumor variants.
Collapse
Affiliation(s)
- Katarina Zelinova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia.,Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Marianna Jagelkova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia.,Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Zuzana Laucekova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Martina Bobrovska
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Zuzana Dankova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Marian Grendar
- Department of Bioinformatics, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, SK-036 01 Martin, Slovakia
| | - Karol Dokus
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia.,Second Department of Obstetrics and Gynecology, Slovak Medical University, Faculty Hospital with Polyclinic of F.D. Roosevelt, 975 17 Banska Bystrica, Slovakia
| |
Collapse
|
29
|
Takeshima K, Hayashida T, Maeda H, Nakashoji A, Yokoe T, Seki T, Takahashi M, Kitagawa Y. Increased frequency of ESR1 mutation in metastatic breast cancer by dosing selective estrogen receptor modulator followed by aromatase inhibitor. Oncol Lett 2020; 20:1231-1238. [PMID: 32724363 PMCID: PMC7377057 DOI: 10.3892/ol.2020.11669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/30/2020] [Indexed: 12/30/2022] Open
Abstract
In several recent studies on metastatic breast cancer (MBC), ligand binding domain mutations of the estrogen receptor, which is coded by the ESR1 gene, were induced by long-term endocrine therapy and resulted in acquired endocrine therapy resistance and poor outcomes. Knowledge of the association between the development of ESR1 mutation and the clinicopathologic features may guide the decision-making process of metastatic breast cancer treatment, including endocrine therapy. The aim of the present study was to evaluate the association between the development of ESR1 mutation and the clinicopathologic characteristics of patients with MBC. To evaluate the association between the development of ESR1 mutation and clinicopathologic features, a cohort of 22 patients with MBC were retrospectively analyzed using next generation sequencing. In 14 of 22 patients, four mutations were detected on the metastatic site, including Tyr537Ser, Glu542Asp, Leu536Arg and Arg548Cys. Univariate analysis demonstrated that the duration of aromatase inhibitor and selective estrogen receptor modulator treatment, as well as the age of treatment initiation for early-stage breast cancer, were significantly associated with the development of ESR1 mutation. ESR1 mutation was identified in all five patients who received selective estrogen receptor modulators in the adjuvant setting followed by aromatase inhibitors in the metastatic setting, as well as in two of the three patients who received no selective estrogen receptor modulators in adjuvant setting followed by aromatase inhibitors in the metastatic setting. In conclusion, the results of the present study suggested that administrating adjuvant selective estrogen receptor modulator followed by aromatase inhibitor for metastasis may increase the frequency of ESR1 mutation.
Collapse
Affiliation(s)
- Kaoru Takeshima
- Department of Surgery, Saitama City Hospital, Saitama 336-0911, Japan
| | - Tetsu Hayashida
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hinako Maeda
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ayako Nakashoji
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Takamichi Yokoe
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomoko Seki
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Maiko Takahashi
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo 160-8582, Japan
| |
Collapse
|
30
|
Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
Collapse
Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
| |
Collapse
|
31
|
Peng X, Li HD, Wu FX, Wang J. Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics. Brief Bioinform 2020; 22:5840077. [PMID: 32427285 DOI: 10.1093/bib/bbaa060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/16/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Advances in sequencing technologies facilitate personalized disease-risk profiling and clinical diagnosis. In recent years, some great progress has been made in noninvasive diagnoses based on cell-free DNAs (cfDNAs). It exploits the fact that dead cells release DNA fragments into the circulation, and some DNA fragments carry information that indicates their tissues-of-origin (TOOs). Based on the signals used for identifying the TOOs of cfDNAs, the existing methods can be classified into three categories: cfDNA mutation-based methods, methylation pattern-based methods and cfDNA fragmentation pattern-based methods. In cfDNA mutation-based methods, the SNP information or the detected mutations in driven genes of certain diseases are employed to identify the TOOs of cfDNAs. Methylation pattern-based methods are developed to identify the TOOs of cfDNAs based on the tissue-specific methylation patterns. In cfDNA fragmentation pattern-based methods, cfDNA fragmentation patterns, such as nucleosome positioning or preferred end coordinates of cfDNAs, are used to predict the TOOs of cfDNAs. In this paper, the strategies and challenges in each category are reviewed. Furthermore, the representative applications based on the TOOs of cfDNAs, including noninvasive prenatal testing, noninvasive cancer screening, transplantation rejection monitoring and parasitic infection detection, are also reviewed. Moreover, the challenges and future work in identifying the TOOs of cfDNAs are discussed. Our research provides a comprehensive picture of the development and challenges in identifying the TOOs of cfDNAs, which may benefit bioinformatics researchers to develop new methods to improve the identification of the TOOs of cfDNAs.
Collapse
|
32
|
Liao H, Li H. Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer. Cancer Manag Res 2020; 12:3547-3560. [PMID: 32547192 PMCID: PMC7244344 DOI: 10.2147/cmar.s249041] [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: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) represents the most commonly diagnosed cancer among females worldwide. Although targeted therapy has greatly improved the efficacy of treating BC, a large proportion of BC patients eventually develop recurrence or metastasis. Traditional invasive tumor tissue biopsy is short of comprehensiveness in tumor assessment due to heterogeneity. Liquid biopsy, an attractive non-invasive approach mainly including circulating tumor cell and circulating tumor DNA (ctDNA), has been widely utilized in a variety of cancers with the advances of sequencing technologies in recent years. The ctDNA that is found circulating in body fluids refers to DNA released from tumor cells and has shown clinical utility in metastatic breast cancer (MBC). With the results of genomic variants detection, ctDNA could be used to predict clinical outcomes, monitor disease progression, and guide treatment for patients with MBC. Moreover, the drug resistance problem may be addressed by ctDNA detection. In this review, we summarized the technological developments and clinical applications of ctDNA in MBC.
Collapse
Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| |
Collapse
|
33
|
Kutasovic JR, McCart Reed AE, Sokolova A, Lakhani SR, Simpson PT. Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer. Cancers (Basel) 2020; 12:E848. [PMID: 32244556 PMCID: PMC7226487 DOI: 10.3390/cancers12040848] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
: Breast cancer is a remarkably complex and diverse disease. Subtyping based on morphology, genomics, biomarkers and/or clinical parameters seeks to stratify optimal approaches for management, but it is clear that every breast cancer is fundamentally unique. Intra-tumour heterogeneity adds further complexity and impacts a patient's response to neoadjuvant or adjuvant therapy. Here, we review some established and more recent evidence related to the complex nature of breast cancer evolution. We describe morphologic and genomic diversity as it arises spontaneously during the early stages of tumour evolution, and also in the context of treatment where the changing subclonal architecture of a tumour is driven by the inherent adaptability of tumour cells to evolve and resist the selective pressures of therapy.
Collapse
Affiliation(s)
- Jamie R. Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Anna Sokolova
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
| |
Collapse
|
34
|
Li A, Schleicher SM, Andre F, Mitri ZI. Genomic Alteration in Metastatic Breast Cancer and Its Treatment. Am Soc Clin Oncol Educ Book 2020; 40:1-14. [PMID: 32213086 DOI: 10.1200/edbk_280463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metastatic breast cancer (mBC) remains responsible for the majority of breast cancer deaths. Whereas clinical outcomes have improved with the development of novel therapies, resistance almost inevitably develops, indicating the need for novel therapeutic approaches for the treatment of mBC. Recent investigations into mBC genomic alterations have revealed novel and potential therapeutic targets. Most notably, therapies against PIK3CA mutation and germline BRCA1/2 mutations have solidified the role of targeted therapy in mBC, with treatments against these alterations now approved by the U.S. Food and Drug Administration (FDA) on the basis of clinical benefit for patients with mBC. Familiarity with relevant genomic alterations in mBC, technologies for mutation detection, methods of interpreting genomic alterations, and an understanding of their clinical impact will aid practicing clinicians in the treatment of mBC as the field of breast oncology moves toward the era of precision medicine.
Collapse
Affiliation(s)
- Allen Li
- Department of Hematology Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| | | | - Fabrice Andre
- Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Zahi I Mitri
- Department of Hematology Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR
| |
Collapse
|
35
|
Molecular Barcode Sequencing of the Whole Ligand Binding Domain of the ESR1 Gene in Cell-Free DNA from Patients with Metastatic Breast Cancer. Transl Oncol 2020; 13:100735. [PMID: 32105989 PMCID: PMC7042480 DOI: 10.1016/j.tranon.2019.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/07/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
ESR1 mutations in breast cancer are known as one of the mechanisms of resistance to aromatase inhibitors. These mutations often occur in the hotspot regions in the ligand binding domain (LBD), but comprehensive mutational analysis has shown that mutations are observed throughout the whole LBD. We previously developed a molecular barcode sequencing (MB-NGS) technique to detect ESR1 hotspot mutations in plasma with high sensitivity. In this study, we have developed a multiplex MB-NGS assay that covers the whole LBD of ESR1. The assay demonstrated that the background errors in the plasma DNA of 10 healthy controls were below 0.1%; thus, the limit of detection was set at 0.1%. We analyzed the plasma DNA of 54 patients with estrogen receptor–positive metastatic breast cancer. Seventeen mutations were detected in 13 patients (24%), with variant allele frequencies ranging from 0.13% to 10.67%, including six rare mutations with a variant allele frequency <1.0% and a novel nonhotspot mutation (A312V). Three patients had double mutations located in the same amplicons, and it was revealed that the double mutations were located in different alleles. ESR1 hotspot mutations were associated with a longer duration of aromatase inhibitor treatment under metastatic conditions and to liver metastasis. The multiplex MB-NGS assay is useful for the sensitive and comprehensive detection of mutations throughout the whole LBD of ESR1. Our assay can be applied to any specific target region of interest using tailor-made primers and can result in minimized sequencing volume and cost.
Collapse
|
36
|
Jeannot E, Darrigues L, Michel M, Stern MH, Pierga JY, Rampanou A, Melaabi S, Benoist C, Bièche I, Vincent-Salomon A, El Ayachy R, Noret A, Epaillard N, Cabel L, Bidard FC, Proudhon C. A single droplet digital PCR for ESR1 activating mutations detection in plasma. Oncogene 2020; 39:2987-2995. [PMID: 32042112 DOI: 10.1038/s41388-020-1174-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 11/09/2022]
Abstract
Activating mutations in the estrogen receptor 1 (ESR1) gene confer resistance to aromatase inhibitors (AI), and may be targeted by selective estrogen receptor downregulators. We designed a multiplex droplet digital PCR (ddPCR), which combines a drop-off assay, targeting the clustered hotspot mutations found in exon 8, with an unconventional assay interrogating the E380Q mutation in exon 5. We assessed its sensitivity in vitro using synthetic oligonucleotides, harboring E380Q, L536R, Y537C, Y537N, Y537S, or D538G mutations. Further validation was performed on plasma samples from a prospective study and compared with next generation sequencing (NGS) data. The multiplex ESR1-ddPCR showed a high sensitivity with a limit of detection ranging from 0.07 to 0.19% in mutant allele frequency. The screening of plasma samples from patients with AI-resistant metastatic breast cancer identified ESR1 mutations in 29% of them, all mutations being confirmed by NGS. In addition, this test identifies patients harboring polyclonal alterations. Furthermore, the monitoring of circulating tumor DNA using this technique during treatment follow-up predicts the clinical benefit of palbociclib-fulvestrant. The multiplex ESR1-ddPCR detects, in a single reaction, the most frequent ESR1 activating mutations with good sensitivity. This method allows real-time liquid biopsy for ESR1 mutation monitoring in large cohorts of patients.
Collapse
Affiliation(s)
- Emmanuelle Jeannot
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.,Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Lauren Darrigues
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France
| | - Marc Michel
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France
| | - Marc-Henri Stern
- INSERM U830, Institut Curie, PSL Research University, Paris, France
| | - Jean-Yves Pierga
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France.,Université de Paris, Paris, France.,Medical Oncology, Department of the Institut Curie, Paris, France
| | - Aurore Rampanou
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France
| | - Samia Melaabi
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Camille Benoist
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Ivan Bièche
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology and Genetics, Institut Curie, PSL Research University, Paris, France
| | - Radouane El Ayachy
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France
| | - Aurélien Noret
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France
| | - Nicolas Epaillard
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France.,Versailles Saint Quentin University, Paris Saclay University, Saint Cloud, France
| | - François-Clément Bidard
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris & Saint Cloud, France.,Versailles Saint Quentin University, Paris Saclay University, Saint Cloud, France
| | - Charlotte Proudhon
- Circulating tumor biomarkers laboratory, Inserm CIC 1428, Institut Curie, PSL Research University, Paris, France.
| |
Collapse
|
37
|
Liu Y, Guo S, Yin C, Guo X, Liu M, Yuan Z, Zhao Z, Jia Y, Xing J. Optimized PCR-Based Enrichment Improves Coverage Uniformity and Mutation Detection in Mitochondrial DNA Next-Generation Sequencing. J Mol Diagn 2020; 22:503-512. [PMID: 32036083 DOI: 10.1016/j.jmoldx.2020.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/03/2019] [Accepted: 01/11/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing-based methods have been commonly used for detecting mutations of mitochondrial genome (mtDNA). PCR amplification is a highly effective method of mtDNA enrichment before sequencing. However, it has been observed that highly variable sequencing depth within PCR amplicons severely reduces the coverage uniformity and accuracy of mutation calling. Therefore, it is necessary to develop an optimized PCR-based strategy for mtDNA sequencing. Herein, the effect of DNA quality on the efficiency of PCR amplification was analyzed and the effects of different primer-design methods, including the number of primer pairs, overlap length of amplicons, and modification of primers, on coverage uniformity and mutation calling in mtDNA sequencing were assessed. Results showed that DNA quality significantly affected the efficiency of PCR amplification. Importantly, over- and under-representation of coverage depth at overlap regions of amplicons were observed when amplicons were not modified and overlap was shorter than two sequencing fragment sizes (800 bp). Then, under-representation was overcome by increasing the overlap length of the amplicons, and over-representation was effectively reduced by 5'-block modification of primers and sticky-end ligation of amplicons. Moreover, findings indicated that these two optimized PCR-based sequencing strategies effectively improved mutation calling in primer-binding regions. Optimized PCR-based mtDNA enrichment and sequencing approaches have been established, which laid a foundation for accurate mutation detection of mtDNA in diseases.
Collapse
Affiliation(s)
- Yang Liu
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, People's Republic of China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Chun Yin
- Department of Cardiovascular Medicine, the 902nd Hospital of PLA Joint Service Support Force, Bengbu, People's Republic of China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Manling Liu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zhidong Yuan
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zheng Zhao
- Third Department of Medical Oncology, Shanxi Provincial Cancer Hospital, Xi'an, People's Republic of China
| | - Yongfeng Jia
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, People's Republic of China.
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China.
| |
Collapse
|
38
|
De Santo I, McCartney A, Migliaccio I, Di Leo A, Malorni L. The Emerging Role of ESR1 Mutations in Luminal Breast Cancer as a Prognostic and Predictive Biomarker of Response to Endocrine Therapy. Cancers (Basel) 2019; 11:E1894. [PMID: 31795152 PMCID: PMC6966519 DOI: 10.3390/cancers11121894] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 02/07/2023] Open
Abstract
Mutations in the hotspot ligand-binding domain of the estrogen receptor (ER) gene ESR1 have recently been recognized as mechanisms of endocrine resistance in endocrine receptor-positive metastatic breast cancer (MBC). Accumulating data suggest these mutations develop under the selective pressure of endocrine treatments, and are infrequent in untreated ER-positive breast cancers. In vitro studies show that these mutations confer ligand-independent activity, resistance to estrogen deprivation, and relative resistance to tamoxifen and fulvestrant. Post-hoc retrospective and prospective analyses of ESR1 mutations in patients with MBC have consistently found that these mutations are markers of poor prognosis and predict resistance to aromatase inhibitors (AIs). These results warrant further investigation and prospective validation in dedicated studies. Moreover, studies are ongoing to clarify the activity of novel drugs in the context of metastatic endocrine resistant luminal breast cancer harboring ESR1 mutations. In this review, we summarize the pre-clinical and clinical findings defining the characteristics of ESR1 mutant breast cancer, and highlight the potential clinical developments in this field.
Collapse
Affiliation(s)
- Irene De Santo
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy;
- “Sandro Pitigliani” Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (A.M.); (A.D.L.)
| | - Amelia McCartney
- “Sandro Pitigliani” Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (A.M.); (A.D.L.)
| | - Ilenia Migliaccio
- “Sandro Pitigliani” Translational Research Unit, Hospital of Prato, 59100 Prato, Italy;
| | - Angelo Di Leo
- “Sandro Pitigliani” Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (A.M.); (A.D.L.)
| | - Luca Malorni
- “Sandro Pitigliani” Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (A.M.); (A.D.L.)
- “Sandro Pitigliani” Translational Research Unit, Hospital of Prato, 59100 Prato, Italy;
| |
Collapse
|
39
|
Hartmaier RJ, Trabucco SE, Priedigkeit N, Chung JH, Parachoniak CA, Vanden Borre P, Morley S, Rosenzweig M, Gay LM, Goldberg ME, Suh J, Ali SM, Ross J, Leyland-Jones B, Young B, Williams C, Park B, Tsai M, Haley B, Peguero J, Callahan RD, Sachelarie I, Cho J, Atkinson JM, Bahreini A, Nagle AM, Puhalla SL, Watters RJ, Erdogan-Yildirim Z, Cao L, Oesterreich S, Mathew A, Lucas PC, Davidson NE, Brufsky AM, Frampton GM, Stephens PJ, Chmielecki J, Lee AV. Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer. Ann Oncol 2019; 29:872-880. [PMID: 29360925 PMCID: PMC5913625 DOI: 10.1093/annonc/mdy025] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer. Patients and methods To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots. Results We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations. Conclusions Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.
Collapse
Affiliation(s)
- R J Hartmaier
- Foundation Medicine Inc., Cambridge; Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA.
| | | | - N Priedigkeit
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | | | | | | | - S Morley
- Foundation Medicine Inc., Cambridge
| | | | - L M Gay
- Foundation Medicine Inc., Cambridge
| | | | - J Suh
- Foundation Medicine Inc., Cambridge
| | - S M Ali
- Foundation Medicine Inc., Cambridge
| | - J Ross
- Foundation Medicine Inc., Cambridge
| | - B Leyland-Jones
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - B Young
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - C Williams
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - B Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, USA
| | - M Tsai
- Minnesota Oncology, Minneapolis, USA
| | - B Haley
- UT Southwestern Medical Center, Dallas, USA
| | - J Peguero
- Oncology Consultants Research Department, Houston, USA
| | | | | | - J Cho
- New Bern Cancer Care, New Bern, USA
| | - J M Atkinson
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - A Bahreini
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA; Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A M Nagle
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - S L Puhalla
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - R J Watters
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, USA
| | - Z Erdogan-Yildirim
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA
| | - L Cao
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Central South University Xiangya School of Medicine, China
| | - S Oesterreich
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - A Mathew
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - P C Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
| | - N E Davidson
- Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - A M Brufsky
- Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | | | | | | | - A V Lee
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| |
Collapse
|
40
|
Abstract
Breast cancer is a highly heterogeneous and dynamic disease, exhibiting unique somatic alterations that lead to disease recurrence and resistance. Tumor biopsy and conventional imaging approaches are not able to provide sufficient information regarding the early detection of recurrence and real time monitoring through tracking sensitive or resistance mechanisms to treatment. Circulating tumor DNA (ctDNA) analysis has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma including DNA mutations and DNA methylation patterns. Numerous studies have reported on the potential of ctDNA analysis in the management of early and advanced stages of breast cancer. Advances in high-throughput technologies, especially next generation sequencing and PCR-based assays, were highly important for the successful application of ctDNA analysis. However, before being integrated into clinical practice, ctDNA analysis needs to be standardized and validated through the performance of multicenter prospective and well-designed clinical studies. This review is focused on the clinical utility of ctDNA analysis, especially at the DNA mutation and methylation level, in breast cancer patients, incorporating the latest advances in technological approaches and involving key studies in the early and metastatic setting.
Collapse
Affiliation(s)
- Eleni Tzanikou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Department of Chemistry, Analysis of Circulating Tumor Cells (ACTC) Lab, Laboratory of Analytical Chemistry, University of Athens, Athens, Greece
| |
Collapse
|
41
|
Li G, Pavlick D, Chung JH, Bauer T, Tan BA, Peguero J, Ward P, Kallab A, Bufill J, Hoffman A, Sadiq A, Edenfield J, He J, Cooke M, Hughes J, Forcier B, Nahas M, Stephens P, Ali SM, Schrock AB, Ross JS, Miller VA, Gregg JP. Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy. J Gastrointest Oncol 2019; 10:831-840. [PMID: 31602320 DOI: 10.21037/jgo.2019.05.05] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor DNA (ctDNA) to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of a sequenced tissue sample obtained from the same tumor. The clinical utility study (CUS) for the FoundationACT™ ctDNA assay (Foundation Medicine, Cambridge, MA, USA; NCT02620527) is a multi-center prospective clinical study for multiple solid tumor types to compare genomic profiling of paired tissue and blood samples from the same patient. In this subset of the study, paired specimens from 96 patients with colorectal cancer (CRC) were analyzed with comprehensive genomic profiling (CGP) of the tumor tissue sample (FoundationOne®) and blood sample (FoundationACT™). Methods Both samples underwent CGP using the hybrid capture-based Illumina Hi-Seq technology. Maximum somatic allele frequency (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both tumor and liquid were compared for each subject. Results Among these patients, 61% were male; 74% had clinical stage IV disease, 19% had clinical stage III disease, and 7% had clinical stage II disease. Time between the tissue biopsy and liquid biopsy (range, 0-709 days) had a significant impact on the positive percent agreement (PPA) between the two assays. Eighty percent of cases had evidence of ctDNA in the blood (MSAF >0). For all cases with MSAF >0, 171 base substitutions and insertions/deletions (indels) were identified in the tumor, and 79% (PPA) of these identical alterations were also identified in matched ctDNA samples; PPA increased to 87% for cases <270 days between the tissue and liquid biopsy, 95% for <90 days, and 100% PPA for <30 days. All known and likely short variants in KRAS, NRAS, and BRAF were analyzed independently as testing of these genes is recommended by the National Comprehensive Cancer Network (NCCN) for patients with CRC and have therapeutic implications. For NCCN genes, PPA was 80% for all time points for short variants; PPA increased to 90% for cases <270 days between the tissue and liquid biopsy. There was high concordance for KRAS G12X between tissue and liquid: overall percent agreement (97%), PPA (93%), negative percent agreement (NPA) (100%), positive predictive value (PPV) (100%), and negative predictive value (NPV) (96%) for the <270 day cohort. Conclusions In cases where tumor tissue profiling is not possible, these results provide compelling evidence that genomic profiling of ctDNA in late stage CRC shows a high concordance with tumor tissue sequencing results and can be used to identify most clinically relevant alterations capable of guiding therapy for these patients.
Collapse
Affiliation(s)
- Gerald Li
- Foundation Medicine, Cambridge, MA, USA
| | | | | | - Todd Bauer
- Sarah Cannon Research Institute, Nashville, TN, USA
| | | | | | | | - Andre Kallab
- Northeast Georgia Medical Center, Gainesville, GA, USA
| | - Jose Bufill
- Northern Indiana Cancer Research Consortium (Michiana), Mishawaka, Indiana, USA
| | | | - Ahad Sadiq
- Fort Wayne Health, Fort Wayne, Indiana, USA
| | | | - Jie He
- Foundation Medicine, Cambridge, MA, USA
| | | | | | | | | | | | | | | | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA, USA.,Upstate Medical University, Syracuse, NY, USA
| | | | - Jeffrey P Gregg
- Foundation Medicine, Cambridge, MA, USA.,UC Davis Health, Department of Pathology and Laboratory Medicine, Sacramento, CA, USA
| |
Collapse
|
42
|
Dustin D, Gu G, Fuqua SAW. ESR1 mutations in breast cancer. Cancer 2019; 125:3714-3728. [PMID: 31318440 DOI: 10.1002/cncr.32345] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022]
Abstract
The acquisition of ligand-independent ESR1 mutations during aromatase inhibitor therapy in metastatic estrogen receptor (ER)-positive breast cancer is a common mechanism of hormonal therapy resistance. Preclinical and clinical studies have demonstrated that ESR1 mutations can preexist in primary tumors and can be enriched during metastasis. Furthermore, ESR1 mutations express a unique transcriptional profile that favors tumor progression, suggesting that selected ESR1 mutations may influence metastasis. Several groups have used sensitive detection methods using patient liquid biopsies to track ESR1 or truncal somatic mutations to predict treatment outcome and tumor progression, and some of these techniques may eventually be used to guide sequential treatment options in patients. Further development and standardization of mutation tracking in circulating tumor DNA is ongoing. Clinically, patients with ESR1 mutations derive clinical benefit when treated with fulvestrant and CDK4/6-targeted therapies, but the development of more potent selective ER degraders and/or new targeted biotherapies are needed to overcome the endocrine-resistant phenotype of ESR1 mutant-bearing tumors. In this review, we discuss the mechanisms of resistance and dissemination of ESR1 mutations as well as the detection methods for ESR1 mutation tracking, newly discovered potential therapeutic targets, and the clinical implications and treatment options for treating patients with ESR1 mutant-bearing tumors.
Collapse
Affiliation(s)
- Derek Dustin
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
| | - Guowei Gu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Suzanne A W Fuqua
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Medicine, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
43
|
Carausu M, Bidard FC, Callens C, Melaabi S, Jeannot E, Pierga JY, Cabel L. ESR1 mutations: a new biomarker in breast cancer. Expert Rev Mol Diagn 2019; 19:599-611. [PMID: 31188645 DOI: 10.1080/14737159.2019.1631799] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: In hormone receptor-positive breast cancer, ESR1 mutations have emerged as a key mechanism of resistance to endocrine therapy. Areas covered: Here, we review currently available data on ESR1 mutations, regarding their functional impact, prevalence at different stages (and according to the material used: tissue-based analysis vs. liquid biopsy), prognostic impact and predictive value of resistance to aromatase inhibitors. Possible strategies to overcome this resistance by using selective estrogen receptor downregulators (such as fulvestrant) are also discussed. Expert opinion: ESR1 mutation detection will probably become a prognostic and predictive biomarker in the future, used in clinical practice for hormone-receptor breast cancer, especially in the metastatic setting. In the future, we should expect to assess ESR1 mutations, using liquid biopsy (by digital-PCR or next-generation sequencing), in the same way as other prognostic or predictive biomarkers, such as EGFR mutations in lung cancer, and possibly even have targeted-therapies against these mutations.
Collapse
Affiliation(s)
- Marcela Carausu
- a Department of Medical Oncology , Institut Curie, PSL Research University , Saint Cloud , France
| | - François-Clément Bidard
- a Department of Medical Oncology , Institut Curie, PSL Research University , Saint Cloud , France.,b Faculty of Medicine , Versailles Saint Quentin en Yvelines University, Paris Saclay University , Paris , France
| | - Celine Callens
- c Department of Genetics , Institut Curie, PSL Research University , Paris , France
| | - Samia Melaabi
- c Department of Genetics , Institut Curie, PSL Research University , Paris , France
| | - Emmanuelle Jeannot
- d Department of Pathology , Institut Curie, PSL Research University , Paris , France
| | - Jean-Yves Pierga
- e Faculty of Medicine , Paris Descartes University , Paris , France.,f Department of Medical Oncology, Institut Curie , PSL Research University , Paris & Saint Cloud , France
| | - Luc Cabel
- a Department of Medical Oncology , Institut Curie, PSL Research University , Saint Cloud , France.,b Faculty of Medicine , Versailles Saint Quentin en Yvelines University, Paris Saclay University , Paris , France
| |
Collapse
|
44
|
Chin RI, Chen K, Usmani A, Chua C, Harris PK, Binkley MS, Azad TD, Dudley JC, Chaudhuri AA. Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA). Mol Diagn Ther 2019; 23:311-331. [PMID: 30941670 PMCID: PMC6561896 DOI: 10.1007/s40291-019-00390-5] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Circulating tumor DNA (ctDNA) is a component of cell-free DNA that is shed by malignant tumors into the bloodstream and other bodily fluids. Levels of ctDNA are typically low, particularly in patients with localized disease, requiring highly sophisticated methods for detection and quantification. Multiple liquid biopsy methods have been developed for ctDNA analysis in solid tumor malignancies and are now enabling detection and assessment of earlier stages of disease, post-treatment molecular residual disease (MRD), resistance to targeted systemic therapy, and tumor mutational burden. Understanding ctDNA biology, mechanisms of release, and clearance and size characteristics, in conjunction with the application of molecular barcoding and targeted error correction, have increased the sensitivity and specificity of ctDNA detection techniques. Combinatorial approaches including integration of ctDNA data with circulating protein biomarkers may further improve assay sensitivity and broaden the scope of ctDNA applications. Circulating viral DNA may be utilized to monitor disease in some virally induced malignancies. In spite of increasingly accurate methods of ctDNA detection, results need to be interpreted with caution given that somatic mosaicisms such as clonal hematopoiesis of indeterminate potential (CHIP) may give rise to genetic variants in the bloodstream unrelated to solid tumors, and the limited concordance observed between different commercial platforms. Overall, highly precise ctDNA detection and quantification methods have the potential to transform clinical practice via non-invasive monitoring of solid tumor malignancies, residual disease detection at earlier timepoints than standard clinical and/or imaging surveillance, and treatment personalization based on real-time assessment of the tumor genomic landscape.
Collapse
Affiliation(s)
- Re-I Chin
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanelle Chua
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tej D Azad
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan C Dudley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA.
- Alvin J. Siteman Cancer Center, Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
45
|
Yang X, Zhang K, Zhang C, Peng R, Sun C. Accuracy of analysis of cfDNA for detection of single nucleotide variants and copy number variants in breast cancer. BMC Cancer 2019; 19:465. [PMID: 31101027 PMCID: PMC6525451 DOI: 10.1186/s12885-019-5698-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/09/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Gene variants are dependable and sensitive biomarkers for target-specific therapies in breast cancer (BC). However, detection of mutations within tissues has many limitations. Plasma circulating free DNA (cfDNA) has been reported in many studies as an alternative tool for detection of mutations. But the diagnostic accuracy of cfDNA for most mutations in BC needs to be reviewed. This study was designed to perform comparative assessment of the diagnostic performance of cfDNA and DNA extracted from tissues for detection of single nucleotide variants (SNV) and copy number variants (CNV). METHODS True-positive (TP), false-positive (FP), false-negative (FN), and true-negative (TN) values were extracted from each selected study. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) were calculated. Subgroup analysis and single study omitted analysis were performed to quantify and explain the study heterogeneity. RESULTS Twenty eligible studies that involved 1055 cases were included in this meta-analysis. SNV studies in early breast cancer (EBC) subgroup are not suitable for meta-analysis owing to high heterogeneity. However, in advanced breast cancer (ABC) subgroup, the pooled sensitivity and specificity of detection of SNVs were 0.78 (0.71-0.84) and 0.92 (0.87-0.95), respectively. The summary receiver operative curve (SROC) exhibited an area under the curve (AUC) of 0.91(0.88-0.93). The pooled results of studies involving subgroups of PIK3CA, TP53, and ESR1 indicate that the diagnostic value of different genes is different, such as AUC for PIK3CA and TP53 were reported to be 0.96 (0.94-0.98) and 0.94 (0.91-0.95), respectively, and ESR1 had the lowest diagnostic value of 0.80 (0.76-0.83). Owing to the low sensitivity and AUC in the cases of CNV, there is no value for cfDNA-based detection of CNV based on insufficient amount of CNV data. CONCLUSION This meta-analysis suggests that the detection of gene mutations in cfDNA have adequate diagnostic accuracy and can be used as an alternative to the tumor tissue for detection of SNV but not for CNV in BC yet.
Collapse
Affiliation(s)
- Xin Yang
- Department of Clinical Lab, Yantai Yuhuangding Hospital, 20 Yudong Road, Yantai, Shandong Province, 264000, People's Republic of China.
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, 100730, People's Republic of China
| | - Caiji Zhang
- Department of Clinical Lab, Yantai Yuhuangding Hospital, 20 Yudong Road, Yantai, Shandong Province, 264000, People's Republic of China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, 100730, People's Republic of China
| | - Chengming Sun
- Department of Clinical Lab, Yantai Yuhuangding Hospital, 20 Yudong Road, Yantai, Shandong Province, 264000, People's Republic of China.
| |
Collapse
|
46
|
Gaillard SL, Andreano KJ, Gay LM, Steiner M, Jorgensen MS, Davidson BA, Havrilesky LJ, Alvarez Secord A, Valea FA, Colon-Otero G, Zajchowski DA, Chang CY, McDonnell DP, Berchuck A, Elvin JA. Constitutively active ESR1 mutations in gynecologic malignancies and clinical response to estrogen-receptor directed therapies. Gynecol Oncol 2019; 154:199-206. [PMID: 30987772 DOI: 10.1016/j.ygyno.2019.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/03/2019] [Accepted: 04/07/2019] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Endocrine therapy is often considered as a treatment for hormone-responsive gynecologic malignancies. In breast cancer, activating mutations in the estrogen receptor (mutESR1) contribute to therapeutic resistance to endocrine therapy, especially aromatase inhibitors (AIs). The purpose of this study was to evaluate the frequency and clinical relevance of ESR1 genomic alterations in gynecologic malignancies. METHODS DNA from FFPE tumor tissue obtained during routine clinical care for 9645 gynecologic malignancies (ovary, fallopian tube, uterus, cervix, vagina, vulvar, and placenta) was analyzed for all classes of genomic alterations (base substitutions (muts), insertions, deletions, rearrangements, and amplifications) in ESR1 by hybrid capture next generation sequencing. A subset of alterations was characterized in laboratory-based transcription assays for response to endocrine therapies. RESULTS A total of 295 ESR1 genomic alterations were identified in 285 (3.0%) cases. mutESR1 were present in 86 (0.9%) cases and were more common in uterine compared to other cancers (2.0% vs <1%, respectively p < 0.001). mutESR1 were enriched in carcinomas with endometrioid versus serous histology (4.4% vs 0.2% respectively, p < 0.0001 in uterine and 3.5% vs 0.3% respectively, p = 0.0004 in ovarian carcinomas). In three of four patients with serial sampling, mutESR1 emerged under the selective pressure of AI therapy. Despite decreased potency of estrogen receptor (ER) antagonists in transcriptional assays, clinical benefit was observed following treatment with selective ER-targeted therapy, in one case lasting >48 months. CONCLUSIONS While the prevalence of ESR1 mutations in gynecologic malignancies is low, there are significant clinical implications useful in guiding therapeutic approaches for these cancers.
Collapse
Affiliation(s)
- Stéphanie L Gaillard
- Duke University Medical Center, Durham, NC, United States of America; Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD, United States of America.
| | | | - Laurie M Gay
- Foundation Medicine, Inc., Cambridge, MA, United States of America
| | - Meghan Steiner
- Duke University Medical Center, Durham, NC, United States of America
| | | | | | | | | | - Fidel A Valea
- Duke University Medical Center, Durham, NC, United States of America
| | | | | | - Ching-Yi Chang
- Duke University Medical Center, Durham, NC, United States of America
| | | | - Andrew Berchuck
- Duke University Medical Center, Durham, NC, United States of America
| | - Julia A Elvin
- Duke University Medical Center, Durham, NC, United States of America
| |
Collapse
|
47
|
Furman C, Hao MH, Prajapati S, Reynolds D, Rimkunas V, Zheng GZ, Zhu P, Korpal M. Estrogen Receptor Covalent Antagonists: The Best Is Yet to Come. Cancer Res 2019; 79:1740-1745. [PMID: 30952631 DOI: 10.1158/0008-5472.can-18-3634] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 02/06/2019] [Indexed: 11/16/2022]
Abstract
The development of tamoxifen and subsequent estrogen receptor alpha (ERα) antagonists represents a tremendous therapeutic breakthrough in the treatment of breast cancer. Despite the ability of ERα antagonists to increase survival rates, resistance to these therapies is an all-too-common occurrence. The majority of resistant tumors, including those with hotspot mutations in the ligand-binding domain of ERα, remain dependent on ERα signaling, indicating that either a more potent or novel class of antagonist could have clinical benefit. With this thought in mind, we developed a novel ERα antagonist that exhibits enhanced potency due to its ability to covalently target a unique cysteine in ER. This review describes the design of this antagonist, H3B-5942, and discusses opportunities for future improvements, which could reduce the risk of escape mutations to this therapeutic modality.
Collapse
Affiliation(s)
| | | | | | | | | | - Guo Z Zheng
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts.
| | | |
Collapse
|
48
|
Alimirzaie S, Bagherzadeh M, Akbari MR. Liquid biopsy in breast cancer: A comprehensive review. Clin Genet 2019; 95:643-660. [PMID: 30671931 DOI: 10.1111/cge.13514] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/04/2019] [Accepted: 01/11/2019] [Indexed: 12/11/2022]
Abstract
Breast cancer is the most common cancer among women worldwide. Due to its complexity in nature, effective breast cancer treatment can encounter many challenges. Traditional methods of cancer detection such as tissue biopsy are not comprehensive enough to capture the entire genomic landscape of breast tumors. However, with the introduction of novel techniques, the application of liquid biopsy has been enhanced, enabling the improvement of various aspects of breast cancer management including early diagnosis and screening, prediction of prognosis, early detection of relapse, serial sampling and efficient longitudinal monitoring of disease progress and response to treatment. Various components of tumor cells released into the blood circulation can be analyzed in liquid biopsy sampling, some of which include circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free RNA, tumor-educated platelets and exosomes. These components can be utilized for different purposes. As an example, ctDNA can be sequenced for genetic profiling of the tumors to enhance individualized treatment and longitudinal screening. CTC plasma count analysis or ctDNA detection after curative tumor resection surgery could facilitate early detection of minimal residual disease, aiding in the initiation of adjuvant therapy to prevent recurrence. Furthermore, CTC plasma count can be assessed to determine the stage and prognosis of breast cancer. In this review, we discuss the advantages and limitations of the various components of liquid biopsy used in breast cancer diagnosis and will expand on aspects that require further focus in future research.
Collapse
Affiliation(s)
- Sahar Alimirzaie
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Ontario, Canada.,Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada
| | - Maryam Bagherzadeh
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
49
|
ESR1 mutations in metastatic lobular breast cancer patients. NPJ Breast Cancer 2019; 5:9. [PMID: 30820448 PMCID: PMC6384916 DOI: 10.1038/s41523-019-0104-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022] Open
Abstract
Invasive lobular breast cancer (ILC) represents the second most common histology of breast cancer after invasive ductal breast cancer (IDC), accounts for up to 15% of all invasive cases and generally express the estrogen receptor (ER, coded by the ESR1 gene). ESR1 mutations have been associated with resistance to endocrine therapy, however these have not been specifically evaluated in ILC. We assessed the frequency of ESR1 mutations by droplet digital PCR in a retrospective multi-centric series of matched primary tumor and recurrence samples (n = 279) from 80 metastatic ER-positive ILC patients. We further compared ESR1 mutations between IDC and ILC patients in metastatic samples from MSKCC-IMPACT (n = 595 IDC and 116 ILC) and in ctDNA from the SoFEA and PALOMA-3 trials (n = 416 IDC and 76 ILC). In the retrospective series, the metastases from seven patients (9%) harbored ESR1 mutations, which were absent from the interrogated primary samples. Five patients (6%) had a mutation in the primary tumor or axillary metastasis, which could not be detected in the matched distant metastasis. In the MSKCC-IMPACT cohort, as well as in the SoFEA and PALOMA-3 trials, there were no differences in prevalence and distribution of the mutations between IDC and ILC, with D538G being the most frequent mutation in both histological subtypes. To conclude, no patient had an identical ESR1 mutation in the early and metastatic disease in the retrospective ILC series. In the external series, there was no difference in terms of prevalence and type of ESR1 mutations between ILC and IDC. Among a cohort of 80 women with metastatic lobular breast cancer, no patient had an identical mutation in the ESR1 gene in both metastases and localized tumors. ESR1 encodes the estrogen receptor targeted by endocrine therapy — thus, tumors harboring mutations in this gene may require different treatment strategies. Christine Desmedt
from KU Leuven, Belgium, and colleagues found that 9% of patients had metastases with ESR1 mutations that were absent in primary breast tumors; another 6% had mutations in the primary tumors or in cancer-invaded lymph nodes that were not detected in distant metastatic sites. Comparisons with other datasets showed that the prevalence and distribution of ESR1 mutations were not significantly different among women with lobular and ductal breast cancer, the two most common subtypes of the disease.
Collapse
|
50
|
Basudan A, Priedigkeit N, Hartmaier RJ, Sokol ES, Bahreini A, Watters RJ, Boisen MM, Bhargava R, Weiss KR, Karsten MM, Denkert C, Blohmer JU, Leone JP, Hamilton RL, Brufsky AM, Elishaev E, Lucas PC, Lee AV, Oesterreich S. Frequent ESR1 and CDK Pathway Copy-Number Alterations in Metastatic Breast Cancer. Mol Cancer Res 2019; 17:457-468. [PMID: 30355675 PMCID: PMC6359977 DOI: 10.1158/1541-7786.mcr-18-0946] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/04/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022]
Abstract
DNA sequencing has identified a limited number of driver mutations in metastatic breast cancer beyond single base-pair mutations in the estrogen receptor (ESR1). However, our previous studies and others have observed that structural variants, such as ESR1 fusions, may also play a role. Therefore, we expanded upon these observations by performing a comprehensive and highly sensitive characterization of copy-number (CN) alterations in a large clinical cohort of metastatic specimens. NanoString DNA hybridization was utilized to measure CN gains, amplifications, and deletions of 67 genes in 108 breast cancer metastases, and in 26 cases, the patient-matched primary tumor. For ESR1, a copyshift algorithm was applied to identify CN imbalances at exon-specific resolution and queried large data sets (>15,000 tumors) that had previously undergone next-generation sequencing (NGS). Interestingly, a subset of ER+ tumors showed increased ESR1 CN (11/82, 13%); three had CN amplifications (4%) and eight had gains (10%). Increased ESR1 CN was enriched in metastatic specimens versus primary tumors, and this was orthogonally confirmed in a large NGS data set. ESR1-amplified tumors showed a site-specific enrichment for bone metastases and worse outcomes than nonamplified tumors. No ESR1 CN amplifications and only one gain was identified in ER- tumors. ESR1 copyshift was present in 5 of the 11 ESR1-amplified tumors. Other frequent amplifications included ERBB2, GRB7, and cell-cycle pathway members CCND1 and CDK4/6, which showed mutually exclusivity with deletions of CDKN2A, CDKN2B, and CDKN1B. IMPLICATIONS: Copy-number alterations of ESR1 and key CDK pathway genes are frequent in metastatic breast cancers, and their clinical relevance should be tested further.
Collapse
Affiliation(s)
- Ahmed Basudan
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Clinical Lab Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nolan Priedigkeit
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ryan J Hartmaier
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Amir Bahreini
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rebecca J Watters
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michelle M Boisen
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Obstetrics and Gynecology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Magee-Women Hospital, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rohit Bhargava
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kurt R Weiss
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Surgical Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | | | - Jose P Leone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ronald L Hamilton
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adam M Brufsky
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Esther Elishaev
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Magee-Women Hospital, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Peter C Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adrian V Lee
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|