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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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2
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Wang R, Wang B, Zhang H, Liao X, Shi B, Zhou Y, Zhou C, Yan Y, Zhang W, Wang K, Ge G, Ren Y, Tang X, Gan B, He J, Niu L. Early evaluation of circulating tumor DNA as marker of therapeutic efficacy and prognosis in breast cancer patients during primary systemic therapy. Breast 2024; 76:103738. [PMID: 38685149 PMCID: PMC11067540 DOI: 10.1016/j.breast.2024.103738] [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: 01/29/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND We assessed the potential role of serial circulating tumor DNA (ctDNA) as a biomarker to monitor treatment response to primary systemic therapy (PST) in breast cancer and evaluated the predictive value of ctDNA to further identify patients with residual disease. METHODS We prospectively enrolled 208 plasma samples collected at three time points (before PST, after 2 cycles of treatment, before surgery) of 72 patients with stage Ⅱ-III breast cancer. Somatic mutations in plasma samples were identified using a customized 128-gene capture panel with next-generation sequencing. The correlation between early change in ctDNA levels and treatment response or long-term clinical outcomes was assessed. RESULTS 37 of 72 (51.4%) patients harbored detectable ctDNA alterations at baseline. Patients with complete response showed a larger decrease in ctDNA levels during PST. The median relative change of variant allele fraction (VAF) was -97.4%, -46.7%, and +21.1% for patients who subsequently had a complete response (n = 11), partial response (n = 11), and no response (n = 15) (p = 0.0012), respectively. In addition, the relative change of VAF between the pretreatment and first on-treatment blood draw exhibited the optimal predictive value to tumor response after PST (area under the curve, AUC = 0.7448, p = 0.02). More importantly, early change of ctDNA levels during treatment have significant prognostic value for patients with BC, there was a significant correlation between early decrease of VAF and longer recurrence-free survival compared to those with an VAF increase (HR = 12.54; 95% CI, 2.084 to 75.42, p = 0.0063). CONCLUSION Early changes of ctDNA are strongly correlated with therapeutic efficacy to PST and clinical outcomes in BC patients. The integration of preoperative ctDNA evaluation could help improving the perioperative management for BC patients receiving PST.
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Affiliation(s)
- Ru Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Bin Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiaoqin Liao
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Bohui Shi
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yuhui Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Can Zhou
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yu Yan
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Wei Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Ke Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Guanqun Ge
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yu Ren
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiaojiang Tang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Baoyu Gan
- Biobank of the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
| | - Ligang Niu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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3
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Giro C, Yamada AMTD, Cruz FJSM, do R Barros LA, da C A Alves B, Fonseca FLA, Del Giglio A. Measuring cfDNA integrity as a biomarker for predicting neoadjuvant chemotherapy response in breast cancer patients: a pilot study. Breast Cancer Res Treat 2024; 206:329-335. [PMID: 38743176 DOI: 10.1007/s10549-024-07366-y] [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: 09/14/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
PURPOSE Circulating cell-free DNA (cfDNA) is a promising biomarker for predicting treatment response and disease outcomes in Breast Cancer (BC) patients undergoing neoadjuvant chemotherapy (NAC). To determine if cfDNA originates from tumors, matching tumor and cfDNA gene mutations are necessary, often requiring tumor DNA sequencing. We assessed plasma cfDNA integrity by measuring concentrations and ratios of larger-to-smaller Alu DNA fractions as a potential biomarker, eliminating the need for prior tumor sequencing. METHODS We included patients with localized and/or locally advanced BC receiving standard NAC alone or in combination with immunotherapy and/or anti-HER2 targeted therapy. Blood samples were collected before treatment, every 2 weeks during treatment, and before surgery. RESULTS Of the 38 evaluated patients, only 28 completed the protocol and underwent surgery after NAC. Seven patients (25%) achieved a pathologic complete response (pCR). We found that cfDNA integrity (cfDNAI) levels at 15 days after starting NAC were significantly higher in patients who achieved pCR (p = 0.045) and correlated significantly with Disease-Free Survival (DFS) in univariate analysis (p = 0.0371). CONCLUSIONS Evaluation of cfDNAI 2 weeks after NAC initiation appears to be an early biomarker for tumor pCR and DFS. Measuring Alu fragments of different lengths may replace techniques requiring prior tumor sequencing to measure ctDNA, reducing costs and complexity of cfDNA serial measurements in BC patients undergoing NAC.
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Affiliation(s)
- Camila Giro
- Instituto Brasileiro de Controle do Câncer (IBCC), São Paulo, SP, Brazil
- Departamento de Oncologia e Hematologia do Centro Universitário FMABC, Av. Príncipe de Gales, 821, Santo André, SP, 09060-650, Brazil
| | | | - Felipe José S M Cruz
- Instituto Brasileiro de Controle do Câncer (IBCC), São Paulo, SP, Brazil
- Departamento de Oncologia e Hematologia do Centro Universitário FMABC, Av. Príncipe de Gales, 821, Santo André, SP, 09060-650, Brazil
| | | | - Beatriz da C A Alves
- Laboratório de Análises Clínicas do Centro Universitário FMABC, Santo André, SP, Brazil
| | - Fernando L A Fonseca
- Laboratório de Análises Clínicas do Centro Universitário FMABC, Santo André, SP, Brazil
- Instituto de Ciências Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
| | - Auro Del Giglio
- Departamento de Oncologia e Hematologia do Centro Universitário FMABC, Av. Príncipe de Gales, 821, Santo André, SP, 09060-650, Brazil.
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Klocker EV, Hasenleithner S, Bartsch R, Gampenrieder SP, Egle D, Singer CF, Rinnerthaler G, Hubalek M, Schmitz K, Bago-Horvath Z, Petzer A, Heibl S, Heitzer E, Balic M, Gnant M. Clinical applications of next-generation sequencing-based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression. Mol Oncol 2024. [PMID: 38867388 DOI: 10.1002/1878-0261.13671] [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: 11/02/2023] [Revised: 03/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
The advancements in the detection and characterization of circulating tumor DNA (ctDNA) have revolutionized precision medicine and are likely to transform standard clinical practice. The non-invasive nature of this approach allows for molecular profiling of the entire tumor entity, while also enabling real-time monitoring of the effectiveness of cancer therapies as well as the identification of resistance mechanisms to guide targeted therapy. Although the field of ctDNA studies offers a wide range of applications, including in early disease, in this review we mainly focus on the role of ctDNA in the dynamic molecular characterization of unresectable locally advanced and metastatic BC (mBC). Here, we provide clinical practice guidance for the rapidly evolving field of molecular profiling of mBC, outlining the current landscape of liquid biopsy applications and how to choose the right ctDNA assay. Additionally, we underline the importance of exploring the clinical relevance of novel molecular alterations that potentially represent therapeutic targets in mBC, along with mutations where targeted therapy is already approved. Finally, we present a potential roadmap for integrating ctDNA analysis into clinical practice.
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Affiliation(s)
- Eva Valentina Klocker
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Austria
| | - Rupert Bartsch
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Simon P Gampenrieder
- Third Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Austria
| | - Daniel Egle
- Department of Gynecology, Breast Cancer Center Tirol, Medical University of Innsbruck, Austria
| | - Christian F Singer
- Department of Gynecology, Breast Cancer Center Vienna, Medical University of Vienna, Austria
| | - Gabriel Rinnerthaler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Michael Hubalek
- Department of Gynecology, Breast Health Center Schwaz, Austria
| | - Katja Schmitz
- Institute of Pathology, University Medical Center Göttingen, Germany
- Tyrolpath Obrist Brunhuber GmbH and Krankenhaus St. Vinzenz, Zams, Austria
| | | | - Andreas Petzer
- Department of Internal Medicine I for Hematology with Stem Cell Transplantation, Hemostaseology and Medical Oncology, Barmherzige Schwestern, Elisabethinen, Ordensklinikum Linz GmbH, Austria
| | - Sonja Heibl
- Department of Internal Medicine IV, Klinikum Wels-Grieskirchen GmbH, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Christian Doppler Laboratory for Liquid Biopsies for early Detection of Cancer, Medical University of Graz, Austria
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
- Division of Hematology and Medical Oncology, University of Pittsburgh School of Medicine, PA, USA
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Austria
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Boissin C, Wang Y, Sharma A, Weitz P, Karlsson E, Robertson S, Hartman J, Rantalainen M. Deep learning-based risk stratification of preoperative breast biopsies using digital whole slide images. Breast Cancer Res 2024; 26:90. [PMID: 38831336 PMCID: PMC11145850 DOI: 10.1186/s13058-024-01840-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Nottingham histological grade (NHG) is a well established prognostic factor in breast cancer histopathology but has a high inter-assessor variability with many tumours being classified as intermediate grade, NHG2. Here, we evaluate if DeepGrade, a previously developed model for risk stratification of resected tumour specimens, could be applied to risk-stratify tumour biopsy specimens. METHODS A total of 11,955,755 tiles from 1169 whole slide images of preoperative biopsies from 896 patients diagnosed with breast cancer in Stockholm, Sweden, were included. DeepGrade, a deep convolutional neural network model, was applied for the prediction of low- and high-risk tumours. It was evaluated against clinically assigned grades NHG1 and NHG3 on the biopsy specimen but also against the grades assigned to the corresponding resection specimen using area under the operating curve (AUC). The prognostic value of the DeepGrade model in the biopsy setting was evaluated using time-to-event analysis. RESULTS Based on preoperative biopsy images, the DeepGrade model predicted resected tumour cases of clinical grades NHG1 and NHG3 with an AUC of 0.908 (95% CI: 0.88; 0.93). Furthermore, out of the 432 resected clinically-assigned NHG2 tumours, 281 (65%) were classified as DeepGrade-low and 151 (35%) as DeepGrade-high. Using a multivariable Cox proportional hazards model the hazard ratio between DeepGrade low- and high-risk groups was estimated as 2.01 (95% CI: 1.06; 3.79). CONCLUSIONS DeepGrade provided prediction of tumour grades NHG1 and NHG3 on the resection specimen using only the biopsy specimen. The results demonstrate that the DeepGrade model can provide decision support to identify high-risk tumours based on preoperative biopsies, thus improving early treatment decisions.
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Affiliation(s)
- Constance Boissin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yinxi Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Abhinav Sharma
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Philippe Weitz
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Emelie Karlsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- MedTechLabs, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- MedTechLabs, BioClinicum, Karolinska University Hospital, Stockholm, Sweden.
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6
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Goetz MP, Hamilton EP, Campone M, Hurvitz SA, Cortes J, Johnston S, Llombart-Cussac A, Kaufman PA, Toi M, Jerusalem G, Graham H, Wang H, Jansen VM, Litchfield LM, Martin M. Landscape of Baseline and Acquired Genomic Alterations in Circulating Tumor DNA with Abemaciclib Alone or with Endocrine Therapy in Advanced Breast Cancer. Clin Cancer Res 2024; 30:2233-2244. [PMID: 37889120 PMCID: PMC11094424 DOI: 10.1158/1078-0432.ccr-22-3573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
PURPOSE To identify potential predictors of response and resistance mechanisms in patients with hormone receptor-positive (HR+), HER2-negative (HER2-) advanced breast cancer (ABC) treated with the cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitor abemaciclib ± endocrine therapy (ET), baseline and acquired genomic alterations in circulating tumor DNA (ctDNA) were analyzed and associated with clinical outcomes. EXPERIMENTAL DESIGN MONARCH 3: postmenopausal women with HR+, HER2- ABC and no prior systemic therapy in the advanced setting were randomly assigned to abemaciclib or placebo plus nonsteroidal aromatase inhibitor (NSAI). nextMONARCH: women with HR+, HER2- metastatic breast cancer that progressed on/after prior ET and chemotherapy were randomly assigned to abemaciclib alone (two doses) or plus tamoxifen. Baseline and end-of-treatment plasma samples from patients in MONARCH 3 and nextMONARCH (monotherapy arms) were analyzed to identify somatic genomic alterations. Association between genomic alterations and median progression-free survival (mPFS) was assessed. RESULTS Most patients had ≥1 genomic alteration detected in baseline ctDNA. In MONARCH 3, abemaciclib+NSAI was associated with improved mPFS versus placebo+NSAI, regardless of baseline alterations. ESR1 alterations were less frequently acquired in the abemaciclib+NSAI arm than placebo+NSAI. Acquired alterations potentially associated with resistance to abemaciclib ± NSAI included RB1 and MYC. CONCLUSIONS In MONARCH 3, certain baseline ctDNA genomic alterations were prognostic for ET but not predictive of abemaciclib response. Further studies are warranted to assess whether ctDNA alterations acquired during abemaciclib treatment differ from other CDK4/6 inhibitors. Findings are hypothesis generating; further exploration is warranted into mechanisms of resistance to abemaciclib and ET. See related commentary by Wander and Bardia, p. 2008.
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Affiliation(s)
| | - Erika P. Hamilton
- Sarah Cannon Research Institute, Tennessee Oncology PLCC, Nashville, Tennessee
| | - Mario Campone
- Institut de Cancerologie de l'Ouest, Angers Cedex, France
| | | | - Javier Cortes
- Oncology Department, International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, Barcelona, Spain
- Department of Medicine, Universidad Europea de Madrid, Faculty of Biomedical and Health Sciences, Madrid, Spain
| | | | | | | | | | | | | | - Hong Wang
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | - Miguel Martin
- Instiuto de Investigacion Santaria Gregorio Maranon, Universidad Complutense, CIBERONC, Madrid, Spain
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Gerratana L, Davis AA, Velimirovic M, Clifton K, Hensing WL, Shah AN, Dai CS, Reduzzi C, D'Amico P, Wehbe F, Medford A, Wander SA, Gradishar WJ, Behdad A, Puglisi F, Ma CX, Bardia A, Cristofanilli M. Interplay between ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype in patients with metastatic breast cancer (MBC): comprehensive circulating tumor DNA (ctDNA) analysis. Breast Cancer Res 2023; 25:112. [PMID: 37784176 PMCID: PMC10546685 DOI: 10.1186/s13058-023-01718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/24/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND although being central for the biology and druggability of hormone-receptor positive, HER2 negative metastatic breast cancer (MBC), ESR1 and PIK3CA mutations are simplistically dichotomized as mutated or wild type in current clinical practice. METHODS The study analyzed a multi-institutional cohort comprising 703 patients with luminal-like MBC characterized for circulating tumor DNA through next generation sequencing (NGS). Pathway classification was defined based on previous work (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Single nucleotide variations (SNVs) were annotated for their oncogenicity through OncoKB. Only pathogenic variants were included in the models. Associations among clinical characteristics, pathway classification, and ESR1/PIK3CA codon variants were explored. RESULTS The results showed a differential pattern of associations for ESR1 and PIK3CA codon variants in terms of co-occurring pathway alterations patterns of metastatic dissemination, and prognosis. ESR1 537 was associated with SNVs in the ER and RAF pathways, CNVs in the MYC pathway and bone metastases, while ESR1 538 with SNVs in the cell cycle pathway and liver metastases. PIK3CA 1047 and 542 were associated with CNVs in the PI3K pathway and with bone metastases. CONCLUSIONS The study demonstrated how ESR1 and PIK3CA codon variants, together with alterations in specific oncogenic pathways, can differentially impact the biology and clinical phenotype of luminal-like MBC. As novel endocrine therapy agents such as selective estrogen receptor degraders (SERDS) and PI3K inhibitors are being developed, these results highlight the pivotal role of ctDNA NGS to describe tumor evolution and optimize clinical decision making.
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Affiliation(s)
- Lorenzo Gerratana
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Andrew A Davis
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Marko Velimirovic
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Katherine Clifton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Whitney L Hensing
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ami N Shah
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Charles S Dai
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Carolina Reduzzi
- Weill Cornell Medicine, 420 E 70th St, LH 204, New York, NY, 10021, USA
| | - Paolo D'Amico
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Firas Wehbe
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arielle Medford
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Seth A Wander
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Amir Behdad
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medical Oncology, CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
- Department of Medicine, University of Udine, Udine, Italy
| | - Cynthia X Ma
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Daneshdoust D, Luo M, Li Z, Mo X, Alothman S, Kallakury B, Schlegel R, Zhang J, Guo D, Furth PA, Liu X, Li J. Unlocking Translational Potential: Conditionally Reprogrammed Cells in Advancing Breast Cancer Research. Cells 2023; 12:2388. [PMID: 37830602 PMCID: PMC10572051 DOI: 10.3390/cells12192388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
Preclinical in vitro models play an important role in studying cancer cell biology and facilitating translational research, especially in the identification of drug targets and drug discovery studies. This is particularly relevant in breast cancer, where the global burden of disease is quite high based on prevalence and a relatively high rate of lethality. Predictive tools to select patients who will be responsive to invasive or morbid therapies (radiotherapy, chemotherapy, immunotherapy, and/or surgery) are relatively lacking. To be clinically relevant, a model must accurately replicate the biology and cellular heterogeneity of the primary tumor. Addressing these requirements and overcoming the limitations of most existing cancer cell lines, which are typically derived from a single clone, we have recently developed conditional reprogramming (CR) technology. The CR technology refers to a co-culture system of primary human normal or tumor cells with irradiated murine fibroblasts in the presence of a Rho-associated kinase inhibitor to allow the primary cells to acquire stem cell properties and the ability to proliferate indefinitely in vitro without any exogenous gene or viral transfection. This innovative approach fulfills many of these needs and offers an alternative that surpasses the deficiencies associated with traditional cancer cell lines. These CR cells (CRCs) can be reprogrammed to maintain a highly proliferative state and reproduce the genomic and histological characteristics of the parental tissue. Therefore, CR technology may be a clinically relevant model to test and predict drug sensitivity, conduct gene profile analysis and xenograft research, and undertake personalized medicine. This review discusses studies that have applied CR technology to conduct breast cancer research.
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Affiliation(s)
- Danyal Daneshdoust
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Mingjue Luo
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Zaibo Li
- Departments of Pathology, Wexner Medical Center, Ohio State University, Columbus, OH 43210, USA
| | - Xiaokui Mo
- Department of Biostatics and Bioinformatics, Wexner Medical Center, Ohio State University, Columbus, OH 43210, USA
| | - Sahar Alothman
- Departments of Oncology and Medicine, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Bhaskar Kallakury
- Departments of Pathology, Lombardi Comprehensive Cancer Center, Center for Cell Reprogramming, Georgetown University, Washington, DC 20057, USA
| | - Richard Schlegel
- Departments of Pathology, Lombardi Comprehensive Cancer Center, Center for Cell Reprogramming, Georgetown University, Washington, DC 20057, USA
| | - Junran Zhang
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
- Department of Radiation Oncology, Wexner Medical Center, Ohio State University, Columbus, OH 43210, USA
| | - Deliang Guo
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
- Department of Radiation Oncology, Wexner Medical Center, Ohio State University, Columbus, OH 43210, USA
| | - Priscilla A. Furth
- Departments of Oncology and Medicine, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Xuefeng Liu
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
- Departments of Pathology, Urology, and Radiation Oncology, Wexner Medical Center, Ohio State University, Columbus, OH 43210, USA
| | - Jenny Li
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
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Chiu J, Su F, Joshi M, Masuda N, Ishikawa T, Aruga T, Zarate JP, Babbar N, Balbin OA, Yap YS. Potential value of ctDNA monitoring in metastatic HR + /HER2 - breast cancer: longitudinal ctDNA analysis in the phase Ib MONALEESASIA trial. BMC Med 2023; 21:306. [PMID: 37580773 PMCID: PMC10426213 DOI: 10.1186/s12916-023-03017-z] [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: 02/07/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND There is increasing interest in the use of liquid biopsies, but data on longitudinal analyses of circulating tumor DNA (ctDNA) remain relatively limited. Here, we report a longitudinal ctDNA analysis of MONALEESASIA, a phase Ib trial evaluating the efficacy and safety of ribociclib plus endocrine therapy (ET) in Asian patients with hormone receptor-positive, human epidermal growth factor receptor-2-negative advanced breast cancer. METHODS MONALEESASIA enrolled premenopausal and postmenopausal Japanese and postmenopausal non-Japanese Asian patients. All patients received ribociclib with ET (letrozole, fulvestrant, or tamoxifen with goserelin). ctDNA was analyzed using a targeted next-generation sequencing panel of 572 cancer-related genes and correlated by best overall response (BOR). RESULTS Five hundred seventy-four cell-free DNA samples from 87 patients were tested. The most frequently altered genes at baseline included PIK3CA (29%) and TP53 (22%). Treatment with ribociclib plus ET decreased ctDNA in most patients at the first on-treatment time point, regardless of dose or ET partner. Patients with partial response and stable disease had lower ctDNA at baseline that remained low until data cutoff if no progressive disease occurred. Most patients with progressive disease as the best response had higher ctDNA at baseline that remained high at the end of treatment. For patients with partial response and stable disease with subsequent progression, ctDNA increased towards the end of treatment in most patients, with a median lead time of 83 days (14-309 days). In some patients with BOR of partial response who experienced disease progression later, specific gene alterations and total ctDNA fraction increased; this was sometimes observed concurrently with the development of new lesions without a change in target lesion size. Patients with alterations in PIK3CA and TP53 at baseline had shorter median progression-free survival compared with patients with wild-type PIK3CA and TP53, 12.7 and 7.3 months vs 19.2 and 19.4 months, respectively (P = .016 and P = .0001, respectively). CONCLUSIONS Higher ctDNA levels and PIK3CA and TP53 alterations detected at baseline were associated with inferior outcomes. On-treatment ctDNA levels were associated with different patterns based on BOR. Longitudinal tracking of ctDNA may be useful for monitoring tumor status and detection of alterations with treatment implications. TRIAL REGISTRATION ClinicalTrials.gov NCT02333370 . Registered on January 7, 2015.
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Affiliation(s)
- Joanne Chiu
- Queen Mary Hospital, 102 Pok Fu Lam Rd, Pok Fu Lam, Hong Kong
| | - Fei Su
- Novartis Pharmaceuticals Corporation, 1 Health Plaza, East Hanover, NJ, USA
| | - Mukta Joshi
- Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA, USA
| | - Norikazu Masuda
- Nagoya University Graduate School of Medicine, Building B, Furocho, Chikusa Ward, Nagoya, Japan
| | - Takashi Ishikawa
- Tokyo Medical University Hospital, 6 Chome-7-1 Nishishinjuku, Shinjuku City, Tokyo, Japan
| | - Tomoyuki Aruga
- Tokyo Metropolitan Komagome Hospital, 3 Chome-18 Honkomagome, Bunkyo City, Tokyo, Japan
| | - Juan Pablo Zarate
- Novartis Pharmaceuticals Corporation, 1 Health Plaza, East Hanover, NJ, USA
| | - Naveen Babbar
- Novartis Pharmaceuticals Corporation, 1 Health Plaza, East Hanover, NJ, USA
| | - O Alejandro Balbin
- Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA, USA
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Blvd, Singapore, Singapore.
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10
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Nicolò E, Munoz-Arcos L, Vagia E, D'Amico P, Reduzzi C, Donahue J, Lorico-Rappa M, Manai M, Behdad A, Zhang Y, Curigliano G, Shah A, Cristofanilli M. Circulating Tumor DNA and Unique Actionable Genomic Alterations in the Longitudinal Monitoring of Metastatic Breast Cancer: A Case of FGFR2-KIAA1598 Gene Fusion. JCO Precis Oncol 2023; 7:e2200702. [PMID: 37437229 DOI: 10.1200/po.22.00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/08/2023] [Accepted: 06/08/2023] [Indexed: 07/14/2023] Open
Affiliation(s)
- Eleonora Nicolò
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY
| | - Laura Munoz-Arcos
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY
| | - Elena Vagia
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Paolo D'Amico
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Carolina Reduzzi
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jeannine Donahue
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Marco Lorico-Rappa
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Royal College of Surgeons School of Medicine, Dublin, Ireland
| | - Maroua Manai
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Amir Behdad
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Youbin Zhang
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Ami Shah
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
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11
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Bai S, Lin S, Lin T, Wang Q, Cheng C, Lin J, Zhang Y, Jiang X, Han X. Clinical diagnostic biomarker "circulating tumor cells" in breast cancer - a meta-analysis. Front Oncol 2023; 13:1137519. [PMID: 37397397 PMCID: PMC10313226 DOI: 10.3389/fonc.2023.1137519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Objective Using meta-analysis, we evaluate circulating tumor cells(CTCs) as a potential diagnostic tool for breast cancer. Methods A document search was conducted using publicly available databases up to May 2021. Specific inclusion and exclusion criteria were formulated and summarize relevant data through literature types, research types, case populations, samples, etc. Subgroup analysis of documents based on regions, enrichment methods, and detection methods. The included research projects were evaluated using DeeKs' bias, and evaluation indicators such as specificity (SPE), sensitivity (SEN), diagnosis odds ratio (DOR) were used as evaluation indicators. Results 16 studies on the use of circulating tumor cells to diagnose breast cancer were included in our meta-analysis. Overall sensitivity value was 0.50 (95%CI:0.48-0.52), specificity value was 0.93 (95%CI:0.92- 0.95), DOR value was 33.41 (95%CI:12.47-89.51), and AUC value was 0.8129. Conclusion In meta-regressions and subgroup analysis, potential heterogeneity factors were analyzed, but the source of heterogeneity is still unclear. CTCs, as a novel tumor marker, have a good diagnostic value, but its enrichment and detection methods still need to continue to be developed to improve detection accuracy. Therefore, CTCs can be used as an auxiliary means of early detection, which is helpful to the diagnosis and screening of breast cancer.
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Affiliation(s)
- Shiyan Bai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Shujin Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Ting Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Qiaowen Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Cui Cheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Junru Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Ying Zhang
- Industrial Management Engineering, National University of Singapore, Singapore, Singapore
| | - Xiwen Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
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12
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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13
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Viglianisi G, Santonocito S, Polizzi A, Troiano G, Amato M, Zhurakivska K, Pesce P, Isola G. Impact of Circulating Cell-Free DNA (cfDNA) as a Biomarker of the Development and Evolution of Periodontitis. Int J Mol Sci 2023; 24:9981. [PMID: 37373135 DOI: 10.3390/ijms24129981] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
In the last few decades, circulating cell-free DNA (cfDNA) has been shown to have an important role in cell apoptosis or necrosis, including in the development and evolution of several tumors and inflammatory diseases in humans. In this regard, periodontitis, a chronic inflammatory disease that can induce the destruction of supporting components of the teeth, could represent a chronic inflammatory stimulus linked to a various range of systemic inflammatory diseases. Recently, a possible correlation between periodontal disease and cfDNA has been shown, representing new important diagnostic-therapeutic perspectives. During the development of periodontitis, cfDNA is released in biological fluids such as blood, saliva, urine and other body fluids and represents an important index of inflammation. Due to the possibility of withdrawing some of these liquids in a non-invasive way, cfDNA could be used as a possible biomarker for periodontal disease. In addition, discovering a proportional relationship between cfDNA levels and the severity of periodontitis, expressed through the disease extent, could open the prospect of using cfDNA as a possible therapeutic target. The aim of this article is to report what researchers have discovered in recent years about circulating cfDNA in the development, evolution and therapy of periodontitis. The analyzed literature review shows that cfDNA has considerable potential as a diagnostic, therapeutic biomarker and therapeutic target in periodontal disease; however, further studies are needed for cfDNA to be used in clinical practice.
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Affiliation(s)
- Gaia Viglianisi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Simona Santonocito
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Alessandro Polizzi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Mariacristina Amato
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Khrystyna Zhurakivska
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Paolo Pesce
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Ospedale S. Martino, 16148 Genoa, Italy
| | - Gaetano Isola
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
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14
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Jagannathan G, White MJ, Xian RR, Emens LA, Cimino-Mathews A. A New Landscape of Testing and Therapeutics in Metastatic Breast Cancer. Clin Lab Med 2023; 43:299-321. [PMID: 37169447 DOI: 10.1016/j.cll.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Predictive biomarker testing on metastatic breast cancer is essential for determining patient eligibility for targeted therapeutics. The National Comprehensive Cancer Network currently recommends assessment of specific biomarkers on metastatic tumor subtypes, including hormone receptors, HER2, and BRCA1/2 mutations, on all newly metastatic breast cancers subtypes; programmed death-ligand 1 on metastatic triple-negative carcinomas; and PIK3CA mutation status on estrogen receptor-positive carcinomas. In select circumstances mismatch repair protein deficiency and/or microsatellite insufficiency, tumor mutation burden, and NTRK translocation status are also testing options. Novel biomarker testing, such as detecting PIK3CA mutations in circulating tumor DNA, is expanding in this rapidly evolving arena.
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Affiliation(s)
- Geetha Jagannathan
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA
| | - Marissa J White
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA
| | - Rena R Xian
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA; Department of Oncology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA
| | - Leisha A Emens
- Department of Oncology, UPMC Hillman Cancer Center/Magee Women's Hospital, 5117 Centre Avenue, Room 1.46e, Pittsburgh, PA 15213, USA
| | - Ashley Cimino-Mathews
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA; Department of Oncology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA.
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15
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Assi T, Khoury R, Ibrahim R, Baz M, Ibrahim T, LE Cesne A. Overview of the role of liquid biopsy in cancer management. Transl Oncol 2023; 34:101702. [PMID: 37267803 DOI: 10.1016/j.tranon.2023.101702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
With the emergence of novel targeted therapeutic options in early-stage and advanced-stage malignancies, researchers have shifted their focus on developing personalized treatment plans through molecular profiling. Circulating tumor DNA (ctDNA) is a cell-free DNA (ctDNA) fragment, originating from tumor cells, and circulating in the bloodstream as well as biological fluids. Over the past decade, many techniques were developed for liquid biopsies through next-generation sequencing. This alternative non-invasive biopsy offers several advantages in various types of tumors over traditional tissue biopsy. The process of liquid biopsy is considered minimally invasive and therefore easily repeatable when needed, providing a more dynamic analysis of the tumor cells. Moreover, it has an advantage in patients with tumors that are not candidates for tissue sampling. Besides, it offers a deeper understanding of tumor burden as well as treatment response, thereby enhancing the detection of minimal residual disease and therapeutic guidance for personalized medicine. Despite its many advantages, ctDNA and liquid biopsy do have some limitations. This paper discusses the basis of ctDNA and the current data available on the subject, as well as its clinical utility. We also reflect on the limitations of using ctDNA in addition to its future perspectives in clinical oncology and precision medicine.
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Affiliation(s)
- Tarek Assi
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Rita Khoury
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Rebecca Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Maria Baz
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Tony Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Axel LE Cesne
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
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16
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Liefaard MC, Moore KS, Mulder L, van den Broek D, Wesseling J, Sonke GS, Wessels LFA, Rookus M, Lips EH. Tumour-educated platelets for breast cancer detection: biological and technical insights. Br J Cancer 2023; 128:1572-1581. [PMID: 36765174 PMCID: PMC10070267 DOI: 10.1038/s41416-023-02174-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier. METHODS Platelet mRNA was sequenced from 266 women with stage I-IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised support vector machine (PSO-SVM) and an elastic net-based classifier (EN) were trained on 71% of the study population. Classifier performance was evaluated in the remainder (29%) of the population, followed by validation in an independent set (37 cases and 36 controls). Potential confounding was assessed in post hoc analyses. RESULTS Both classifiers reached an area under the curve (AUC) of 0.85 upon internal validation. Reproducibility in the independent validation set was poor with an AUC of 0.55 and 0.54 for the PSO-SVM and EN classifier, respectively. Post hoc analyses indicated that 19% of the variance in gene expression was associated with hospital. Genes related to platelet activity were differentially expressed between hospitals. CONCLUSIONS We could not validate two TEP-based breast cancer classifiers in an independent validation cohort. The TEP protocol is sensitive to within-protocol variation and revision might be necessary before TEPs can be reconsidered for breast cancer detection.
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Affiliation(s)
- Marte C Liefaard
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kat S Moore
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Clinical Chemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Matti Rookus
- Department of Psychosocial and Epidemiology Research, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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17
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Nair MG, Ramesh RS, Naidu CM, Mavatkar AD, V. P. S, Ramamurthy V, Somashekaraiah VM, C. E. A, Raghunathan K, Panigrahi A, Das M, Dhar SK, Prabhu JS. Estimation of ALU Repetitive Elements in Plasma as a Cost-Effective Liquid Biopsy Tool for Disease Prognosis in Breast Cancer. Cancers (Basel) 2023; 15:cancers15041054. [PMID: 36831397 PMCID: PMC9953974 DOI: 10.3390/cancers15041054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Liquid biopsy is widely recognized as an efficient diagnostic method in oncology for disease detection and monitoring. Though the examination of circulating tumor cells (CTC) is mostly implemented for the assessment of genomic aberrations, the need of complex methodologies for their detection has impeded its acceptance in low-resource settings. We evaluated cell-free DNA (cfDNA) as a liquid biopsy tool and investigated its utility in breast cancer patients. METHODS Total cell-free DNA was extracted from the plasma of breast cancer patients (n = 167) with a median follow-up of more than 5 years, at various stages of the disease. Quantitative PCR was performed to estimate the copy numbers of two fractions of ALU repetitive elements (ALU 115 and ALU 247), and DNA integrity (DI) was calculated as the ratio of ALU 247/115. Mutations in TP53 and PIK3CA in the cfDNA were estimated by next-gen sequencing (NGS) in a subset of samples. Associations of the levels of both the ALU fragments with various clinico-pathological factors and disease-free survival at various stages were examined. Nomogram models were constructed with clinical variables and ALU 247 levels to predict disease-free survival and the best performing model was evaluated by decision curve analysis. RESULTS DI and ALU 247 levels were significantly lower (p < 0.0001) in the post-operative plasma when compared to their pre-surgery levels. DI and ALU 247 were found to be significantly higher in patients with metastasis (p < 0.05). Patients with higher levels of ALU 247 in their post-operative plasma had significant poor disease-free survival (p = 0.005). Higher levels of ALU 247 in the circulation also correlated with low tumor-infiltrating lymphocytes (TIL) within their primary tumors in the ER-negative breast cancer subtype (p = 0.01). Cox proportional hazard analysis confirmed ALU 247 as an independent variable of disease-free survival both in univariate and multivariate analysis [HR 1.3 (95% CI 1.047 to 1.613, p = 0.017)]. The nomogram model showed that the addition of ALU 247 with other variables significantly improved (C-index 0.823) the predictive ability of the model. CONCLUSION Our results confirm the utility of cfDNA as an evolving liquid biopsy tool for molecular analysis. Evaluation of larger fragments of cfDNA estimated through ALU 247 can provide vital information concurrent with the pathological process of disease evolution in breast cancer and warrants expansion to other cancer types.
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Affiliation(s)
- Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
- Correspondence: (M.G.N.); (J.S.P.)
| | - Rakesh S. Ramesh
- Department of Surgical Oncology, St. John’s Medical College and Hospital, Bangalore 560034, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Snijesh V. P.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Vishakha Ramamurthy
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Vidya M. Somashekaraiah
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | - Anupama C. E.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
| | | | - Anuradha Panigrahi
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Manjula Das
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Sujan K. Dhar
- Molecular Immunology Program, MSMF, Narayana Health City, Bangalore 560099, India
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, India
- Correspondence: (M.G.N.); (J.S.P.)
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18
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Li G, Wu S, Chen W, Duan X, Sun X, Li S, Mai Z, Wu W, Zeng G, Liu H, Chen T. Designing Intelligent Nanomaterials to Achieve Highly Sensitive Diagnoses and Multimodality Therapy of Bladder Cancer. SMALL METHODS 2023; 7:e2201313. [PMID: 36599700 DOI: 10.1002/smtd.202201313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Bladder cancer (BC) is among the most common malignant tumors of the genitourinary system worldwide. In recent years, the rate of BC incidence has increased, and the recurrence rate is high, resulting in poor quality of life for patients. Therefore, how to develop an effective method to achieve synchronous precise diagnoses and BC therapies is a difficult problem to solve clinically. Previous reports usually focus on the role of nanomaterials as drug delivery carriers, while a summary of the functional design and application of nanomaterials is lacking. Summarizing the application of functional nanomaterials in high-sensitivity diagnosis and multimodality therapy of BC is urgently needed. This review summarizes the application of nanotechnology in BC diagnosis, including the application of nanotechnology in the sensoring of BC biomarkers and their role in monitoring BC. In addition, conventional and combination therapies strategy in potential BC therapy are analyzed. Moreover, different kinds of nanomaterials in BC multimodal therapy according to pathological features of BC are also outlined. The goal of this review is to present an overview of the application of nanomaterials in the theranostics of BC to provide guidance for the application of functional nanomaterials to precisely diagnose and treat BC.
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Affiliation(s)
- Guanlin Li
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Sicheng Wu
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Wenzhe Chen
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Xiaolu Duan
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Xinyuan Sun
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Shujue Li
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Zanlin Mai
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Wenzheng Wu
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, P. R. China
| | - Guohua Zeng
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
| | - Hongxing Liu
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou, 510631, P. R. China
| | - Tianfeng Chen
- Department of Urology, Guangzhou Institute of Urology, Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, P. R. China
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou, 510631, P. R. China
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19
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Cerma K, Piacentini F, Moscetti L, Barbolini M, Canino F, Tornincasa A, Caggia F, Cerri S, Molinaro A, Dominici M, Omarini C. Targeting PI3K/AKT/mTOR Pathway in Breast Cancer: From Biology to Clinical Challenges. Biomedicines 2023; 11:biomedicines11010109. [PMID: 36672617 PMCID: PMC9855880 DOI: 10.3390/biomedicines11010109] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
Breast cancer (BC) is the most common women cancer and cause of cancer death. Despite decades of scientific progress in BC treatments, the clinical benefit of new drugs is modest in several cases. The phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway mutations are frequent in BC (20-40%) and are significant causes of aggressive tumor behavior, as well as treatment resistance. Improving knowledge of the PI3K/AKT/mTOR pathway is an urgent need. This review aims to highlight the central role of PI3K-mTORC1/C2 mutations in the different BC subtypes, in terms of clinical outcomes and treatment efficacy. The broad base of knowledge in tumor biology is a key point for personalized BC therapy in the precision medicine era.
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Affiliation(s)
- Krisida Cerma
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
| | - Federico Piacentini
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
- Division of Medical Oncology, University Hospital of Modena, 41122 Modena, Italy
- GOIRC (Gruppo Oncologico Italiano di Ricerca Clinica), 43126 Parma, Italy
| | - Luca Moscetti
- Division of Medical Oncology, University Hospital of Modena, 41122 Modena, Italy
- GOIRC (Gruppo Oncologico Italiano di Ricerca Clinica), 43126 Parma, Italy
| | - Monica Barbolini
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
- Division of Medical Oncology, University Hospital of Modena, 41122 Modena, Italy
| | - Fabio Canino
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
| | - Antonio Tornincasa
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
| | - Federica Caggia
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
| | - Sara Cerri
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
| | - Alessia Molinaro
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
| | - Massimo Dominici
- Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, 41122 Modena, Italy
- Division of Medical Oncology, University Hospital of Modena, 41122 Modena, Italy
| | - Claudia Omarini
- Division of Medical Oncology, University Hospital of Modena, 41122 Modena, Italy
- GOIRC (Gruppo Oncologico Italiano di Ricerca Clinica), 43126 Parma, Italy
- Correspondence: ; Tel.: +39-059-422-2845
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20
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Khan H, Shah MR, Barek J, Malik MI. Cancer biomarkers and their biosensors: A comprehensive review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Valenza C, Trapani D, Curigliano G. Circulating tumour DNA dynamics for assessment of molecular residual disease and for intercepting resistance in breast cancer. Curr Opin Oncol 2022; 34:595-605. [PMID: 36083118 DOI: 10.1097/cco.0000000000000905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Longitudinal evaluation of circulating tumour DNA (ctDNA) represents a promising tool for monitoring tumour evolution. In patients with breast cancer, ctDNA dynamics for the assessment of molecular residual disease (MRD) and resistances may, respectively, help clinicians in treatment modulation of adjuvant treatments, and in anticipating resistance to ongoing treatments and switch treatments before clinical progression, to improve disease control. Anyway, the introduction of this dynamic biomarker into clinical practice requires the demonstration of analytical validity, clinical validity and clinical utility. RECENT FINDINGS In early breast cancer setting, several observational studies demonstrated the clinical validity of MRD monitoring through ctDNA in identifying patients at a higher risk of relapse, but many clinical trials evaluating the clinical utility are still ongoing, and few data resulted in inconclusive results.Instead, ctDNA dynamics for intercepting resistance have not been fully evaluated in terms of clinical validity, because monitoring schedules of most observational studies are not intensive. The only trial assessing their clinical utility (PADA-1) demonstrated a benefit in terms of progression-free survival, portraying a new landscape for clinical trials in this space. SUMMARY Rigorous clinical trials with adequate assays and patient-relevant endpoints are paramount to demonstrate the clinical utility of ctDNA dynamics and eventually increase clinical outcomes.
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Affiliation(s)
- Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS
- Department of Oncology and Haematology, University of Milan, Milan, Italy
| | - Dario Trapani
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS
- Department of Oncology and Haematology, University of Milan, Milan, Italy
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22
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Silva ATF, Rodrigues CM, Ferreira ICC, Santos LLD, Santos DW, Araújo TG, Canto PPL, Paiva CE, Goulart LR, Maia YCP. A Novel Detection Method of Breast Cancer through a Simple Panel of Biomarkers. Int J Mol Sci 2022; 23:ijms231911983. [PMID: 36233281 PMCID: PMC9570447 DOI: 10.3390/ijms231911983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Circulating tumor cells (CTCs) have been identified as responsible for the spread of tumors to other organs of the body. In this sense, the development of sensitive and specific assays for their detection is important to reduce the number of deaths due to metastases. Here, we assessed whether the detection of CTCs in peripheral blood can serve in the construction of a panel of diagnosis and monitoring treatments of breast cancer (BC), focusing on the expression of markers of epithelial-mesenchymal transition. Through analyzing the blood from women without breast alterations (control), women with benign alterations, women with breast cancer without chemotherapy, and women with breast cancer with chemotherapy, we identified the best markers by transcriptional levels and determined three profiles of CTCs (mesenchymal, intermediate, and epithelial) by flow cytometry which, combined, can be used for diagnosis and therapy monitoring with sensitivity and specificity between 80% and 100%. Therefore, we have developed a method for detecting breast cancer based on the analysis of CTC profiles by epithelial-mesenchymal transition markers which, combined, can be used for the diagnosis and monitoring of therapy.
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Affiliation(s)
- Alinne T. F. Silva
- Molecular Biology and Nutrition Research Group, School of Medicine, Graduate Program in Health Science, Av. Amazonas sn, Block 2E, 2º Floor, Room 210, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
| | - Cláudia M. Rodrigues
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
| | - Izabella C. C. Ferreira
- Molecular Biology and Nutrition Research Group, School of Medicine, Graduate Program in Health Science, Av. Amazonas sn, Block 2E, 2º Floor, Room 210, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
| | - Letícia L. D. Santos
- Molecular Biology and Nutrition Research Group, School of Medicine, Graduate Program in Health Science, Av. Amazonas sn, Block 2E, 2º Floor, Room 210, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
| | - Donizeti W. Santos
- Obstetric Division, University Hospital, Federal University of Uberlandia, Av. Pará, 1720, Block 2H, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
| | - Thaise G. Araújo
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
| | - Paula P. L. Canto
- Department of Clinical Oncology, Clinics Hospital, Federal University of Uberlandia, Av. Pará, 1720, Oncology Sector, Room 9, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
| | - Carlos E. Paiva
- Department of Clinical Oncology, Graduate Program in Oncology, Palliative Care and Quality of Life Research Group (GPQual), Barretos Cancer Hospital, R. Antenor Duarte Vilela, 1331, Doutor Paulo Prata, Barretos 14784-400, Sao Paulo, Brazil
| | - Luiz R. Goulart
- Molecular Biology and Nutrition Research Group, School of Medicine, Graduate Program in Health Science, Av. Amazonas sn, Block 2E, 2º Floor, Room 210, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
| | - Yara C. P. Maia
- Molecular Biology and Nutrition Research Group, School of Medicine, Graduate Program in Health Science, Av. Amazonas sn, Block 2E, 2º Floor, Room 210, Campus Umuarama, Uberlandia 38405-320, Minas Gerais, Brazil
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Federal University of Uberlandia, Av. Amazonas sn, Block 2E, 2º Floor, Room 248, Campus Umuarama, Uberlandia 38405-302, Minas Gerais, Brazil
- Correspondence: ; Tel.: +34-3225-8628
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23
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Liu C, Yu Y, Wang G, Liu J, Liu R, Liu L, Yang X, Li H, Gao C, Lu Y, Zhuang J. From tumor mutational burden to characteristic targets analysis: Identifying the predictive biomarkers and natural product interventions in cancer management. Front Nutr 2022; 9:989989. [PMID: 36204371 PMCID: PMC9530334 DOI: 10.3389/fnut.2022.989989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/19/2022] [Indexed: 12/24/2022] Open
Abstract
High-throughput next-generation sequencing (NGS) provides insights into genome-wide mutations and can be used to identify biomarkers for the prediction of immune and targeted responses. A deeper understanding of the molecular biological significance of genetic variation and effective interventions is required and ultimately needs to be associated with clinical benefits. We conducted a retrospective observational study of patients in two cancer cohorts who underwent NGS in a “real-world” setting. The association between differences in tumor mutational burden (TMB) and clinical presentation was evaluated. We aimed to identify several key mutation targets and describe their biological characteristics and potential clinical value. A pan-cancer dataset was downloaded as a verification set for further analysis and summary. Natural product screening for the targeted intervention of key markers was also achieved. The majority of tumor patients were younger adult males with advanced cancer. The gene identified with the highest mutation rate was TP53, followed by PIK3CA, EGFR, and LRP1B. The association of TMB (0–103.7 muts/Mb) with various clinical subgroups was determined. More frequent mutations, such as in LRP1B, as well as higher levels of ferritin and neuron-specific enolase, led to higher TMB levels. Further analysis of the key targets, LRP1B and APC, was performed, and mutations in LRP1B led to better immune benefits compared to APC. APC, one of the most frequently mutated genes in gastrointestinal tumors, was further investigated, and the potential interventions by cochinchinone B and rottlerin were clarified. In summary, based on the analysis of the characteristics of gene mutations in the “real world,” we obtained the potential association indicators of TMB, found the key signatures LRP1B and APC, and further described their biological significance and potential interventions.
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Affiliation(s)
- Cun Liu
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang, China
| | - Yang Yu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ge Wang
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Jingyang Liu
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiaoxu Yang
- School of Life Sciences and Technology, Weifang Medical University, Weifang, China
| | - Huayao Li
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang, China
| | - Chundi Gao
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi Lu
- Department of Clinical Nutrition, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Traditional Chinese Medicine Oncology, Zhejiang Cancer Hospital, Hangzhou, China
- *Correspondence: Yi Lu,
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
- Jing Zhuang,
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24
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Hai L, Li L, Liu Z, Tong Z, Sun Y. Whole-genome circulating tumor DNA methylation landscape reveals sensitive biomarkers of breast cancer. MedComm (Beijing) 2022; 3:e134. [PMID: 35756163 PMCID: PMC9205580 DOI: 10.1002/mco2.134] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 01/12/2023] Open
Abstract
The changes in circulating tumor DNA (ctDNA) methylation are believed to be early events in breast cancer initiation, which makes them suitable as promising biomarkers for early diagnosis. However, applying ctDNA in breast cancer early diagnosis remains highly challenging due to the contamination of background DNA from blood and low DNA methylation signals. Here, we report an improved way to extract ctDNA, reduce background contamination, and build a whole‐genome bisulfite sequencing (WGBS) library from different stages of breast cancer. We first compared the DNA methylation data of 74 breast cancer patients with those of seven normal controls to screen candidate methylation CpG site biomarkers for breast cancer diagnosis. The obtained 26 candidate ctDNA methylation biomarkers produced high accuracy in breast cancer patients (area under the curve [AUC] = 0.889; sensitivity: 100%; specificity: 75%). Furthermore, we revealed potential ctDNA methylated CpG sites for detecting early‐stage breast cancer (AUC = 0.783; sensitivity: 93.44%; specificity: 50%). In addition, different subtypes of breast cancer could be well distinguished by the ctDNA methylome, which was obtained through our improved ctDNA‐WGBS method. Overall, we identified high specificity and sensitivity breast cancer‐specific methylation CpG site biomarkers, and they will be expected to have the potential to be translated to clinical practice.
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Affiliation(s)
- Luo Hai
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China
| | - Lingyu Li
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China
| | - Zongzhi Liu
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China.,University of Chinese Academy of Sciences Beijing China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics Chinese Academy of Sciences Beijing China
| | - Zhongsheng Tong
- Department of Breast Oncology Tianjin Medical University Cancer Institute and Hospital Tianjin China
| | - Yingli Sun
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen China.,University of Chinese Academy of Sciences Beijing China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics Chinese Academy of Sciences Beijing China
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25
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Cardinali B, De Luca G, Tasso R, Coco S, Garuti A, Buzzatti G, Sciutto A, Arecco L, Villa F, Carli F, Reverberi D, Quarto R, Dono M, Del Mastro L. Targeting PIK3CA Actionable Mutations in the Circulome: A Proof of Concept in Metastatic Breast Cancer. Int J Mol Sci 2022; 23:ijms23116320. [PMID: 35682999 PMCID: PMC9181240 DOI: 10.3390/ijms23116320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
The study of circulating cancer-derived components (circulome) is considered the new frontier of liquid biopsy. Despite the recognized role of circulome biomarkers, their comparative molecular profiling is not yet routine. In advanced breast cancer (BC), approximately 40% of hormone-receptor-positive, HER2-negative BC cases harbor druggable PIK3CA mutations suitable for combined alpelisib/fulvestrant treatment. This pilot study investigates PIK3CA mutations in circulating tumor DNA (ctDNA), tumor cells (CTCs), and extracellular vesicles (EVs) with the aim of determining which information on molecular targetable profiling could be recollected in each of them. The in-depth molecular analysis of four BC patients demonstrated, as a proof-of-concept study, that it is possible to retrieve mutational information in the three components. Patient-specific PIK3CA mutations were found in both tissue and ctDNA and in 3/4 cases, as well as in CTCs, in the classical population (large-sized CD45−/EpCAM+/− cells), and/or in the “non-conventional” sub-population (smaller-sized CD44+/EpCAM−/CD45− cells). Consistent mutational profiles of EVs with CTCs suggest that they may have been released by CTCs. This preliminary evidence on the molecular content of the different circulating biomaterials suggests their possible function as a mirror of the intrinsic heterogeneity of BC. Moreover, this study demonstrates, through mutational assessment, the tumor origin of the different CTC sub-populations sustaining the translational value of the circulome for a more comprehensive picture of the disease.
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Affiliation(s)
- Barbara Cardinali
- Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy; (A.S.); (L.A.); (L.D.M.)
- Correspondence: (B.C.); (G.D.L.); Tel.: +39-0105558101 (B.C.); +39-0105558940 (G.D.L.)
| | - Giuseppa De Luca
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
- Correspondence: (B.C.); (G.D.L.); Tel.: +39-0105558101 (B.C.); +39-0105558940 (G.D.L.)
| | - Roberta Tasso
- Department of Experimental Medicine (DIMES), University of Genova, 5-16126 Genova, Italy; (R.T.); (R.Q.)
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Anna Garuti
- Clinica Oncologia Medica ad Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Giulia Buzzatti
- Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Andrea Sciutto
- Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy; (A.S.); (L.A.); (L.D.M.)
| | - Luca Arecco
- Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy; (A.S.); (L.A.); (L.D.M.)
| | - Federico Villa
- Molecular Oncology and Angiogenesis Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Franca Carli
- Surgical Pathology Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Daniele Reverberi
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Rodolfo Quarto
- Department of Experimental Medicine (DIMES), University of Genova, 5-16126 Genova, Italy; (R.T.); (R.Q.)
- Cellular Oncology Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy
| | - Mariella Dono
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy;
| | - Lucia Del Mastro
- Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, 10-16132 Genova, Italy; (A.S.); (L.A.); (L.D.M.)
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genova, 5-16126 Genova, Italy
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26
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Hu D, Guo E, Yang B, Qin X, Fu Y, Fan J, Zhuang X, Yao Q, Lu F, Li W, Xiao R, Wu X, Yang X, Wang Z, Liu C, You L, Zang R, Zhou Q, Zhao W, Chen G, Sun C. Mutation profiles in circulating cell‐free
DNA
predict acquired resistance to Olaparib in high‐grade serous ovarian carcinoma. Cancer Sci 2022; 113:2849-2861. [PMID: 35661486 PMCID: PMC9357630 DOI: 10.1111/cas.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/23/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xu Qin
- Department of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xucui Zhuang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qianqian Yao
- Department of Medical Science Shanghai AccuraGen Biotechnology Co., Ltd Shanghai China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wenting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xue Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xiaohang Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Lixin You
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rongyu Zang
- Department of Gynecologic Oncology, Zhongshan Hospital Fudan University Shanghai China
| | - Qi Zhou
- Department of Gynecology Oncology Chongqing University Cancer Hospital Chongqing China
| | - Weidong Zhao
- Department of Gynecologic Oncology Anhui Provincial Cancer Hospital Hefei China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
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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 .
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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.
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Hildebrandt MG, Naghavi-Behzad M, Vogsen M. A role of FDG-PET/CT for response evaluation in metastatic breast cancer? Semin Nucl Med 2022; 52:520-530. [PMID: 35525631 DOI: 10.1053/j.semnuclmed.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/27/2022] [Indexed: 01/19/2023]
Abstract
Breast cancer prognosis is steadily improving due to early detection of primary cancer in screening programs and revolutionizing treatment development. In the metastatic setting, therapy improvements render breast cancer a chronic disease. Although FDG-PET/CT has emerged as a highly accurate method for staging metastatic breast cancer, there has been no change in response evaluation methods for decades. FDG-PET/CT has proven high prognostic values in patients with metastatic breast cancer when using quantitative PET methods. It has also shown a higher predictive value than conventional CT when applying the respective response evaluation criteria, RECIST and PERCIST. Response categorization using FDG-PET/CT is more sensitive in detecting progressive and regressive disease, while conventional imaging such as CT and bone scintigraphy deem stable disease more often. These findings reflect the higher accuracy of FDG-PET/CT for response evaluation in this patient group. But does the higher accuracy of FDG-PET/CT translate into a patient benefit when implementing it for monitoring response to palliative treatment? We have evidence of survival benefit from a retrospective study indicating the superiority of using FDG-PET/CT compared with conventional imaging for response evaluation in metastatic breast cancer patients. The survival benefit seems to result from earlier detection of progression with FDG-PET/CT than conventional imaging, leading to an earlier change in treatment with potentially better efficacy of the subsequent treatment line. FDG-PET/CT can be used semiquantitatively as suggested in PERCIST. However, we still need to improve clinically applicable methods based on neural network modeling to better integrate the quantitative information in a smart and standardized way, enabling relevant comparability between scans, patients, and institutions. Such innovation is warranted to support imaging specialists in diagnostic response assessment. Prospective multicenter studies analyzing patients' survival, quality of life, societal and patient costs of replacing conventional imaging with FDG-PET/CT are needed before firm conclusions can be drawn on which type of scan to recommend in future clinical guidelines.
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Affiliation(s)
- Malene Grubbe Hildebrandt
- Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Center for Personalized Response Monitoring in Oncology, PREMIO, Odense University Hospital, Odense, Denmark; Center for Innovative Medical Technology, CIMT, Odense University Hospital, Odense, Denmark.
| | - Mohammad Naghavi-Behzad
- Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Center for Personalized Response Monitoring in Oncology, PREMIO, Odense University Hospital, Odense, Denmark
| | - Marianne Vogsen
- Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Center for Personalized Response Monitoring in Oncology, PREMIO, Odense University Hospital, Odense, Denmark; Department of Oncology, Odense University Hospital, Odense, Denmark
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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Elzehery R, Effat N, El Farahaty R, Elsayed Farag R, Abo-Hashem EM, Elhelaly R. Circulating Cell-Free DNA and DNA Integrity as Molecular Diagnostic Tools in Hepatocellular Carcinoma. Am J Clin Pathol 2022; 158:254-262. [PMID: 35403666 DOI: 10.1093/ajcp/aqac037] [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: 12/26/2021] [Accepted: 03/02/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES We assessed the ability to use circulating cell-free DNA (cfDNA) and the DNA integrity index (DNAII) to detect the transition from liver cirrhosis (LC) to hepatocellular carcinoma (HCC). METHODS Circulating cfDNA and DNAII were measured in 50 patients with advanced LC and 50 patients with HCC who were followed for 1 month after transarterial chemoembolization (TACE). Fifty healthy participants served as a control group. Real-time quantitative polymerase chain reaction (PCR) was used to measure circulating cfDNA concentration, and Alu-PCR was used to measure the concentration of Alu repeats, both short fragments (115 base pairs [bp]) and long fragments (247 bp). We compared liquid biopsy results with the relevant traditional markers. RESULTS The HCC group showed significantly higher circulating cfDNA concentrations and DNAII values compared with the LC and control groups. No significant differences were found in circulating cfDNA concentrations and DNAII values between the LC and control groups. Circulating cfDNA concentrations decreased significantly after treatment (TACE); areas under the curve of circulating cfDNA concentration and DNAII values were significantly better than those of ɑ-fetoprotein and vascular endothelial growth factor in discriminating between LC and HCC. CONCLUSIONS The combined use of DNAII with proteins induced by vitamin K absence or antagonist showed better diagnostic performance in HCC. Circulating cfDNA could have a potential role in monitoring HCC treatment.
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Affiliation(s)
| | - Narmin Effat
- Department of Clinical Pathology, Mansoura, Egypt
| | | | - Raghda Elsayed Farag
- Department of Tropical Medicine, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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31
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Kasi PM, Fehringer G, Taniguchi H, Starling N, Nakamura Y, Kotani D, Powles T, Li BT, Pusztai L, Aushev VN, Kalashnikova E, Sharma S, Malhotra M, Demko ZP, Aleshin A, Rodriguez A, Billings PR, Grothey A, Taieb J, Cunningham D, Yoshino T, Kopetz S. Impact of Circulating Tumor DNA-Based Detection of Molecular Residual Disease on the Conduct and Design of Clinical Trials for Solid Tumors. JCO Precis Oncol 2022; 6:e2100181. [PMID: 35263168 PMCID: PMC8926064 DOI: 10.1200/po.21.00181] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Earlier detection of cancer recurrence using circulating tumor DNA (ctDNA) to detect molecular residual disease (MRD) has the potential to dramatically affect cancer management. We review evidence supporting the use of ctDNA as a biomarker for detection of MRD and highlight the potential impact that ctDNA testing could have on the conduct of clinical trials.
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Affiliation(s)
- Pashtoon M Kasi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA
| | | | - Hiroya Taniguchi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Naureen Starling
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Daisuke Kotani
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Thomas Powles
- Barts Cancer Institute, Queen Mary University of London ECMC, Barts Health, London, United Kingdom
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT
| | | | | | | | | | | | | | | | | | - Axel Grothey
- West Cancer Center and Research Institute, Germantown, TN
| | - Julien Taieb
- Georges Pompidou European Hospital, SIRIC-CARPEM, Université de Paris, Paris, France
| | - David Cunningham
- The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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32
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The potential of liquid biopsy in the management of cancer patients. Semin Cancer Biol 2022; 84:69-79. [DOI: 10.1016/j.semcancer.2022.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
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Chedid J, Allam S, Chamseddine N, Bou Zerdan M, El Nakib C, Assi HI. Role of circulating tumor DNA and circulating tumor cells in breast cancer: History and updates. SAGE Open Med 2022; 10:20503121221077838. [PMID: 35223029 PMCID: PMC8874178 DOI: 10.1177/20503121221077838] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/17/2022] [Indexed: 11/15/2022] Open
Abstract
Circulating tumor DNA, cell-free DNA, and circulating tumor cells have been at the epitome of recent research in breast cancer. These forms of liquid biopsies have been used in monitoring disease progression, estimating the risk of relapse, and response to treatment. Much has been done in relation to serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. Some studies have also explored their use in monitoring treatment response. As the field of liquid biopsies expands, more prospective studies are needed to tailor management in an individualistic approach. In this literature review, the authors explore the multiple uses of circulating tumor DNA and circulating tumor cells in breast cancer.
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Affiliation(s)
- Julien Chedid
- Department of Obstetrics and Gynecology, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Sabine Allam
- Faculty of Medicine, University of Balamand, Beirut, Lebanon
| | - Nathalie Chamseddine
- Department of Obstetrics and Gynecology, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Maroun Bou Zerdan
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Clara El Nakib
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hazem I Assi
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
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Jagannathan G, White MJ, Xian RR, Emens LA, Cimino-Mathews A. A New Landscape of Testing and Therapeutics in Metastatic Breast Cancer. Surg Pathol Clin 2022; 15:105-120. [PMID: 35236627 DOI: 10.1016/j.path.2021.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Predictive biomarker testing on metastatic breast cancer is essential for determining patient eligibility for targeted therapeutics. The National Comprehensive Cancer Network currently recommends assessment of specific biomarkers on metastatic tumor subtypes, including hormone receptors, HER2, and BRCA1/2 mutations, on all newly metastatic breast cancers subtypes; programmed death-ligand 1 on metastatic triple-negative carcinomas; and PIK3CA mutation status on estrogen receptor-positive carcinomas. In select circumstances mismatch repair protein deficiency and/or microsatellite insufficiency, tumor mutation burden, and NTRK translocation status are also testing options. Novel biomarker testing, such as detecting PIK3CA mutations in circulating tumor DNA, is expanding in this rapidly evolving arena.
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Affiliation(s)
- Geetha Jagannathan
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA
| | - Marissa J White
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA
| | - Rena R Xian
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA; Department of Oncology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA
| | - Leisha A Emens
- Department of Oncology, UPMC Hillman Cancer Center/Magee Women's Hospital, 5117 Centre Avenue, Room 1.46e, Pittsburgh, PA 15213, USA
| | - Ashley Cimino-Mathews
- Department of Pathology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA; Department of Oncology, The Johns Hopkins University School of Medicine, 401 N Broadway, Weinberg 2242, Baltimore, MD 21287, USA.
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35
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Immunotherapy for early triple negative breast cancer: research agenda for the next decade. NPJ Breast Cancer 2022; 8:23. [PMID: 35181659 PMCID: PMC8857212 DOI: 10.1038/s41523-022-00386-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/11/2022] [Indexed: 12/31/2022] Open
Abstract
For decades, the systemic treatment of localized triple negative breast cancer (TNBC) has exclusively relied on chemotherapy. Recent advancements, however, are rapidly reshaping the treatment algorithms for this disease. The addition of pembrolizumab to neoadjuvant chemotherapy has indeed shown to significantly improve event-free survival for stage II–III TNBC, leading to its establishment as new standard of care in this setting. This landmark advancement has however raised several important scientific questions. Indeed, we desperately need strategies to identify upfront patients deriving benefit from the addition of immunotherapy. Moreover, the best integration of pembrolizumab with further recent advancements (capecitabine, olaparib) is yet to be defined. Lastly, extensive efforts are needed to minimize the impact on patients of immune-related adverse events and financial toxicity. The next decade of clinical research will be key to overcome these challenges, and ultimately learn how to optimally integrate immunotherapy in the treatment landscape of TNBC.
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Papakonstantinou A, Saoudi Gonzalez N, Pimentel I, Suñol A, Zamora E, Ortiz C, Espinosa-Bravo M, Peg V, Vivancos A, Saura C, Villacampa G, Oliveira M. Prognostic value of ctDNA detection in patients with early breast cancer undergoing neoadjuvant therapy: a systematic review and meta-analysis. Cancer Treat Rev 2022; 104:102362. [DOI: 10.1016/j.ctrv.2022.102362] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
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Contemporary Outcomes After Multimodality Therapy in Patients With Breast Cancer Presenting With Ipsilateral Supraclavicular Node Involvement. Int J Radiat Oncol Biol Phys 2022; 112:66-74. [PMID: 34710521 PMCID: PMC8688264 DOI: 10.1016/j.ijrobp.2021.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/03/2021] [Accepted: 08/12/2021] [Indexed: 01/03/2023]
Abstract
PURPOSE Patients with breast cancer and ipsilateral supraclavicular (SCV) node involvement at the time of diagnosis (TNM cN3c) have historically had poor outcomes. Radiation therapy (RT) has an important role because SCV nodes are not routinely surgically dissected. However, optimal locoregional management, contemporary outcomes, and prognostic factors are not well defined. METHODS AND MATERIALS We reviewed the data of patients with cN3c breast cancer treated at our institution between 2014 and 2019 with curative intent, including neoadjuvant chemotherapy, surgery, and adjuvant RT. All patients received comprehensive regional RT, including to the SCV nodes. Institutional guidelines recommend a 10-Gy or 16-Gy boost to resolved and unresolved N3 nodes, respectively. Overall survival (OS), recurrence-free survival (RFS), locoregional recurrence-free survival (LRRFS), and supraclavicular recurrence-free survival (SCRFS) were analyzed. RESULTS Data from 173 consecutive patients were analyzed with a median follow-up time of 2.8 years. The median age was 54 years, 76 patients (44%) were estrogen receptor positive/human epidermal growth factor receptor 2 negative, 100 patients (58%) had T3/4 disease, and 10 patients (6%) underwent a neck dissection. In addition, 156 patients (90%) received a cumulative SCV dose of ≥60 Gy. The 5-year OS, SCRFS, LRRFS, and RFS rates were 73%, 95%, 86%, and 50%, respectively. The 5-year OS rate for a cumulative SCV dose of ≥60 Gy versus <60 Gy was 75% versus 39% (P = .04). In the multivariable analysis, a cumulative SCV dose of ≥60 Gy, extranodal extension, receptor status, and Eastern Cooperative Oncology Group performance status were associated with OS. The 5-year SCRFS rates with and without neck dissection were 100% versus 95% (P = .57). Among patients with a postchemotherapy SCV node size of ≥1 cm without neck dissection, the 5-year SCRFS rate was 83%. CONCLUSIONS In one of the largest series of patients with cN3c breast cancer, multimodality therapy using adjuvant RT with a SCV boost resulted in a 5-year LRRFS rate of 86%. There is a limited role for neck dissection as the 5-year SCRFS rate was 95% overall and 83% for residual SCV disease ≥1 cm after chemotherapy with RT alone. A cumulative SCV dose of ≥60 Gy was associated with improved OS, but not SCRFS, LRRFS, or RFS. A SCV boost should be considered in these patients as treatment was well-tolerated. Despite advances in systemic therapy, nearly half of patients developed distant metastases, highlighting the need for close observation after treatment.
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Allouchery V, Perdrix A, Calbrix C, Berghian A, Lequesne J, Fontanilles M, Leheurteur M, Etancelin P, Sarafan-Vasseur N, Di Fiore F, Clatot F. Circulating PIK3CA mutation detection at diagnosis in non-metastatic inflammatory breast cancer patients. Sci Rep 2021; 11:24041. [PMID: 34911971 PMCID: PMC8674263 DOI: 10.1038/s41598-021-02643-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/11/2021] [Indexed: 01/04/2023] Open
Abstract
Inflammatory breast cancer (IBC) is an aggressive BC subtype with poor outcomes. A targetable somatic PIK3CA mutation is reported in 30% of IBC, allowing for treatment by PI3Kα-specific inhibitors, such as alpelisib. The aim of this study was to evaluate the detection rate of circulating PIK3CA mutation in locally-advanced IBC (LAIBC) patients harbouring a PIK3CA mutation on initial biopsy. This monocentric retrospective study was based on available stored plasma samples and tumour biopsies at diagnosis from all LAIBC patients treated with neo-adjuvant chemotherapy (NCT) between 2008 and 2018 at the Centre Henri Becquerel. PIK3CA mutations (E542K, E545K, H1047R/L) were assessed by droplet digital PCR (ddPCR) in plasma samples and tumoral tissue at diagnosis. A total of 55 patients were included. Overall, 14/55 patients (25%) had a PIK3CA mutation identified on baseline biopsy (H1047R = 8; H1047L = 3; E545K = 2; E542K = 1). Among them, 11 (79%) patients had enough DNA for circulating DNA analyses, and corresponding circulating PIK3CA mutations were found in 6/11 (55%). Among the 41 patients without PIK3CA mutations on biopsy, 32 (78%) had enough DNA for circulating DNA analysis, and no circulating PIK3CA mutation was identified. Our results revealed no prognostic or predictive value of PIK3CA mutations at the diagnosis of non-metastatic IBC but highlighted the prognostic value of the cfDNA rate at diagnosis. Our study showed that a corresponding circulating PIK3CA mutation was identified in 55% of LAIBC patients with PIK3CA-mutated tumours, while no circulating mutation was found among patients with PI3KCA wild-type tumours.
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Affiliation(s)
- Violette Allouchery
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.
| | - Anne Perdrix
- IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Céline Calbrix
- IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Anca Berghian
- Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Justine Lequesne
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - Maxime Fontanilles
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.,IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France
| | - Marianne Leheurteur
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France
| | | | - Nasrin Sarafan-Vasseur
- IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.,IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France
| | - Florian Clatot
- Department of Medical Oncology, Centre Henri Becquerel, 1 Rue d'Amiens, 76038, Rouen Cedex 1, France.,IRON Group, Inserm U1245, UNIROUEN, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Normandie Université, Rouen, France
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Chivu-Economescu M, Necula L, Matei L, Dragu D, Bleotu C, Diaconu CC. Clinical Applications of Liquid Biopsy in Gastric Cancer. Front Med (Lausanne) 2021; 8:749250. [PMID: 34651002 PMCID: PMC8505538 DOI: 10.3389/fmed.2021.749250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy represents an exciting new area in the field of cancer diagnosis and management, offering a less invasive and more convenient approach to obtain a time-point image of the tumor burden and its genomic profile. Samples collected from several body fluids, mostly blood, can be used to gain access to circulating tumor cells and DNA, non-coding RNAs, microRNAs, and exosomes, at any moment, offering a dynamic picture of the tumor. For patients with GC, the use of blood-based biopsies may be particularly beneficial since tissue biopsies are difficult to obtain and cause real distress to the patient. With advantages such as repeatability and minimal invasion, it is no wonder that the field of liquid biopsy has received tremendous attention. However, the abundance of studies, involving a wide range of assays with different principles, prevented for the moment the reproducibility of the results and therefore the translation into the clinic of liquid biopsy. In this review, we present the latest technical development and data on circulating biomarkers available through liquid biopsy in gastric cancer with an emphasis on their clinical utility in areas such as cancer screening, prognostic stratification, and therapeutic management.
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Affiliation(s)
- Mihaela Chivu-Economescu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Laura Necula
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania.,Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Lilia Matei
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Denisa Dragu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Coralia Bleotu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Carmen C Diaconu
- Department of Cellular and Molecular Pathology, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
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Aboelwafa RA, Zakaria NH, Hagazy N, Zaki II, Rady AS, Sharaki OA. Clinical significance of estrogen receptor 1 gene mutations in hormonal resistant breast cancer patients. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Sun L, Wu A, Bean GR, Hagemann IS, Lin CY. Molecular Testing in Breast Cancer: Current Status and Future Directions. J Mol Diagn 2021; 23:1422-1432. [PMID: 34454106 DOI: 10.1016/j.jmoldx.2021.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/01/2021] [Accepted: 07/22/2021] [Indexed: 11/28/2022] Open
Abstract
Molecular testing in breast cancer is a rapidly developing field that is becoming increasingly integral to patient care. This article provides an overview of currently available molecular assays and testing modalities that have prognostic, predictive, and therapeutic value. These include multigene assays for invasive breast cancer (Oncotype DX, MammaPrint, Prosigna, and Breast Cancer Index) and ductal carcinoma in situ (Oncotype DX DCIS and DCISionRT) and companion tests to detect PIK3CA mutations and NTRK fusions. The various assays related to immune checkpoint inhibitors, consisting of immunohistochemistry with anti-programmed death-ligand 1 antibodies SP142 and 22C3 and detection of microsatellite instability, mismatch repair deficiency, and tumor mutational burden are also discussed. Finally, the practical utility and hopeful promise of next-generation sequencing panels and circulating tumor (cell-free) DNA assays are evaluated. This review should serve as a useful and practical reference for practicing pathologists, molecular pathologists, clinicians, and researchers.
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Affiliation(s)
- Lulu Sun
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Ariel Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Gregory R Bean
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Ian S Hagemann
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Chieh-Yu Lin
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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Valencia GA, Rioja P, Morante Z, Araujo JM, Vallejos HD, Guerra H, Gomez HL. PIK3CA mutation in non-metastatic triple-negative breast cancer as a potential biomarker of early relapse: A case report. World J Clin Oncol 2021; 12:702-711. [PMID: 34513603 PMCID: PMC8394163 DOI: 10.5306/wjco.v12.i8.702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Currently, the detection of PIK3CA mutations is of special interest in personalized medicine because it is frequently found in triple-negative breast cancer (TNBC). The PI3KCA mutation is an independent negative prognostic factor for survival in metastatic breast cancer, and its prognostic value in liquid biopsy as a biomarker of treatment and early relapse is under investigation, both for metastatic disease and neoadjuvant scenario with curative intent.
CASE SUMMARY A 54-year-old female patient with TNBC clinical stage IIIA, who, after receiving neoadjuvant chemotherapy (based on anthracyclines and taxanes), surgery, radiotherapy, and adjuvant capecitabine, was detected with a PI3KCA mutation in tissue and peripheral blood (ctDNA in liquid biopsy). After 10 mo, the patient had disease relapse of left cervical node disease.
CONCLUSION The detection of PIK3CA mutation in TNBC after neoadjuvant treatment might be associated with early relapse or rapid disease progression.
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Affiliation(s)
| | - Patricia Rioja
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima 15000, Peru
| | - Zaida Morante
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima 15000, Peru
| | - Jhajaira M Araujo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima 15067, Peru
| | - Heberth Daniel Vallejos
- Department of Medical Oncology, Russian Scientific Center of Radiology and Radiotherapy, Konkovo 117485, Moscow, Russia
| | - Henry Guerra
- Department of Pathology, Instituto Nacional de Enfermedades Neoplásicas, Lima 15000, Peru
| | - Henry L Gomez
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima 15000, Peru
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Zhang X, Zhao D, Yin Y, Yang T, You Z, Li D, Chen Y, Jiang Y, Xu S, Geng J, Zhao Y, Wang J, Li H, Tao J, Lei S, Jiang Z, Chen Z, Yu S, Fan JB, Pang D. Circulating cell-free DNA-based methylation patterns for breast cancer diagnosis. NPJ Breast Cancer 2021; 7:106. [PMID: 34400642 PMCID: PMC8367945 DOI: 10.1038/s41523-021-00316-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023] Open
Abstract
Mammography is used to detect breast cancer (BC), but its sensitivity is limited, especially for dense breasts. Circulating cell-free DNA (cfDNA) methylation tests is expected to compensate for the deficiency of mammography. We derived a specific panel of markers based on computational analysis of the DNA methylation profiles from The Cancer Genome Atlas (TCGA). Through training (n = 160) and validation set (n = 69), we developed a diagnostic prediction model with 26 markers, which yielded a sensitivity of 89.37% and a specificity of 100% for differentiating malignant disease from normal lesions [AUROC = 0.9816 (95% CI: 96.09-100%), and AUPRC = 0.9704 (95% CI: 94.54–99.46%)]. A simplified 4-marker model including cg23035715, cg16304215, cg20072171, and cg21501525 had a similar diagnostic power [AUROC = 0.9796 (95% CI: 95.56–100%), and AUPRC = 0.9220 (95% CI: 91.02–94.37%)]. We found that a single cfDNA methylation marker, cg23035715, has a high diagnostic power [AUROC = 0.9395 (95% CI: 89.72–99.27%), and AUPRC = 0.9111 (95% CI: 88.45–93.76%)], with a sensitivity of 84.90% and a specificity of 93.88%. In an independent testing dataset (n = 104), the obtained diagnostic prediction model discriminated BC patients from normal controls with high accuracy [AUROC = 0.9449 (95% CI: 90.07–98.91%), and AUPRC = 0.8640 (95% CI: 82.82–89.98%)]. We compared the diagnostic power of cfDNA methylation and mammography. Our model yielded a sensitivity of 94.79% (95% CI: 78.72–97.87%) and a specificity of 98.70% (95% CI: 86.36–100%) for differentiating malignant disease from normal lesions [AUROC = 0.9815 (95% CI: 96.75–99.55%), and AUPRC = 0.9800 (95% CI: 96.6–99.4%)], with better diagnostic power and had better diagnostic power than that of using mammography [AUROC = 0.9315 (95% CI: 89.95–96.34%), and AUPRC = 0.9490 (95% CI: 91.7–98.1%)]. In addition, hypermethylation profiling provided insights into lymph node metastasis stratifications (p < 0.05). In conclusion, we developed and tested a cfDNA methylation model for BC diagnosis with better performance than mammography.
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Affiliation(s)
- Xianyu Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dezhi Zhao
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Yanling Yin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ting Yang
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Zilong You
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dalin Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanbo Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yongdong Jiang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Hui Li
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Jinsheng Tao
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Shan Lei
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Zeyu Jiang
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Zhiwei Chen
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China.,AnchorDx, Inc., Fremont, California, USA
| | - Shihui Yu
- Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Jian-Bing Fan
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China. .,Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China.
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
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Nteliopoulos G, Page K, Hills A, Howarth K, Emmett W, Green E, Martinson LJ, Fernadez-Garcia D, Hastings R, Guttery DS, Kenny L, Stebbing J, Cleator S, Rehman F, Gleason KLT, Sanela A, Ion C, Rushton AJ, Rosenfeld N, Coombes RC, Shaw JA. Comparison of two targeted ultra-deep sequencing technologies for analysis of plasma circulating tumour DNA in endocrine-therapy-resistant breast cancer patients. Breast Cancer Res Treat 2021; 188:465-476. [PMID: 34097174 PMCID: PMC8260509 DOI: 10.1007/s10549-021-06220-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/30/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE There is growing interest in the application of circulating tumour DNA (ctDNA) as a sensitive tool for monitoring tumour evolution and guiding targeted therapy in patients with cancer. However, robust comparisons of different platform technologies are still required. Here we compared the InVisionSeq™ ctDNA Assay with the Oncomine™ Breast cfDNA Assay to assess their concordance and feasibility for the detection of mutations in plasma at low (< 0.5%) variant allele fraction (VAF). METHODS Ninety-six plasma samples from 50 patients with estrogen receptor (ER)-positive metastatic breast cancer (mBC) were profiled using the InVision Assay. Results were compared to the Oncomine assay in 30 samples from 26 patients, where there was sufficient material and variants were covered by both assays. Longitudinal samples were analysed for 8 patients with endocrine resistance. RESULTS We detected alterations in 59/96 samples from 34/50 patients analysed with the InVision assay, most frequently affecting ESR1, PIK3CA and TP53. Complete or partial concordance was found in 28/30 samples analysed by both assays, and VAF values were highly correlated. Excellent concordance was found for most genes, and most discordant calls occurred at VAF < 1%. In longitudinal samples from progressing patients with endocrine resistance, we detected consistent alterations in sequential samples, most commonly in ESR1 and PIK3CA. CONCLUSION This study shows that both ultra-deep next-generation sequencing (NGS) technologies can detect genomic alternations even at low VAFs in plasma samples of mBC patients. The strong agreement of the technologies indicates sufficient reproducibility for clinical use as prognosic and predictive biomarker.
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Affiliation(s)
- Georgios Nteliopoulos
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | - Karen Page
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Allison Hills
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | | | | | | | - Luke J Martinson
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Daniel Fernadez-Garcia
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Robert Hastings
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - David S Guttery
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Laura Kenny
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Justin Stebbing
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Susan Cleator
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Farah Rehman
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Kelly L T Gleason
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Andrijac Sanela
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Charlotte Ion
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Amelia J Rushton
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | | | - R Charles Coombes
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, London, UK
| | - Jacqueline A Shaw
- Department of Genetics and Genome Biology and Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Targeted Next-Generation Sequencing of Circulating Tumor DNA Mutations among Metastatic Breast Cancer Patients. ACTA ACUST UNITED AC 2021; 28:2326-2336. [PMID: 34202466 PMCID: PMC8293138 DOI: 10.3390/curroncol28040214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/13/2021] [Accepted: 06/18/2021] [Indexed: 01/02/2023]
Abstract
Liquid biopsy through the detection of circulating tumor DNA (ctDNA) has potential advantages in cancer monitoring and prediction. However, most previous studies in this area were performed with a few hotspot genes, single time point detection, or insufficient sequencing depth. In this study, we performed targeted next-generation sequencing (NGS) with a customized panel in metastatic breast cancer (MBC) patients. Fifty-four plasma samples were taken before chemotherapy and after the third course of treatment for detection and analysis. Paired lymphocytes were also included to eliminate clonal hematopoiesis (CH)-related alternatives. A total of 1182 nonsynonymous mutations in 419 genes were identified. More ctDNA mutations were detected in patients with tumors > 3 cm (p = 0.035) and HER2(−) patients (p = 0.029). For a single gene, the distribution of ctDNA mutations was also correlated with clinical characteristics. Multivariate regression analysis revealed that HER2 status was significantly associated with mutation burden (OR 0.02, 95% CI 0–0.62, p = 0.025). The profiles of ctDNA mutations exhibited marked discrepancies between two time points, and baseline ctDNA was more sensitive and specific than that after chemotherapy. Finally, elevated ctDNA mutation level was positively correlated with poor survival (p < 0.001). Mutations in ctDNA could serve as a potential biomarker for the evaluation, prediction, and clinical management guidance of MBC patients with chemotherapy.
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46
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Gerratana L, Davis AA, Zhang Q, Basile D, Rossi G, Strickland K, Franzoni A, Allegri L, Mu Z, Zhang Y, Flaum LE, Damante G, Gradishar WJ, Platanias LC, Behdad A, Yang H, Puglisi F, Cristofanilli M. Longitudinal Dynamics of Circulating Tumor Cells and Circulating Tumor DNA for Treatment Monitoring in Metastatic Breast Cancer. JCO Precis Oncol 2021; 5:943-952. [PMID: 34136741 PMCID: PMC8202557 DOI: 10.1200/po.20.00345] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/10/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy-based biomarkers, including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), are increasingly important for the characterization of metastatic breast cancer (MBC). The aim of the study was to explore CTCs and ctDNA dynamics to better understand their potentially complementary role in describing MBC. METHODS The study retrospectively analyzed 107 patients with MBC characterized with paired CTCs and ctDNA assessments and a second prospective cohort, which enrolled 48 patients with MBC. CTCs were immunomagnetically isolated and ctDNA was quantified and then characterized through next-generation sequencing in the retrospective cohort and droplet digital polymerase chain reaction in the prospective cohort. Matched pairs variations at baseline, at evaluation one (EV1), and at progression were tested through the Wilcoxon test. The prognostic role of ctDNA parameters was also investigated. RESULTS Mutant allele frequency (MAF) had a significant decrease between baseline and EV1 and a significant increase between EV1 and progression. Number of detected alterations steadily increased across timepoints, CTCs enumeration (nCTCs) significantly increased only between EV1 and progression. MAF dynamics across the main altered genes was then investigated. Plasma DNA yield did not vary across timepoints both in the retrospective cohort and in the prospective cohort, while the short fragments fraction showed a potential role as a prognostic biomarker. CONCLUSION nCTCs and ctDNA provide complementary information about prognosis and treatment benefit. Although nCTCs appeared to assess tumor biology rather than tumor burden, MAF may be a promising biomarker for the dynamic assessment of treatment response and resistance.
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Affiliation(s)
- Lorenzo Gerratana
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL.,Department of Medicine, University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, Italy
| | - Andrew A Davis
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL.,Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Qiang Zhang
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Debora Basile
- Department of Medicine, University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, Italy
| | - Giovanna Rossi
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, PA.,Breast International Group (BIG), Brussels, Belgium
| | - Kimberly Strickland
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, PA.,Novant Health Cancer Institute, Charlotte, NC
| | | | | | - Zhaomei Mu
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Youbin Zhang
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Lisa E Flaum
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Giuseppe Damante
- Department of Medicine, University of Udine, Udine, Italy.,Institute of Human Genetics, ASUFC University Hospital, Udine, Italy
| | - William John Gradishar
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Leonidas C Platanias
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Amir Behdad
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Department of Pathology, Northwestern University, Chicago, IL
| | - Hushan Yang
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Fabio Puglisi
- Department of Medicine, University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, Italy
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
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Han BW, Cai GX, Liu Q, Yang X, Guo ZW, Huang LM, Li K, Ouyang GJ, Yang XX, Ye GL, Wu YS. Noninvasive discrimination of benign and malignant breast lesions using genome-wide nucleosome profiles of plasma cell-free DNA. Clin Chim Acta 2021; 520:95-100. [PMID: 34107314 DOI: 10.1016/j.cca.2021.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Breast malignancy is the most frequently diagnosed malignancy in women worldwide, and the diagnosis relies on invasive examinations. However, most clinical breast changes in women are benign, and invasive diagnostic approaches cause unnecessary suffering for the patients. Thus, a novel noninvasive approach for discriminating malignant breast lesions from benign lesions is needed. METHODS We performed cell-free DNA (cfDNA) sequencing on plasma samples from 173 malignant breast lesion patients, 158 benign breast lesion patients, and 102 healthy women. We then analyzed the cfDNA-based nucleosome profiles, which reflect the various tissues of origin and transcription factor activities. Moreover, by using machine learning classifiers along with the cfDNA sequencing data, we built classifiers for discriminating benign from malignant breast lesions. Receiver operating characteristic curve analyses were used to evaluate the performance of the classifiers. RESULTS cfDNA-based nucleosome profiles reflected the various tissues of origin and transcription factor activities in benign and malignant breast lesions. The cfDNA-based transcription factor activities and breast malignancy-specific transcription factor-binding site accessibility profiles could accurately distinguish benign and malignant breast lesions, with area under the curve values of 0.777 and 0.824, respectively. CONCLUSIONS Our proof-of-principle study established a methodology for noninvasively discriminating benign from malignant breast lesions.
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Affiliation(s)
- Bo-Wei Han
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Geng-Xi Cai
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China; Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qing Liu
- Department of Pathology, The First People's Hospital of Foshan, Foshan 528000, China
| | - Xu Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Zhi-Wei Guo
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Li-Min Huang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China; Guangzhou XGene Co., Ltd., Guangzhou 510500, China
| | - Guo-Jun Ouyang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou 510663, China
| | - Xue-Xi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Guo-Lin Ye
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China.
| | - Ying-Song Wu
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
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Cattin S, Fellay B, Calderoni A, Christinat A, Negretti L, Biggiogero M, Badellino A, Schneider AL, Tsoutsou P, Pellanda AF, Rüegg C. Circulating immune cell populations related to primary breast cancer, surgical removal, and radiotherapy revealed by flow cytometry analysis. Breast Cancer Res 2021; 23:64. [PMID: 34090509 PMCID: PMC8180078 DOI: 10.1186/s13058-021-01441-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Advanced breast cancer (BC) impact immune cells in the blood but whether such effects may reflect the presence of early BC and its therapeutic management remains elusive. METHODS To address this question, we used multiparametric flow cytometry to analyze circulating leukocytes in patients with early BC (n = 13) at the time of diagnosis, after surgery, and after adjuvant radiotherapy, compared to healthy individuals. Data were analyzed using a minimally supervised approach based on FlowSOM algorithm and validated manually. RESULTS At the time of diagnosis, BC patients have an increased frequency of CD117+CD11b+ granulocytes, which was significantly reduced after tumor removal. Adjuvant radiotherapy increased the frequency of CD45RO+ memory CD4+ T cells and CD4+ regulatory T cells. FlowSOM algorithm analysis revealed several unanticipated populations, including cells negative for all markers tested, CD11b+CD15low, CD3+CD4-CD8-, CD3+CD4+CD8+, and CD3+CD8+CD127+CD45RO+ cells, associated with BC or radiotherapy. CONCLUSIONS This study revealed changes in blood leukocytes associated with primary BC, surgical removal, and adjuvant radiotherapy. Specifically, it identified increased levels of CD117+ granulocytes, memory, and regulatory CD4+ T cells as potential biomarkers of BC and radiotherapy, respectively. Importantly, the study demonstrates the value of unsupervised analysis of complex flow cytometry data to unravel new cell populations of potential clinical relevance.
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Affiliation(s)
- Sarah Cattin
- Pathology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Benoît Fellay
- Central Laboratory, Hôpital Fribourgeois, CH-1700, Fribourg, Switzerland
| | | | | | - Laura Negretti
- Radiation Oncology Department, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland
| | - Maira Biggiogero
- Radiation Oncology Department, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland.,Clinical Research unit, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland
| | - Alberto Badellino
- Radiation Oncology Department, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland.,Clinical Research unit, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland
| | - Anne-Lise Schneider
- Breast and Oncology Center, Hôpital Neuchatelois, CH-2300, La Chaux-de-Fonds, Switzerland
| | - Pelagia Tsoutsou
- Breast and Oncology Center, Hôpital Neuchatelois, CH-2300, La Chaux-de-Fonds, Switzerland.,Present Address: Service de Radio-Oncologie, Hôpitaux Universitaires de Genève, CH-1205, Geneva, Switzerland
| | - Alessandra Franzetti Pellanda
- Radiation Oncology Department, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland.,Clinical Research unit, Clinica Luganese Moncucco, CH-6900, Lugano, Switzerland
| | - Curzio Rüegg
- Pathology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, CH-1700, Fribourg, Switzerland.
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Perspectives on the Systemic Staging in Newly Diagnosed Breast Cancer. Clin Breast Cancer 2021; 21:309-316. [PMID: 33962905 DOI: 10.1016/j.clbc.2021.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/06/2021] [Accepted: 03/23/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer is a complex disease, and accurate systemic staging is an essential aspect of the evaluation of a patient with newly diagnosed breast cancer. Considering that the chance of having metastatic disease at breast cancer diagnosis is different in each patient and depends on a variety of anatomic and biologic factors, it is crucial to understand that some populations may benefit from more intensive staging because their pretest probability of metastatic disease is higher than that of the average patient. Identifying these patients with de novo stage IV breast cancer is associated with substantial prognostic and therapeutic implications. Unfortunately, recent advances in understanding breast cancer heterogeneity and molecular biology have not been incorporated in the international guidelines and recommendations about imaging examinations for detecting de novo metastatic breast cancer. This review article discusses important issues regarding the rationale for performing systemic staging, addresses current and innovative imaging methods, and proposes an algorithm for systemic staging in patients with newly diagnosed breast cancer.
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Pizzutilo EG, Pedrani M, Amatu A, Ruggieri L, Lauricella C, Veronese SM, Signorelli D, Cerea G, Giannetta L, Siena S, Sartore-Bianchi A. Liquid Biopsy for Small Cell Lung Cancer either De Novo or Transformed: Systematic Review of Different Applications and Meta-Analysis. Cancers (Basel) 2021; 13:2265. [PMID: 34066817 PMCID: PMC8125928 DOI: 10.3390/cancers13092265] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The potential added value of liquid biopsy (LB) is not well determined in the case of small cell lung cancer (SCLC), an aggressive tumor that can occur either de novo or from the histologic transformation of non-small cell lung cancer (NSCLC). METHODS A systematic review of studies adopting LB in patients with SCLC have been performed to assess the clinical utility of circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs). RESULTS After a screening of 728 records, 62 studies (32 evaluating CTCs, 27 ctDNA, and 3 both) met predetermined eligibility criteria. Only four studies evaluated LB in the diagnostic setting for SCLC, while its prognostic significance was evaluated in 38 studies and prominently supported by both ctDNA and CTCs. A meta-analysis of 11 studies as for CTCs enumeration showed an HR for overall survival of 2.63 (1.71-4.05), with a potential publication bias. The feasibility of tumor genomic profiling and the predictive role of LB in terms of response/resistance to chemotherapy was assessed in 11 and 24 studies, respectively, with greater consistency for those regarding ctDNA. Intriguingly, several case reports suggest that LB can indirectly capture the transition to SCLC in NSCLC treated with EGFR tyrosine kinase inhibitors. CONCLUSIONS While dedicated trials are needed, LB holds potential clinical roles in both de novo and transformed SCLC. CtDNA analysis appears the most valuable and practicable tool for both disease monitoring and genomic profiling.
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Affiliation(s)
- Elio Gregory Pizzutilo
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Martino Pedrani
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Lorenzo Ruggieri
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Calogero Lauricella
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Silvio Marco Veronese
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Diego Signorelli
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Giulio Cerea
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Laura Giannetta
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
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