1
|
Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [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: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
Collapse
Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| |
Collapse
|
2
|
Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
Collapse
Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| |
Collapse
|
3
|
Damodaran S, O'Sullivan CC, Elkhanany A, Anderson IC, Barve M, Blau S, Cherian MA, Peguero JA, Goetz MP, Plourde PV, Portman DJ, Moore HCF. Open-label, phase II, multicenter study of lasofoxifene plus abemaciclib for treating women with metastatic ER+/HER2- breast cancer and an ESR1 mutation after disease progression on prior therapies: ELAINE 2. Ann Oncol 2023; 34:1131-1140. [PMID: 38072513 DOI: 10.1016/j.annonc.2023.09.3103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Acquired ESR1 mutations in estrogen receptor-positive (ER+) metastatic breast cancer (mBC) drive treatment resistance and tumor progression; new treatment strategies are needed. Lasofoxifene, a next-generation, oral, endocrine therapy and tissue-specific ER antagonist, provided preclinical antitumor activity, alone or combined with a cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) in ESR1-mutated mBC. PATIENTS AND METHODS In the open-label, phase II, ELAINE 2 trial (NCT04432454), women with ESR1-mutated, ER+/human epidermal growth factor receptor 2-negative (HER2-) mBC who progressed on prior therapies (including CDK4/6i) received lasofoxifene 5 mg/day and abemaciclib 150 mg b.i.d until disease progression/toxicity. The primary endpoint was safety/tolerability. Secondary endpoints included progression-free survival (PFS), clinical benefit rate (CBR), and objective response rate (ORR). RESULTS Twenty-nine women (median age 60 years) participated; all but one were previously treated with a CDK4/6i (median duration 2 years). The lasofoxifene-abemaciclib combination was well tolerated with primarily grade 1/2 treatment-emergent adverse events (TEAEs), most commonly diarrhea, nausea, fatigue, and vomiting. One patient (with no prior CDK4/6i) discontinued treatment due to grade 2 diarrhea. No deaths occurred during the study. Median PFS was 56.0 weeks [95% confidence interval (CI) 31.9 weeks-not estimable; ∼13 months]; PFS rates at 6, 12, and 18 months were 76.1%, 56.1%, and 38.8%, respectively. CBR at 24 weeks was 65.5% (95% CI 47.3% to 80.1%). In 18 patients with measurable lesions, ORR was 55.6% (95% CI 33.7% to 75.4%). ESR1-mutant circulating tumor DNA (ctDNA) allele fraction decreased from baseline to week 4 in 21/26 (80.8%) patients. CONCLUSIONS Lasofoxifene plus abemaciclib had an acceptable safety profile, was well tolerated, and exhibited meaningful antitumor activity in women with ESR1-mutated, ER+/HER2- mBC after disease progression on prior CDK4/6i. Observed decreases in ESR1-mutant ctDNA with lasofoxifene concordant with clinical response suggest target engagement. If the ELAINE 2 findings are confirmed in the initiated, phase III, ELAINE 3 trial, these data could be practice-changing and help address a critical unmet need.
Collapse
Affiliation(s)
- S Damodaran
- Department of Breast Medical Oncology, The University of Texas, MD Anderson Cancer Center, Houston.
| | | | - A Elkhanany
- Baylor College of Medicine, Duncan Cancer Center - Breast, Houston
| | | | - M Barve
- Mary Crowley Cancer Research, Dallas
| | - S Blau
- Oncology Division, Northwest Medical Specialties, PPLC, Puyallup
| | - M A Cherian
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus
| | - J A Peguero
- Department of Research, Oncology Consultants PA, Houston
| | - M P Goetz
- Department of Oncology, Mayo Clinic, Rochester
| | | | | | - H C F Moore
- Cleveland Clinic Taussig Cancer Institute, Cleveland, USA
| |
Collapse
|
4
|
Heft Neal ME, Walline HM, Haring CT. Circulating Tumor DNA in Human Papillomavirus-Mediated Oropharynx Cancer: Leveraging Early Data to Inform Future Directions. Cancer J 2023; 29:215-219. [PMID: 37471611 DOI: 10.1097/ppo.0000000000000670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
ABSTRACT Circulating tumor DNA (ctDNA) has become an area of intense study in many solid malignancies including head and neck cancer. This is of particular interest for human papillomavirus-mediated oropharyngeal squamous cell carcinoma as this cohort of patients has excellent survival and is undergoing current clinical trials aimed at treatment de-escalation. Recent studies have demonstrated the prognostic implications of pretreatment ctDNA and the utility of monitoring ctDNA during and posttreatment; however, there is a need for a more critical understanding of ctDNA as it is beginning to be incorporated into clinical trials. This review discusses the current state of ctDNA in oropharynx cancer focusing on ctDNA kinetics and minimal residual disease detection and ends with a discussion of future applications.
Collapse
Affiliation(s)
| | - Heather M Walline
- From the Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI
| | - Catherine T Haring
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, OH
| |
Collapse
|
5
|
Lother D, Robert M, Elwood E, Smith S, Tunariu N, Johnston SRD, Parton M, Bhaludin B, Millard T, Downey K, Sharma B. Imaging in metastatic breast cancer, CT, PET/CT, MRI, WB-DWI, CCA: review and new perspectives. Cancer Imaging 2023; 23:53. [PMID: 37254225 DOI: 10.1186/s40644-023-00557-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Breast cancer is the most frequent cancer in women and remains the second leading cause of death in Western countries. It represents a heterogeneous group of diseases with diverse tumoral behaviour, treatment responsiveness and prognosis. While major progress in diagnosis and treatment has resulted in a decline in breast cancer-related mortality, some patients will relapse and prognosis in this cohort of patients remains poor. Treatment is determined according to tumor subtype; primarily hormone receptor status and HER2 expression. Menopausal status and site of disease relapse are also important considerations in treatment protocols. MAIN BODY Staging and repeated evaluation of patients with metastatic breast cancer are central to the accurate assessment of disease extent at diagnosis and during treatment; guiding ongoing clinical management. Advances have been made in the diagnostic and therapeutic fields, particularly with new targeted therapies. In parallel, oncological imaging has evolved exponentially with the development of functional and anatomical imaging techniques. Consistent, reproducible and validated methods of assessing response to therapy is critical in effectively managing patients with metastatic breast cancer. CONCLUSION Major progress has been made in oncological imaging over the last few decades. Accurate disease assessment at diagnosis and during treatment is important in the management of metastatic breast cancer. CT (and BS if appropriate) is generally widely available, relatively cheap and sufficient in many cases. However, several additional imaging modalities are emerging and can be used as adjuncts, particularly in pregnancy or other diagnostically challenging cases. Nevertheless, no single imaging technique is without limitation. The authors have evaluated the vast array of imaging techniques - individual, combined parametric and multimodal - that are available or that are emerging in the management of metastatic breast cancer. This includes WB DW-MRI, CCA, novel PET breast cancer-epitope specific radiotracers and radiogenomics.
Collapse
Affiliation(s)
| | - Marie Robert
- Institut de Cancérologie de l'Ouest, St Herblain, France
| | | | - Sam Smith
- The Royal Marsden Hospital, London & Sutton, UK
| | - Nina Tunariu
- The Royal Marsden Hospital, London & Sutton, UK
- The Institute of Cancer Research (ICR), London & Sutton, UK
| | - Stephen R D Johnston
- The Royal Marsden Hospital, London & Sutton, UK
- The Institute of Cancer Research (ICR), London & Sutton, UK
| | | | | | | | - Kate Downey
- The Royal Marsden Hospital, London & Sutton, UK
- The Institute of Cancer Research (ICR), London & Sutton, UK
| | - Bhupinder Sharma
- The Royal Marsden Hospital, London & Sutton, UK.
- The Institute of Cancer Research (ICR), London & Sutton, UK.
| |
Collapse
|
6
|
Li K, Cao L, Li C, Wu J, Chen B, Zhang G, Li X, Wen L, Jia M, Wei G, Lin J, Li Y, Zhang Y, Mok H, Ren C, Wang Y, Qi X, Guo L, Che Y, Liao N. Genomic alteration profile and PD-L1 expression among different breast cancer subtypes in Chinese population and their correlations. Cancer Med 2023; 12:5195-5208. [PMID: 36404592 PMCID: PMC10028068 DOI: 10.1002/cam4.5314] [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: 05/05/2022] [Revised: 08/02/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUD There were limitations existing in programmed cell-death ligand 1 (PD-L1) as predictive biomarkers for breast cancer (BC), hence exploring the correlation between PD-L1 levels and other biomarkers in BC may become a very useful therapeutic clinical tool. METHODS A total of 301 Chinese patients with different BC subtypes including 47 HR+/HER2+, 185 HR+/HER2-, 38 HR-/HER2+, and 31 triple-negative breast cancer (TNBC) were enrolled in our study. Next-generation sequencing based Yuansu450 gene panel was used for genomic alteration identification and PD-L1 expression was tested using immunohistochemistry. RESULTS The most prevalent BC-related mutations were TP53 mutations, followed by mutations in PIK3CA, ERBB2, CDK12, and GATA3 in our Chinese cohort. We found that mutations DDR2 and MYCL were only mutated in HR-/HER2+ subtype, whereas H3-3A and NRAS mutations were only occurred in HR-/HER2- subtype. The percentage of patients with PD-L1-positive expression was higher in patients with HR-/HER2- mainly due to the percentage of PD-L1-high level. Mutational frequencies of TP53, MYC, FAT4, PBRM1, PREX2 were observed to have significant differences among patients with different BC subtypes based on PD-L1 levels. Moreover, a positive correlation was observed between TMB and PD-L1 level in HR+/HER2- subtype, and showed that the proportion of patients with high PD-L1 expression was higher than that of patients with low PD-L1 expression in the HR+/HER2- and HR+/HER2+ cohorts with high Ki67 expression. CONCLUSIONS The genomic alterations based on PD-L1 and other biomarkers of different cohorts may provide more possibilities for the treatment of BC with different subtypes.
Collapse
Affiliation(s)
- Kai Li
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Li Cao
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Cheukfai Li
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Jundong Wu
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and TreatmentCancer Hospital of Shantou University Medical CollegeShantouChina
| | - Bo Chen
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Guochun Zhang
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Xueri Li
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Lingzhu Wen
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Minghan Jia
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Guangnan Wei
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
- School of MedicineSouth China University of TechnologyGuangzhouChina
| | - Jiali Lin
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
- The Second School of Clinical MedicineSouthern Medical UniversityGuangzhouChina
| | - Yingzi Li
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yuchen Zhang
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Hsiaopei Mok
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Chongyang Ren
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yulei Wang
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | | | | | | | - Ning Liao
- Department of Breast Cancer, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| |
Collapse
|
7
|
Giannoni-Luza S, Acosta O, Murillo Carrasco AG, Danos P, Cotrina Concha JM, Miller HG, Pinto JA, Aguilar A, Araujo JM, Fujita R, Buleje J. Chip-based digital Polymerase Chain Reaction as quantitative technique for the detection of PIK3CA mutations in breast cancer patients. Heliyon 2022; 8:e11396. [DOI: 10.1016/j.heliyon.2022.e11396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
|
8
|
Jiang H, Ouyang Q, Yin Y, Tong Z, Shen K, Yuan Z, Geng C, Liu Y, Song G, Ran R, Li W, Qu Q, Wang M, Meng L, Tong Y, Li H. Proxalutamide in patients with AR-positive metastatic breast cancer: Results from an open-label multicentre phase Ib study and biomarker analysis. Eur J Cancer 2022; 176:1-12. [PMID: 36182805 DOI: 10.1016/j.ejca.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 12/15/2022]
Abstract
AIM Proxalutamide is a novel second-generation non-steroidal androgen receptor (AR) antagonist. This study aimed to evaluate the preliminary efficacy and safety of proxalutamide in patients with AR-positive metastatic breast cancer (AR+ mBC). METHODS In this open-label, dose-expansion, multicentre phase Ib trial, patients with AR+ mBC (immunohistochemistry [IHC] ≥1%) received proxalutamide orally once daily. Two proxalutamide dose cohorts (cohort A: 200 mg; cohort B: 300 mg) were sequentially investigated. Primary endpoints were disease control rate (DCR) at 8 and 16 weeks and recommended phase II dose (RP2D). RESULTS Forty-five patients with three median lines (range, 1-13) prior systemic therapy were enrolled (cohort A, n = 30; cohort B, n = 15). Among 39 evaluable patients, DCR at 8 and 16 weeks was 25.6% (95% confidence interval [CI], 11.9-39.4%), with 26.9% in cohort A and 23.1% in cohort B. No patient achieved partial response or complete response. Proxalutamide 200 mg/day was determined as RP2D. The 6-month progression-free survival (PFS) rate was 19.6% (95% CI, 10.2-37.5%). In the triple-negative subgroup, DCR at 8 weeks was 38.5%, with median PFS of 9.1 months (95% CI, 7.8-NA) in those who achieved response at 8 weeks (n = 5). Most common grade 3/4 adverse events were aspartate aminotransferase increase (8.9%) and γ-glutamyltransferase increase (8.9%). By biomarker analysis, patients with moderate AR expression of IHC (26%-75%), PIK3CA pathogenic mutations, or <60 ng/ml cell-free DNA yield showed longer PFS. CONCLUSION Proxalutamide showed promising anti-tumour activity with good tolerability in patients with heavily pretreated AR+ mBC, supporting further investigation. TRIAL REGISTRATION This clinical study was prospectively registered at chinadrugtrials.org.cn (Identifier: CTR20170757) and clinical trials.gov (Identifier: NCT04103853).
Collapse
Affiliation(s)
- Hanfang Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Quchang Ouyang
- Department of Breast Oncology, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Yongmei Yin
- Department of Breast Oncology, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Zhongshen Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Kunwei Shen
- Department of Breast Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhongyu Yuan
- Department of Breast Oncology, Sun-Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Cuizhi Geng
- Department of Breast Centre, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yaxin Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Guohong Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ran Ran
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei Li
- Department of Breast Oncology, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Qing Qu
- Department of Breast Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Meiyu Wang
- Suzhou Kintor Pharmaceuticals, Inc., Suzhou, Jiangsu, China
| | - Luping Meng
- Suzhou Kintor Pharmaceuticals, Inc., Suzhou, Jiangsu, China
| | - Youzhi Tong
- Suzhou Kintor Pharmaceuticals, Inc., Suzhou, Jiangsu, China.
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
| |
Collapse
|
9
|
Castaneda CA, Castillo M, Bernabe LA, Suarez N, Romero A, Sanchez J, Torres E, Enciso J, Tello K, Enciso N, Velarde M, De La Cruz M, Dunstan J, Cotrina JM, Abugattas J, Pinillos MA, Roque K, Fuentes H, Poquioma E, Guerra H, Gomez HL. Association between PIK3CA Mutations in Blood and Tumor-Infiltrating Lymphocytes in Peruvian Breast Cancer Patients. Asian Pac J Cancer Prev 2022; 23:3331-3337. [PMID: 36308356 PMCID: PMC9924322 DOI: 10.31557/apjcp.2022.23.10.3331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE To evaluate the relationship between circulating tumor DNA (ctDNA) presence and tumor features including tumor-infiltrating lymphocyte (TIL) levels in Peruvian breast cancer patients. MATERIALS AND METHODS This was a prospective study conducted at the Instituto Nacional de Enfemedades Neoplasicas, Peru. We evaluated level of TIL and PIK3CA mutations in ctDNA. Clinical characteristics, including outcome data, were collected from the patient file. Survival was calculated from the date of blood sample drawn to the event time. Data collected were analyzed using SPSS software version 25. RESULTS We analyzed plasma samples from 183 breast cancer patients. most cases were of Luminal-B (44.8%) phenotype and stage II (41.5%), and median stromal TIL was 30%. PIK3CA mutation in ctDNA was detected in 35% cases (most with E545K) and was associated with lower TIL level (p=0.04). PIK3CA in ctDNA tended to be associated with advanced stages (p=0.09) in the whole series and with higher recurrence rates (p=0.053) in the non-metastatic setting. Patients with presence of PIK3CA in ctDNA tended to have shorter survival (p=0.083). CONCLUSION Presence of PIK3CA mutation in ctDNA was frequently found in our Peruvian breast cancer series, was associated with lower TIL levels and tended to predict poor outcomes.
Collapse
Affiliation(s)
- Carlos A. Castaneda
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru. ,Faculty of Medical Sciences, Universidad Cientifica del Sur, Lima 15067, Peru. ,For Correspondence:
| | - Miluska Castillo
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Luis A. Bernabe
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Nancy Suarez
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Atocha Romero
- Department of Medical Oncology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain.
| | - Joselyn Sanchez
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Ebert Torres
- Department of Pathology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Javier Enciso
- Laboratorio de Cultivo Celular e Inmunologia, Universidad Cientifica del Sur, Lima 15067, Peru.
| | - Katherine Tello
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Nataly Enciso
- Laboratorio de Cultivo Celular e Inmunologia, Universidad Cientifica del Sur, Lima 15067, Peru.
| | - Marco Velarde
- Department of Breast and Soft Tissues, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Miguel De La Cruz
- Department of Breast and Soft Tissues, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Jorge Dunstan
- Department of Breast and Soft Tissues, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Jose M. Cotrina
- Department of Breast and Soft Tissues, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Julio Abugattas
- Department of Breast and Soft Tissues, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Miguel A. Pinillos
- Department of Breast and Soft Tissues, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Katia Roque
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Hugo Fuentes
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Ebert Poquioma
- Department of Epidemiology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Henry Guerra
- Department of Pathology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| | - Henry L. Gomez
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru.
| |
Collapse
|
10
|
Galvano A, Castellana L, Gristina V, La Mantia M, Insalaco L, Barraco N, Perez A, Cutaia S, Calò V, Bazan Russo TD, Francini E, Incorvaia L, Mirisola MG, Vieni S, Rolfo C, Bazan V, Russo A. The diagnostic accuracy of PIK3CA mutations by circulating tumor DNA in breast cancer: an individual patient data meta-analysis. Ther Adv Med Oncol 2022; 14:17588359221110162. [PMID: 36188485 PMCID: PMC9516428 DOI: 10.1177/17588359221110162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Background The circulating tumor DNA (ctDNA) diagnostic accuracy for detecting phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutations in breast cancer (BC) is under discussion. We aimed to compare plasma and tissue PIK3CA alterations, encompassing factors that could affect the results. Methods Two reviewers selected studies from different databases until December 2020. We considered BC patients with matched tumor tissue and plasma ctDNA. We performed meta-regression and subgroup analyses to explore sources of heterogeneity concerning tumor burden, diagnostic technique, sample size, sampling time, biological subtype, and hotspot mutation. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the related area under the curve (AUC) were elaborated for the overall population and each subgroup. Results The pooled analysis was carried out on 25 cohorts for a total of 1966 patients. The overall ctDNA sensitivity and specificity were 0.73 (95% CI: 0.70-0.77) and 0.87 (95% CI: 0.85-0.89). The AUC was 0.93. Pooled concordance, negative predictive value and positive predictive value values were 0.87 (95% CI: 0.82-0.92), 0.86 (95% CI: 0.81-0.90), and 0.89 (95% CI: 0.81-0.95) with pooled PLR, NLR, and DOR of 7.94 (95% CI: 4.90-12.86), 0.33 (95% CI: 0.25-0.45), and 33.41 (95% CI: 17.23-64.79), respectively. The pooled results consistently favored next-generation sequencing (NGS)- over polymerase chain reaction-based methodologies. The best ctDNA performance in terms of sensitivity, specificity, and AUC (0.85, 0.99, and 0.94, respectively) was observed in the low-time sampling subgroup (⩽18 days between tissue and plasma collection). Meta-regression and subgroup analyses highlighted sampling time as a possible major cause of heterogeneity. Conclusions These findings reliably estimate the high ctDNA accuracy for the detection of PIK3CA mutations. A ctDNA-first approach for the assessment of PIK3CA mutational status by NGS may accurately replace tissue tumor sampling, representing the preferable strategy at diagnosis of metastatic BC in patients who present with visceral involvement and at least two metastatic lesions, primarily given low clinical compliance or inaccessible metastatic sites.
Collapse
Affiliation(s)
- Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Luisa Castellana
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Maria La Mantia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Lavinia Insalaco
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Nadia Barraco
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Alessandro Perez
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Sofia Cutaia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valentina Calò
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Edoardo Francini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lorena Incorvaia
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Mario Giuseppe Mirisola
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Salvatore Vieni
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viviana Bazan
- Department of Experimental Biomedicine and Clinical Neurosciences, School of Medicine, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Via del Vespro 129, Palermo 90127, Italy
| |
Collapse
|
11
|
Wang Y, Xu Y, Zhang Y. A novel ferroptosis-related long noncoding RNA signature for relapse free survival prediction in patients with breast cancer. Medicine (Baltimore) 2022; 101:e29573. [PMID: 35945765 PMCID: PMC9351903 DOI: 10.1097/md.0000000000029573] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ferroptosis is the process of cell death dependent on iron. Growing evidence suggests that ferroptosis plays vital roles in the biological process of many cancers. However, just a small number of ferroptosis-related lncRNAs have been explored in depth. Ferroptosis-related lncRNAs in breast cancer (BC) were identified by co-expression analysis based on The Cancer Genome Atlas database (TCGA). The whole set was divided into a training set and a test set with a 1:1 ratio. Univariate Cox regression and LASSO analyses were performed to establish a signature in the 3 sets. Kaplan-Meier analysis and receiver operating characteristic (ROC) for the 3 sets validated the effectiveness and robustness of the signature. Besides, we also explore the relationship between this and clinical characteristics, immune cell infiltration and tumor microenvironment. Meanwhile, the nomogram was drawn by screening indicators of independent recurrent prediction. Finally, we evaluated the relationships between the signature and tumor microenvironment. We identified 391 ferroptosis-related lncRNAs and constructed a 5 lncRNAs-based signature in the training, test, and whole sets, stratifying patients into high-risk and low-risk groups. According to survival analysis, patients in the high-risk groups had worse relapse free survival (RFS) compared to the low risk-groups. The ROC curves indicated that the recurrent signature had a promising predictive capability for BC patients. Moreover, an independent factors-based nomogram model could offer the quantitative prediction and net benefit for the recurrence of BC patients. Finally, the microenvironment, including tumor mutational burden (TMB), immune cell functions and immune checkpoints, showed big differences between the 2 groups. The 5 ferroptosis-related lncRNAs and their signature might be novel promising biomarkers and immunotherapy targets for patients with BC.
Collapse
Affiliation(s)
- Yuzhi Wang
- Department of Laboratory Medicine, People’s Hospital of Deyang City, Deyang, Sichuan, P. R. China
| | - Yunfei Xu
- Department of Laboratory Medicine, Chengdu Women’s and Children’s Central Hospital, Chengdu, Sichuan, P. R. China
| | - Yi Zhang
- Department of Blood Transfusion, People’s Hospital of Deyang City, Deyang, Sichuan, P. R. China
- *Correspondence: Yi Zhang, People’s Hospital of Deyang City, No. 173, Section 1, Taishan North Road, Deyang City, Sichuan 618000, China (e-mail: )
| |
Collapse
|
12
|
Sánchez-Herrero E, Serna-Blasco R, Robado de Lope L, González-Rumayor V, Romero A, Provencio M. Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front Oncol 2022; 12:943253. [PMID: 35936733 PMCID: PMC9350013 DOI: 10.3389/fonc.2022.943253] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells release nucleic acids, freely or associated with other structures such as vesicles into body fluids, including blood. Among these nucleic acids, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker for tumor molecular profiling. However, certain biological characteristics of ctDNA are still unknown. Here, we provide an overview of the current knowledge about ctDNA biological features, including size and structure as well as the mechanisms of ctDNA shedding and clearance, and the physio-pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is essential for the development of new methods that enable the analysis of ctDNA.
Collapse
Affiliation(s)
- Estela Sánchez-Herrero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- +D Department, Atrys Health, Barcelona, Spain
| | - Roberto Serna-Blasco
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | - Lucia Robado de Lope
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | | | - Atocha Romero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
- *Correspondence: Atocha Romero, ; orcid.org/0000-0002-1634-7397
| | - Mariano Provencio
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
| |
Collapse
|
13
|
Yan T, Yu L, Zhang N, Peng C, Su G, Jing Y, Zhang L, Wu T, Cheng J, Guo Q, Shi X, Lu Y. The advanced development of molecular targeted therapy for hepatocellular carcinoma. Cancer Biol Med 2022. [PMID: 35699406 DOI: 10.20892/j.issn.2095-3941.2021.0661.pmid:35699406;pmcid:pmc9257319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC), one of the most common malignant tumors in China, severely threatens the life and health of patients. In recent years, precision medicine, clinical diagnoses, treatments, and innovative research have led to important breakthroughs in HCC care. The discovery of new biomarkers and the promotion of liquid biopsy technologies have greatly facilitated the early diagnosis and treatment of HCC. Progress in targeted therapy and immunotherapy has provided more choices for precise HCC treatment. Multiomics technologies, such as genomics, transcriptomics, and metabolomics, have enabled deeper understanding of the occurrence and development mechanisms, heterogeneity, and genetic mutation characteristics of HCC. The continued promotion and accurate typing of HCC, accurate guidance of treatment, and accurate prognostication have provided more treatment opportunities and prolonged survival timelines for patients with HCC. Innovative HCC research providing an in-depth understanding of the biological characteristics of HCC will be translated into accurate clinical practices for the diagnosis and treatment of HCC.
Collapse
Affiliation(s)
- Tao Yan
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Lingxiang Yu
- The Second Department of Hepatobiliary Surgery, Senior Department of Hepatology, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Ning Zhang
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Caiyun Peng
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Guodong Su
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Yi Jing
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Linzhi Zhang
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Tong Wu
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Jiamin Cheng
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Qian Guo
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | | | - Yinying Lu
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- National Clinical Medical Research Center for Infectious Diseases, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| |
Collapse
|
14
|
Yan T, Yu L, Zhang N, Peng C, Su G, Jing Y, Zhang L, Wu T, Cheng J, Guo Q, Shi X, Lu Y. The advanced development of molecular targeted therapy for hepatocellular carcinoma. Cancer Biol Med 2022; 19:j.issn.2095-3941.2021.0661. [PMID: 35699406 PMCID: PMC9257319 DOI: 10.20892/j.issn.2095-3941.2021.0661] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/18/2022] [Indexed: 11/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC), one of the most common malignant tumors in China, severely threatens the life and health of patients. In recent years, precision medicine, clinical diagnoses, treatments, and innovative research have led to important breakthroughs in HCC care. The discovery of new biomarkers and the promotion of liquid biopsy technologies have greatly facilitated the early diagnosis and treatment of HCC. Progress in targeted therapy and immunotherapy has provided more choices for precise HCC treatment. Multiomics technologies, such as genomics, transcriptomics, and metabolomics, have enabled deeper understanding of the occurrence and development mechanisms, heterogeneity, and genetic mutation characteristics of HCC. The continued promotion and accurate typing of HCC, accurate guidance of treatment, and accurate prognostication have provided more treatment opportunities and prolonged survival timelines for patients with HCC. Innovative HCC research providing an in-depth understanding of the biological characteristics of HCC will be translated into accurate clinical practices for the diagnosis and treatment of HCC.
Collapse
Affiliation(s)
- Tao Yan
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Lingxiang Yu
- The Second Department of Hepatobiliary Surgery, Senior Department of Hepatology, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Ning Zhang
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Caiyun Peng
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Guodong Su
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Yi Jing
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Linzhi Zhang
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Tong Wu
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Jiamin Cheng
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Qian Guo
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | | | - Yinying Lu
- Comprehensive Liver Cancer Center, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- National Clinical Medical Research Center for Infectious Diseases, the 5th Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| |
Collapse
|
15
|
Provencio M, Calvo V, Romero A, Spicer JD, Cruz-Bermúdez A. Treatment Sequencing in Resectable Lung Cancer: The Good and the Bad of Adjuvant Versus Neoadjuvant Therapy. Am Soc Clin Oncol Educ Book 2022; 42:1-18. [PMID: 35561296 DOI: 10.1200/edbk_358995] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The treatment scenario for patients with resectable non-small cell lung cancer has changed dramatically with the incorporation of immunotherapy. The introduction of immunotherapy into treatment algorithms has yielded improved clinical outcomes in several phase II and III trials in both adjuvant (Impower010 and PEARLS) and neoadjuvant settings (JHU/MSK, LCMC3, NEOSTAR, Columbia/MGH, NADIM, and CheckMate-816), leading to new U.S. Food and Drug Administration approvals in this sense. Different treatment options are now available for patients, making the optimal treatment scenario a matter of intense debate. In this review, we summarize the main results concerning treatment sequencing in resectable non-small cell lung cancer from the past 30 years in the preimmunotherapy era, focusing on recent advances after incorporation of immunotherapy. Finally, the utility of several parameters (PD-L1, tumor mutational burden, radiomics, circulating tumor DNA, T-cell receptor, and immune populations) as predictive biomarkers for therapy personalization is discussed.
Collapse
Affiliation(s)
- Mariano Provencio
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Virginia Calvo
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Atocha Romero
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Jonathan D Spicer
- Division of Thoracic Surgery, McGill University Health Centre, Montréal, Quebec, Canada
| | - Alberto Cruz-Bermúdez
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| |
Collapse
|
16
|
Li C, Wang H, Jiang Y, Fu W, Liu X, Zhong R, Cheng B, Zhu F, Xiang Y, He J, Liang W. Advances in lung cancer screening and early detection. Cancer Biol Med 2022; 19:j.issn.2095-3941.2021.0690. [PMID: 35535966 PMCID: PMC9196057 DOI: 10.20892/j.issn.2095-3941.2021.0690] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022] Open
Abstract
Lung cancer is associated with a heavy cancer-related burden in terms of patients' physical and mental health worldwide. Two randomized controlled trials, the US-National Lung Screening Trial (NLST) and Nederlands-Leuvens Longkanker Screenings Onderzoek (NELSON), indicated that low-dose CT (LDCT) screening results in a statistically significant decrease in mortality in patients with lung cancer, LDCT has become the standard approach for lung cancer screening. However, many issues in lung cancer screening remain unresolved, such as the screening criteria, high false-positive rate, and radiation exposure. This review first summarizes recent studies on lung cancer screening from the US, Europe, and Asia, and discusses risk-based selection for screening and the related issues. Second, an overview of novel techniques for the differential diagnosis of pulmonary nodules, including artificial intelligence and molecular biomarker-based screening, is presented. Third, current explorations of strategies for suspected malignancy are summarized. Overall, this review aims to help clinicians understand recent progress in lung cancer screening and alleviate the burden of lung cancer.
Collapse
Affiliation(s)
- Caichen Li
- Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
| | - Huiting Wang
- Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
| | - Yu Jiang
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
| | - Wenhai Fu
- Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Xiwen Liu
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
| | - Ran Zhong
- Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
| | - Bo Cheng
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
| | - Feng Zhu
- Department of Internal Medicine, Detroit Medical Center Sinai-Grace Hospital, Detroit, Michigan 48235, USA
| | - Yang Xiang
- Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Jianxing He
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Wenhua Liang
- Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
- Dongguan Affiliated Hospital of Southern Medical University, Dongguan People Hospital, Dongguan 523059, China
- Department of Oncology, the First People’s Hospital of Zhaoqing, Zhaoqing 526020, China
| |
Collapse
|
17
|
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: 19] [Impact Index Per Article: 9.5] [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.
Collapse
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
| |
Collapse
|
18
|
Hayashi T, Yoshida Y, Yamada T, Tanaka K, Shimaoka H, Kajitani R, Munechika T, Nagano H, Matsumoto Y, Komono A, Sakamoto R, Aisu N, Yoshimatsu G, Yoshimura F, Hasegawa S. Relationship between perioperative oncological evaluation and recurrence using circulating tumor DNA with KRAS mutation in patients with colorectal cancer. Cancer Med 2022; 11:3126-3135. [PMID: 35312176 PMCID: PMC9385586 DOI: 10.1002/cam4.4677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
Background The detection of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) by liquid biopsy may have prognostic information. In this perioperative study, we evaluate if there is a relationship between mutant allele frequency (MAF) of Kirsten rat sarcoma viral oncogene homolog (KRAS) and tumor recurrence and how that could be useful in the early detection of recurrence. Methods Among 304 cases of colorectal cancer surgery, ctDNA was sampled from the perioperative blood of 84 patients with CRC with KRAS mutation (exon 4 p.A146T, exon 4 p.A146V, exon 2 p.G12A, exon 2 p.G12C, exon 2 p.G12D, exon 2 p.G12S, exon 2 p.G12V, exon 2 p.G13D, exon 3 p.Q61H) and analyzed using the digital polymerase chain reaction system. The median observation period was 26 months. Results Although the relationship between the perioperative MAF of KRAS and recurrence was not proved, tumor diameter, tumor depth, and stage were correlated with the preoperative MAF of KRAS (p = 0.034, p = 0.002, p = 0.008). However, tumor diameter, tumor depth, and stage did not correlate with MAF of KRAS at postoperative day 30. Conclusions In this study, pathological tumor size, tumor depth, and stage were correlated with preoperative MAF of KRAS, but it was unreliable to predict recurrence by detection of ctDNA with KRAS mutation in the perioperative period of colorectal surgery.
Collapse
Affiliation(s)
- Takaomi Hayashi
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Yoichiro Yoshida
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Teppei Yamada
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Keita Tanaka
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Hideki Shimaoka
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Ryuji Kajitani
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Taro Munechika
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Hideki Nagano
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Yoshiko Matsumoto
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Akira Komono
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Ryohei Sakamoto
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Naoya Aisu
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Gumpei Yoshimatsu
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Fumihiro Yoshimura
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Suguru Hasegawa
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| |
Collapse
|
19
|
Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
Collapse
Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
| |
Collapse
|
20
|
Hoshino I, Yokota H, Iwatate Y, Mori Y, Kuwayama N, Ishige F, Itami M, Uno T, Nakamura Y, Tatsumi Y, Shimozato O, Nagase H. Prediction of the differences in tumor mutation burden between primary and metastatic lesions by radiogenomics. Cancer Sci 2021; 113:229-239. [PMID: 34689378 PMCID: PMC8748253 DOI: 10.1111/cas.15173] [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: 08/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor mutational burden (TMB) is gaining attention as a biomarker for responses to immune checkpoint inhibitors in cancer patients. In this study, we evaluated the status of TMB in primary and liver metastatic lesions in patients with colorectal cancer (CRC). In addition, the status of TMB in primary and liver metastatic lesions was inferred by radiogenomics on the basis of computed tomography (CT) images. The study population included 24 CRC patients with liver metastases. DNA was extracted from primary and liver metastatic lesions obtained from the patients and TMB values were evaluated by next‐generation sequencing. The TMB value was considered high when it equaled to or exceeded 10/100 Mb. Radiogenomic analysis of TMB was performed by machine learning using CT images and the construction of prediction models. In 7 out of 24 patients (29.2%), the TMB status differed between the primary and liver metastatic lesions. Radiogenomic analysis was performed to predict whether TMB status was high or low. The maximum values for the area under the receiver operating characteristic curve were 0.732 and 0.812 for primary CRC and CRC with liver metastasis, respectively. The sensitivity, specificity, and accuracy of the constructed models for TMB status discordance were 0.857, 0.600, and 0.682, respectively. Our results suggested that accurate inference of the TMB status is possible using radiogenomics. Therefore, radiogenomics could facilitate the diagnosis, treatment, and prognosis of patients with CRC in the clinical setting.
Collapse
Affiliation(s)
- Isamu Hoshino
- Division of Gastroenterological Surgery, Chiba Cancer Center, Chiba, Japan
| | - Hajime Yokota
- Department of Diagnostic Radiology and Radiation Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yosuke Iwatate
- Division of Hepato-Biliary-Pancreatic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Yasukuni Mori
- Faculty of Engineering, Graduate School of Engineering, Chiba University, Chiba, Japan
| | - Naoki Kuwayama
- Division of Gastroenterological Surgery, Chiba Cancer Center, Chiba, Japan
| | - Fumitaka Ishige
- Division of Hepato-Biliary-Pancreatic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Makiko Itami
- Division of Clinical Pathology, Chiba Cancer Center, Chiba, Japan
| | - Takashi Uno
- Department of Diagnostic Radiology and Radiation Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuki Nakamura
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba Cancer Center, Chiba, Japan
| | - Yasutoshi Tatsumi
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba Cancer Center, Chiba, Japan
| | - Osamu Shimozato
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba Cancer Center, Chiba, Japan
| | - Hiroki Nagase
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba Cancer Center, Chiba, Japan
| |
Collapse
|
21
|
Oncological evaluation in the perioperative period using cfDNA with BRAF V600E mutation in patients with colorectal cancer. Sci Rep 2021; 11:13263. [PMID: 34168268 PMCID: PMC8225636 DOI: 10.1038/s41598-021-92795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022] Open
Abstract
The detection of circulating cell-free DNA (cfDNA) by liquid biopsy is reported to provide prognostic information in colorectal cancer (CRC). Although the frequency of BRAF V600E mutation in CRC is less than 10%, it is associated with poor responses to conventional chemotherapy. We conducted a prospective study to investigate the relationship between the perioperative mutant allele frequency (MAF) of BRAF V600E and tumor recurrence, and to evaluate the possibility of early detection of recurrence. Among 362 patients who underwent radical resection, cfDNA was extracted from the perioperative blood of 11 CRC patients with BRAF V600E mutation and analyzed using the digital polymerase chain reaction (dPCR) system. The median follow-up time was 22 months, and there were four cases of recurrence. Although there was no correlation between recurrence and the perioperative MAF of BRAF V600E, tumor diameter was correlated with the MAF (p = 0.024), and the MAF increased with time in two patients from whom additional samples were obtained prior to recurrence. In this study, we identified a correlation between the pathological tumor diameter and the MAF, but it was difficult to predict recurrence by measuring cfDNA with BRAF V600E mutation in the perioperative period of radical resection of CRC.
Collapse
|
22
|
Watanabe K, Nakamura Y, Low SK. Clinical implementation and current advancement of blood liquid biopsy in cancer. J Hum Genet 2021; 66:909-926. [PMID: 34088974 DOI: 10.1038/s10038-021-00939-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022]
Abstract
Liquid biopsies have been receiving tremendous attentions as easy, rapid, and non-invasive tools for cancer diagnosis. Liquid biopsy can be performed repeatedly for disease monitoring and is expected to overcome the limitations of tissue biopsies. With the advancement of next generation sequencing technologies, it is now possible to detect minute amount of tumor-derived circulation tumor DNA (ctDNA) from blood samples. Importantly, ctDNA detection could be complementary to tissue biopsies or tumor biomarkers particularly in cases of which tumor biopsy is clinically difficult to obtain. Here, we introduce the up-to-date technologies used in cfDNA-based liquid biopsy and review the clinical utilities of ctDNA in cancer screening, detection of minimal residual diseases, selection of molecular-targeted drugs, as well as monitoring of treatment responsiveness. We also discuss the challenges and future perspectives of liquid biopsy implementation in clinical setting.
Collapse
Affiliation(s)
- Kazunori Watanabe
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yusuke Nakamura
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Siew-Kee Low
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
| |
Collapse
|
23
|
A Systematic Review of the Use of Circulating Cell-Free DNA Dynamics to Monitor Response to Treatment in Metastatic Breast Cancer Patients. Cancers (Basel) 2021; 13:cancers13081811. [PMID: 33920135 PMCID: PMC8069506 DOI: 10.3390/cancers13081811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/24/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
Monitoring treatment response in metastatic breast cancer currently consists mainly of radiological and clinical assessments. These methods have high inter-observer variation, suboptimal sensitivity to determine response to treatment and give little insight into the biological characteristics of the tumor. Assessing circulating tumor DNA (ctDNA) over time could be employed to address these limitations. Several ways to quantify and characterize ctDNA exist, based on somatic mutations, copy number variations, methylation, and global circulating cell-free DNA (cfDNA) fragment sizes and concentrations. These methods are being explored and technically validated, but to date none of these methods are applied clinically. We systematically reviewed the literature on the use of quantitative ctDNA measurements over time to monitor response to systemic therapy in patients with metastatic breast cancer. Cochrane, Embase, PubMed and Google Scholar databases were searched to find studies focusing on the use of cfDNA to longitudinally monitor treatment response in advanced breast cancer patients until October 2020. This resulted in a total of 33 studies which met the inclusion criteria. These studies were heterogeneous in (pre-)processing procedures, applied techniques and design. An association between ctDNA and treatment response was found in most of the included studies, independent of the applied assay. To implement ctDNA-based response monitoring into daily clinical practice for metastatic breast cancer patients, sample (pre-) processing procedures need to be standardized and large prospectively collected sample cohorts with well annotated clinical follow-up are required to establish its clinical validity.
Collapse
|
24
|
Provencio M, Pérez-Barrios C, Barquin M, Calvo V, Franco F, Sánchez E, Sánchez R, Marsden D, Cristóbal Sánchez J, Martin Acosta P, Laza-Briviesca R, Cruz-Bermúdez A, Romero A. Next-generation sequencing for tumor mutation quantification using liquid biopsies. Clin Chem Lab Med 2021; 58:306-313. [PMID: 31469650 DOI: 10.1515/cclm-2019-0745] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 11/15/2022]
Abstract
Background Non-small cell lung cancer (NSCLC) patients benefit from targeted therapies both in first- and second-line treatment. Nevertheless, molecular profiling of lung cancer tumors after first disease progression is seldom performed. The analysis of circulating tumor DNA (ctDNA) enables not only non-invasive biomarker testing but also monitoring tumor response to treatment. Digital PCR (dPCR), although a robust approach, only enables the analysis of a limited number of mutations. Next-generation sequencing (NGS), on the other hand, enables the analysis of significantly greater numbers of mutations. Methods A total of 54 circulating free DNA (cfDNA) samples from 52 NSCLC patients and two healthy donors were analyzed by NGS using the Oncomine™ Lung cfDNA Assay kit and dPCR. Results Lin's concordance correlation coefficient and Pearson's correlation coefficient between mutant allele frequencies (MAFs) assessed by NGS and dPCR revealed a positive and linear relationship between the two data sets (ρc = 0.986; 95% confidence interval [CI] = 0.975-0.991; r = 0.987; p < 0.0001, respectively), indicating an excellent concordance between both measurements. Similarly, the agreement between NGS and dPCR for the detection of the resistance mutation p.T790M was almost perfect (K = 0.81; 95% CI = 0.62-0.99), with an excellent correlation in terms of MAFs (ρc = 0.991; 95% CI = 0.981-0.992 and Pearson's r = 0.998; p < 0.0001). Importantly, cfDNA sequencing was successful using as low as 10 ng cfDNA input. Conclusions MAFs assessed by NGS were highly correlated with MAFs assessed by dPCR, demonstrating that NGS is a robust technique for ctDNA quantification using clinical samples, thereby allowing for dynamic genomic surveillance in the era of precision medicine.
Collapse
Affiliation(s)
- Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Clara Pérez-Barrios
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
- Laboratory Medicine Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Miguel Barquin
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Virginia Calvo
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Fabio Franco
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Estela Sánchez
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Ricardo Sánchez
- Laboratorio de Hematología Traslacional, Servicio de Hematología, Instituto de Investigación Hospital 12 de Octubre (I+12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Daniel Marsden
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Juan Cristóbal Sánchez
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Paloma Martin Acosta
- Pathology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Raquel Laza-Briviesca
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Alberto Cruz-Bermúdez
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Atocha Romero
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
- Medical Oncology Department, Puerta de Hierro Hospital, C/ Manuel de Falla 1, Majadahonda, Madrid 28222, Spain
| |
Collapse
|
25
|
PEG3 mutation is associated with elevated tumor mutation burden and poor prognosis in breast cancer. Biosci Rep 2021; 40:225944. [PMID: 32729618 PMCID: PMC7419805 DOI: 10.1042/bsr20201648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Breast cancer is the second most common malignancy in women and considered as a severe health burden. PEG3 mutations have been observed in several cancers. However, the associations of PEG3 mutation with tumor mutation burden (TMB) and prognosis in breast cancer have not been investigated. Methods: In our study, the somatic mutation data of 986 breast cancer patients from The Cancer Genome Atlas (TCGA) were analyzed. Results: It showed that PEG3 had a relatively high mutation rate (2%). After calculated the TMB in PEG3 mutant and PEG3 wild-type groups, we found the TMB value was significantly higher in PEG3 mutant samples than that in PEG3 wild-type samples (P = 5.6e-07), which was independent of the confounding factors including age, stage, mutations of BRCA1, BRCA2 and POLE (odd ratio, 0.45; 95% CI, 0.20–0.98; P=0.044). Survival analysis revealed that PEG3 mutant samples had inferior survival outcome compared with the PEG3 wild-type samples after adjusted for the confounding factors above (hazard ratio, 0.27; 95% CI: 0.12–0.57; P<0.001). Conclusion: These results illustrated that PEG3 mutation was associated with high TMB and inferior prognosis, suggesting PEG3 mutation might play a guiding role in prognosis prediction and immunotherapy selection in breast cancer.
Collapse
|
26
|
Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
Collapse
Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
27
|
Martins I, Ribeiro IP, Jorge J, Gonçalves AC, Sarmento-Ribeiro AB, Melo JB, Carreira IM. Liquid Biopsies: Applications for Cancer Diagnosis and Monitoring. Genes (Basel) 2021; 12:349. [PMID: 33673461 PMCID: PMC7997281 DOI: 10.3390/genes12030349] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The minimally-or non-invasive detection of circulating tumor-derived components in biofluids, such as blood, liquid biopsy is a revolutionary approach with significant potential for the management of cancer. Genomic and transcriptomic alterations can be accurately detected through liquid biopsies, which provide a more comprehensive characterization of the heterogeneous tumor profile than tissue biopsies alone. Liquid biopsies could assist diagnosis, prognosis, and treatment selection, and hold great potential to complement current surveilling strategies to monitor disease evolution and treatment response in real-time. In particular, these are able to detect minimal residual disease, to predict progression, and to identify mechanisms of resistance, allowing to re-orient treatment strategies in a timelier manner. In this review we gathered current knowledge regarding the role and potential of liquid biopsies for the diagnosis and follow-up of cancer patients. The presented findings emphasize the strengths of liquid biopsies, revealing their chance of improving the diagnosis and monitoring of several tumor types in the near future. However, despite growing evidence supporting their value as a management tool in oncology, some limitations still need to be overcome for their implementation in the routine clinical setting.
Collapse
Affiliation(s)
- Ivana Martins
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Joana Jorge
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Haematology Department, Coimbra University Hospital Centre (CHUC), 3004-531 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| |
Collapse
|
28
|
Abstract
Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.
Collapse
|
29
|
Tellez-Gabriel M, Knutsen E, Perander M. Current Status of Circulating Tumor Cells, Circulating Tumor DNA, and Exosomes in Breast Cancer Liquid Biopsies. Int J Mol Sci 2020; 21:E9457. [PMID: 33322643 PMCID: PMC7763984 DOI: 10.3390/ijms21249457] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer among women worldwide. Although the five-, ten- and fifteen-year survival rates are good for breast cancer patients diagnosed with early-stage disease, some cancers recur many years after completion of primary therapy. Tumor heterogeneity and clonal evolution may lead to distant metastasis and therapy resistance, which are the main causes of breast cancer-associated deaths. In the clinic today, imaging techniques like mammography and tissue biopsies are used to diagnose breast cancer. Even though these methods are important in primary diagnosis, they have limitations when it comes to longitudinal monitoring of residual disease after treatment, disease progression, therapy responses, and disease recurrence. Over the last few years, there has been an increasing interest in the diagnostic, prognostic, and predictive potential of circulating cancer-derived material acquired through liquid biopsies in breast cancer. Thanks to the development of sensitive devices and platforms, a variety of tumor-derived material, including circulating cancer cells (CTCs), circulating DNA (ctDNA), and biomolecules encapsulated in extracellular vesicles, can now be extracted and analyzed from body fluids. Here we will review the most recent studies on breast cancer, demonstrating the clinical potential and utility of CTCs and ctDNA. We will also review literature illustrating the potential of circulating exosomal RNA and proteins as future biomarkers in breast cancer. Finally, we will discuss some of the advantages and limitations of liquid biopsies and the future perspectives of this field in breast cancer management.
Collapse
Affiliation(s)
- Marta Tellez-Gabriel
- Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, 9011 Tromsø, Norway; (E.K.); (M.P.)
| | | | | |
Collapse
|
30
|
Xie H, Mahoney DW, Foote PH, Burger KN, Doering KA, Taylor WR, Then SS, Cao X, McGlinch M, Berger CK, Wu TT, Hubbard JM, Allawi HT, Kaiser MW, Lidgard GP, Ahlquist DA, Kisiel JB. Novel Methylated DNA Markers in the Surveillance of Colorectal Cancer Recurrence. Clin Cancer Res 2020; 27:141-149. [PMID: 33028593 DOI: 10.1158/1078-0432.ccr-20-2589] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/04/2020] [Accepted: 10/01/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE We aimed to assess the concordance of colorectal cancer-associated methylated DNA markers (MDM) in primary and metastatic colorectal cancer for feasibility in detection of distantly recurrent/metastatic colorectal cancer in plasma. EXPERIMENTAL DESIGN A panel of previously discovered colorectal cancer-associated MDMs was selected. MDMs from primary and paired metastatic colorectal cancer tissue were assayed with quantitative methylation-specific PCR. Plasma MDMs were measured blindly by target enrichment long-probe quantitative-amplified signal assays. Random forest modeling was used to derive a prediction algorithm of MDMs in archival plasma samples from primary colorectal cancer cases. This algorithm was validated in prospectively collected plasma samples from recurrent colorectal cancer cases. The accuracy of the algorithm was summarized as sensitivity, specificity, and area under the curve (AUC). RESULTS Of the 14 selected MDMs, the concordance between primary and metastatic tissue was considered moderate or higher for 12 MDMs (86%). At a preset specificity of 95% (91%-98%), a panel of 13 MDMs, in plasma from 97 colorectal cancer cases and 200 controls, detected stage IV colorectal cancer with 100% (80%-100%) sensitivity and all stages of colorectal cancer with an AUC of 0.91 (0.87-0.95), significantly higher than carcinoembryonic antigen [AUC, 0.72 (0.65-0.79)]. This panel, in plasma from 40 cases and 60 healthy controls, detected recurrent/metastatic colorectal cancer with 90% (76%-97%) sensitivity, 90% (79%-96%) specificity, and an AUC of 0.96 (0.92-1.00). The panel was positive in 0.30 (0.19-0.43) of 60 patients with no evidence of disease in post-operative patients with colorectal cancer. CONCLUSIONS Plasma assay of novel colorectal cancer-associated MDMs can reliably detect both primary colorectal cancer and distantly recurrent colorectal cancer with promising accuracy.
Collapse
Affiliation(s)
- Hao Xie
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Patrick H Foote
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Kelli N Burger
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Karen A Doering
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Sara S Then
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Xiaoming Cao
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Maria McGlinch
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Calise K Berger
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tsung-Teh Wu
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
31
|
Xie H, Kim RD. The Application of Circulating Tumor DNA in the Screening, Surveillance, and Treatment Monitoring of Colorectal Cancer. Ann Surg Oncol 2020; 28:1845-1858. [PMID: 32776184 DOI: 10.1245/s10434-020-09002-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
Precision medicine with genetic profiling of tumor tissue has become an essential part of routine clinical practice in colorectal cancer. However, tissue genetic profiling suffers from clonal evolution, tumor heterogeneity, and time needed to deliver critical information for prompt clinical decision making. In contrast, liquid biopsy with plasma circulating tumor DNA provides genetic and epigenetic information from both the primary and metastatic colorectal cancer, which can potentially capture tumor heterogeneity and evolution with time and treatment. In addition, liquid biopsy with circulating tumor DNA is minimally invasive, quicker, and easily repeatable with high patient compliance to provide both qualitative and quantitative molecular information in real-time. We provide an overview on the potential clinical applications of circulating tumor DNA in the screening, surveillance, and treatment monitoring of colorectal cancer.
Collapse
Affiliation(s)
- Hao Xie
- Division of Medical Oncology, Mayo Clinic, Rochester, USA
| | - Richard D Kim
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA.
| |
Collapse
|
32
|
Plasma DNA as a "liquid biopsy" incompletely complements tumor biopsy for identification of mutations in a case series of four patients with oligometastatic breast cancer. Breast Cancer Res Treat 2020; 182:665-677. [PMID: 32562118 DOI: 10.1007/s10549-020-05714-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Circulating tumor DNA in plasma may present a minimally invasive opportunity to identify tumor-derived mutations to inform selection of targeted therapies for individual patients, particularly in cases of oligometastatic disease where biopsy of multiple tumors is impractical. To assess the utility of plasma DNA as a "liquid biopsy" for precision oncology, we tested whether sequencing of plasma DNA is a reliable surrogate for sequencing of tumor DNA to identify targetable genetic alterations. METHODS Blood and biopsies of 1-3 tumors were obtained from 4 evaluable patients with advanced breast cancer. One patient provided samples from an additional 7 tumors post-mortem. DNA extracted from plasma, tumor tissues, and buffy coat of blood were used for probe-directed capture of all exons in 149 cancer-related genes and massively parallel sequencing. Somatic mutations in DNA from plasma and tumors were identified by comparison to buffy coat DNA. RESULTS Sequencing of plasma DNA identified 27.94 ± 11.81% (mean ± SD) of mutations detected in a tumor(s) from the same patient; such mutations tended to be present at high allelic frequency. The majority of mutations found in plasma DNA were not found in tumor samples. Mutations were also found in plasma that matched clinically undetectable tumors found post-mortem. CONCLUSIONS The incomplete overlap of genetic alteration profiles of plasma and tumors warrants caution in the sole reliance of plasma DNA to identify therapeutically targetable alterations in patients and indicates that analysis of plasma DNA complements, but does not replace, tumor DNA profiling. TRIAL REGISTRATION Subjects were prospectively enrolled in trial NCT01836640 (registered April 22, 2013).
Collapse
|
33
|
Sánchez-Herrero E, Blanco Clemente M, Calvo V, Provencio M, Romero A. Next-generation sequencing to dynamically detect mechanisms of resistance to ALK inhibitors in ALK-positive NSCLC patients: a case report. Transl Lung Cancer Res 2020; 9:366-372. [PMID: 32420077 PMCID: PMC7225153 DOI: 10.21037/tlcr.2020.02.07] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tyrosine kinase inhibitors (TKIs) of the anaplastic lymphoma kinase gene (ALK) have significantly improved the quality of life and survival of non-small cell lung cancer (NSCLC) patients whose tumors harbor an ALK translocation. However, most of these patients relapse within 2 to 3 years as the tumor acquires resistance mutations. Unlike beaming and digital PCR (dPCR), which only allow a few mutations to be analyzed, next-generation sequencing (NGS) approaches enable the simultaneous screening of multiple genetic alterations even when the frequencies of the variants are very low. We present the case of a 52-year-old man who was diagnosed with an ALK-positive NSCLC and was treated with crizotinib and, subsequently, ceritinib. The analysis of serial liquid biopsies by NGS detected two asynchronous mutations arising in the ALK locus during disease progression, namely p.Gly1269Ala (c.3806G>C) and p.Gly1202Arg (c.3604G>A), that conferred resistance to crizotinib and ceritinib, respectively. The resistance mutations were detected independently at different times, and could be imputed to different metastatic lesions, thereby highlighting the importance of heterogeneity in advance disease. Plasma levels of ALK resistance mutations correlated well with tumor responses assessed by CT scans and bone scintigraphy, demonstrating that non-invasive tumor molecular profiling by NGS allows the efficient dynamic monitoring of ALK-positive NSCLC patients, and outperforms dPCR and beaming because more somatic mutations can be tracked over the course of the treatment. In conclusion, this case report illustrates the usefulness NGS to guide therapeutic decisions in ALK-positive NSCLC patients based tumor molecular profile upon disease progression.
Collapse
Affiliation(s)
- Estela Sánchez-Herrero
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain
| | - Mariola Blanco Clemente
- Medical Oncology Department, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain
| | - Virginia Calvo
- Medical Oncology Department, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain
| | - Mariano Provencio
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain.,Medical Oncology Department, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain
| | - Atocha Romero
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain.,Medical Oncology Department, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain
| |
Collapse
|
34
|
Knuever J, Weiss J, Persa OD, Kreuzer K, Mauch C, Hallek M, Schlaak M. The use of circulating cell-free tumor DNA in routine diagnostics of metastatic melanoma patients. Sci Rep 2020; 10:4940. [PMID: 32188904 PMCID: PMC7080785 DOI: 10.1038/s41598-020-61818-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 03/02/2020] [Indexed: 11/09/2022] Open
Abstract
Modern advances in technology such as next-generation sequencing and digital PCR make detection of minor circulating cell-free tumor DNA amounts in blood from cancer patients possible. Samples can be obtained minimal-invasively, tested for treatment-determining genetic alterations and are considered to reflect the genetic constitution of the whole tumor mass. Furthermore, tumor development can be determined by a time course of the quantified circulating cell-free tumor DNA. However, systematic studies which prove the clinical relevance of monitoring patients using liquid biopsies are still lacking. In this study, we collected 115 samples from 47 late stage melanoma patients over 1.5 years alongside therapy-associated clinical routine monitoring. Mutation status was confirmed by molecular analysis of primary tumor material. We can show that detectable levels of circulating cell-free tumor DNA correlate with clinical development over time. Increasing levels of circulating cell-free tumor DNA during melanoma treatment with either targeted therapy (BRAF/MEK inhibitors) or immunotherapy, during recovery time or the intervals between last treatment cycle and second-line treatment point towards clinical progression before the progression becomes obvious in imaging. Therefore, this is a further possibility to closely screen our patients for tumor progression during therapy, in therapy-free phases and in earlier stages before therapy initiation.
Collapse
Affiliation(s)
- Jana Knuever
- Department of Dermatology and Venerology, University of Cologne, Cologne, Germany.
- Center of Integrated Oncology (CIO), Cologne, Germany.
| | - Jonathan Weiss
- Center of Integrated Oncology (CIO), Cologne, Germany
- Clinic I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Oana-Diana Persa
- Department of Dermatology and Venerology, University of Cologne, Cologne, Germany
- Center of Integrated Oncology (CIO), Cologne, Germany
| | - Karl Kreuzer
- Center of Integrated Oncology (CIO), Cologne, Germany
- Clinic I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Cornelia Mauch
- Department of Dermatology and Venerology, University of Cologne, Cologne, Germany
- Center of Integrated Oncology (CIO), Cologne, Germany
| | - Michael Hallek
- Center of Integrated Oncology (CIO), Cologne, Germany
- Clinic I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Max Schlaak
- Department of Dermatology and Venerology, University of Cologne, Cologne, Germany
- Center of Integrated Oncology (CIO), Cologne, Germany
- Department of Dermatology and Allergology, Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| |
Collapse
|
35
|
Sánchez-Herrero E, Provencio M, Romero A. Clinical utility of liquid biopsy for the diagnosis and monitoring of EML4-ALK NSCLC patients. ADVANCES IN LABORATORY MEDICINE 2020; 1:20190019. [PMID: 37362555 PMCID: PMC10197761 DOI: 10.1515/almed-2019-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/04/2019] [Indexed: 06/28/2023]
Abstract
Background Genomic rearrangement in anaplastic lymphoma kinase (ALK) gene occurs in 3-7% of patients with non-small-cell lung cancer (NSCLC). The detection of this alteration is crucial as ALK positive NSCLC patients benefit from ALK inhibitors, which improve both the patient's quality of life and overall survival (OS) compared to traditional chemotherapy. Content In routine clinical practice, ALK rearrangements are detected using tissue biopsy. Nevertheless, the availability of tumor tissue is compromised in NSCLC patients due to surgical complications or difficult access to the cancer lesion. In addition, DNA quality and heterogeneity may impair tumor biopsies testing. These limitations can be overcome by liquid biopsy, which refers to non-invasive approaches for tumor molecular profiling. In this paper we review currently available technology for non-invasive ALK testing, in NSCLC patients, based on the analysis of circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), circulating tumor cells (CTCs), tumor-educated platelets (TEPs) and extracellular vesicles (EVs) such as exosomes. Summary and outlook Non-invasive tumor molecular profiling is crucial to improve outcomes and quality of life of NSCLC patients whose tumors harbor a translocation involving ALK locus.
Collapse
Affiliation(s)
- Estela Sánchez-Herrero
- Molecular Oncology Laboratory, Biomedical Sciences Research Institute Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Mariano Provencio
- Medical Oncology Department, Puerta de Hierro Majadahonda University Hospital, C/ Manuel de Falla 1, Majadahonda, Madrid 28222, Spain
| | - Atocha Romero
- Medical Oncology Department, Puerta de Hierro Majadahonda University Hospital, C/ Manuel de Falla 1, Majadahonda, Madrid 28222, Spain
| |
Collapse
|
36
|
Oliveira KC, Ramos IB, Silva JM, Barra WF, Riggins GJ, Palande V, Pinho CT, Frenkel-Morgenstern M, Santos SE, Assumpcao PP, Burbano RR, Calcagno DQ. Current Perspectives on Circulating Tumor DNA, Precision Medicine, and Personalized Clinical Management of Cancer. Mol Cancer Res 2020; 18:517-528. [DOI: 10.1158/1541-7786.mcr-19-0768] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/13/2019] [Accepted: 01/23/2020] [Indexed: 11/16/2022]
|
37
|
Abstract
The great promise of digital PCR is the potential for unparalleled precision enabling accurate measurements for detection and quantification of genetic material. This chapter walks the reader through the fundamentals of digital PCR technology including digital PCR modeling using Poisson statistics. It describes a highly successful implementation of digital PCR technology using the chip-based nanofluidic Applied Biosystems™ QuantStudio™ 3D digital PCR system. It reviews the large number of applications where digital PCR is poised to make significant impacts. These include applications where detection of rare genetic targets is prioritized such as liquid biopsy, rare mutation detection, confirmation of NGS variant detection, detection of fusion transcripts, detection of chimerism and GMO detection and monitoring. These further include applications where accurate quantification of genetic targets is prioritized such as generation of references and standards, copy number variation, and NGS Library quantification.
Collapse
Affiliation(s)
- Marion Laig
- Thermo Fisher Scientific, South San Francisco, CA, USA.
| | | | | |
Collapse
|
38
|
Lim ZF, Ma PC. Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy. J Hematol Oncol 2019; 12:134. [PMID: 31815659 PMCID: PMC6902404 DOI: 10.1186/s13045-019-0818-2] [Citation(s) in RCA: 289] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
The biggest hurdle to targeted cancer therapy is the inevitable emergence of drug resistance. Tumor cells employ different mechanisms to resist the targeting agent. Most commonly in EGFR-mutant non-small cell lung cancer, secondary resistance mutations on the target kinase domain emerge to diminish the binding affinity of first- and second-generation inhibitors. Other alternative resistance mechanisms include activating complementary bypass pathways and phenotypic transformation. Sequential monotherapies promise to temporarily address the problem of acquired drug resistance, but evidently are limited by the tumor cells' ability to adapt and evolve new resistance mechanisms to persist in the drug environment. Recent studies have nominated a model of drug resistance and tumor progression under targeted therapy as a result of a small subpopulation of cells being able to endure the drug (minimal residual disease cells) and eventually develop further mutations that allow them to regrow and become the dominant population in the therapy-resistant tumor. This subpopulation of cells appears to have developed through a subclonal event, resulting in driver mutations different from the driver mutation that is tumor-initiating in the most common ancestor. As such, an understanding of intratumoral heterogeneity-the driving force behind minimal residual disease-is vital for the identification of resistance drivers that results from branching evolution. Currently available methods allow for a more comprehensive and holistic analysis of tumor heterogeneity in that issues associated with spatial and temporal heterogeneity can now be properly addressed. This review provides some background regarding intratumoral heterogeneity and how it leads to incomplete molecular response to targeted therapies, and proposes the use of single-cell methods, sequential liquid biopsy, and multiregion sequencing to discover the link between intratumoral heterogeneity and early adaptive drug resistance. In summary, minimal residual disease as a result of intratumoral heterogeneity is the earliest form of acquired drug resistance. Emerging technologies such as liquid biopsy and single-cell methods allow for studying targetable drivers of minimal residual disease and contribute to preemptive combinatorial targeting of both drivers of the tumor and its minimal residual disease cells.
Collapse
Affiliation(s)
- Zuan-Fu Lim
- WVU Cancer Institute, West Virginia University, Morgantown, WV, 26506, USA.,Cancer Cell Biology Program, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.,Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Penn State University, P.O. Box 850, Mail Code CH46, 500 University Drive, Hershey, PA, 17033-0850, USA
| | - Patrick C Ma
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Penn State University, P.O. Box 850, Mail Code CH46, 500 University Drive, Hershey, PA, 17033-0850, USA.
| |
Collapse
|
39
|
Jahangiri L, Hurst T. Assessing the Concordance of Genomic Alterations between Circulating-Free DNA and Tumour Tissue in Cancer Patients. Cancers (Basel) 2019; 11:cancers11121938. [PMID: 31817150 PMCID: PMC6966532 DOI: 10.3390/cancers11121938] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Somatic alterations to the genomes of solid tumours, which in some cases represent actionable drivers, provide diagnostic and prognostic insight into these complex diseases. Spatial and longitudinal tracking of somatic genomic alterations (SGAs) in patient tumours has emerged as a new avenue of investigation, not only as a disease monitoring strategy, but also to improve our understanding of heterogeneity and clonal evolution from diagnosis through disease progression. Furthermore, analysis of circulating-free DNA (cfDNA) in the so-called "liquid biopsy" has emerged as a non-invasive method to identify genomic information to inform targeted therapy and may also capture the heterogeneity of the primary and metastatic tumours. Considering the potential of cfDNA analysis as a translational laboratory tool in clinical practice, establishing the extent to which cfDNA represents the SGAs of tumours, particularly actionable driver alterations, becomes a matter of importance, warranting standardisation of methods and practices. Here, we assess the utilisation of cfDNA for molecular profiling of SGAs in tumour tissue across a broad range of solid tumours. Moreover, we examine the underlying factors contributing to discordance of detected SGAs between cfDNA and tumour tissue.
Collapse
Affiliation(s)
- Leila Jahangiri
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Lab blocks level 3, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Correspondence:
| | - Tara Hurst
- Department of Life Sciences, Birmingham City University, Birmingham B15 3TN, UK;
| |
Collapse
|
40
|
Liu Z, Xie Z, Zhao S, Ye D, Cai X, Cheng B, Li C, Xiong S, Li J, Liang H, Chen Z, Liang P, Liu J, He J, Liang W. Presence of allele frequency heterogeneity defined by ctDNA profiling predicts unfavorable overall survival of NSCLC. Transl Lung Cancer Res 2019; 8:1045-1050. [PMID: 32010581 DOI: 10.21037/tlcr.2019.12.10] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background The generation of subclonal (low-frequency) mutations is driven by tumor mutations and the relationship between the heterogeneity of tumor mutation abundance and non-small cell lung cancer (NSCLC) remains unknown. We investigate the role of allele frequency heterogeneity (AFH) defined by circulating tumor DNA (ctDNA) profiling in predicting prognosis in advanced NSCLC patients. Methods Publicly available data set of POPLAR (N=211) and OAK (N=642) trials were used for analyzing. A low ratio of allele frequency (AF) of a mutation to the maximum-somatic-allele-frequency (MSAF) was used to define the presence of AFH. The prognostic value of AF/MSAF ratio that was below a defined cutoff point in overall survival (OS) was evaluated using Cox-proportional hazards regression; and the structural break point was determined by LOESS regression and Chow test. The derived AFH was also explored in an independent cohort (N=259) of advanced NSCLC receiving first-line EGFR-TKIs from the First Affiliated Hospital of Guangzhou Medical University. Results In the POPLAR and OAK cohort, low AF/MSAF ratio was found to be significantly associated with unfavorable OS in univariate and multivariate analysis. The structural break point analysis demonstrated that AF/MSAF <10% could yield the optimal value to stratify patients with poor OS, which was applied for defining the presence of AFH. The presence of AFH significantly correlated with unfavorable OS in advanced NSCLC regardless of treatment arms (overall: HR 1.52, immunotherapy: HR 1.81, chemotherapy: HR 1.32, all P<0.05). In the exploratory EGFR-TKIs cohort, the presence of AFH was also significantly associated with shorter OS (HR 1.72, P=0.039). Conclusions Our results demonstrate that the presence of AFH predict unfavorable prognosis in advanced NSCLC despite which drug the patients used. The presence of AFH defined by ctDNA might provide an easily-accessible biomarker for risk stratification in the current clinical practice.
Collapse
Affiliation(s)
- Zhichao Liu
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China.,Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhanhong Xie
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Shen Zhao
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Dawei Ye
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Bo Cheng
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Shan Xiong
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Jianfu Li
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Hengrui Liang
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Zisheng Chen
- Department of Respiratory Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, China
| | - Peng Liang
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, the First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| |
Collapse
|
41
|
The Factors Predicting Concordant Epidermal Growth Factor Receptor (EGFR) Mutation Detected in Liquid/Tissue Biopsy and the Related Clinical Outcomes in Patients of Advanced Lung Adenocarcinoma with EGFR Mutations. J Clin Med 2019; 8:jcm8111758. [PMID: 31652678 PMCID: PMC6912667 DOI: 10.3390/jcm8111758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022] Open
Abstract
Liquid biopsy to identify epidermal growth factor receptor (EGFR) gene mutations from circulating tumor DNA (ctDNA) for lung adenocarcinoma is less invasive than traditional tissue biopsy. Most patients have concordant results in liquid/tissue biopsy, while the clinical significance of concordant results remains unclear. Our study aimed to evaluate the predicting factors and clinical outcomes associated with concordant results in liquid/tissue biopsy in newly diagnosed lung adenocarcinoma patients with EGFR mutations. In the 80 patients of stage III or IV lung adenocarcinoma, 51 patients had EGFR mutations detected in tissue samples, while 33 (65%) of them had concordant results shown in liquid biopsy. Multivariable regression analysis showed that lymph node involvement (adjusted odds ratio (95% CI): 8.71 (1.88–40.35), p = 0.0057) and bone metastasis (adjusted odds ratio (95% CI): 9.65 (1.72–54.05), p = 0.0099) were the independent predicting factors for concordant results. Forty of these 51 patients were stage IV and were treated with EGFR tyrosine kinase inhibitors (TKIs). The concordant results in liquid/tissue samples were associated with significantly poorer progression-free survival (PFS) in univariate analysis. However, multivariable analysis showed that lymph node involvement was the only independent predicting factor for poorer PFS, while concordant results in liquid/tissue samples were excluded during variable selection. The concordant results in liquid/tissue samples might indicate a larger tumor burden, which actually contributes to poorer PFS.
Collapse
|
42
|
A Predictor of Early Disease Recurrence in Patients With Breast Cancer Using a Cell-free RNA and Protein Liquid Biopsy. Clin Breast Cancer 2019; 20:108-116. [PMID: 31607655 DOI: 10.1016/j.clbc.2019.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Circulating biomarkers have been increasingly used in the clinical management of breast cancer. The present study evaluated whether RNAs and a protein present in the plasma of patients with breast cancer might have utility as prognostic biomarkers complementary to existing clinical tests. PATIENTS AND METHODS We performed microarray profiling of small noncoding RNAs in plasma samples from 30 patients with breast cancer and 10 control individuals. Two small noncoding RNAs, including microRNA (miR)-923, were selected and quantified in plasma samples from an evaluation cohort of 253 patients with breast cancer, using droplet digital polymerase chain reaction. We also measured cancer antigen (CA) 15-3 protein levels in these samples. Cox regression survival analysis was used to determine which markers were associated with patient prognosis. RESULTS As independent markers of prognosis, the plasma levels of miR-923 and CA 15-3 at the time of surgery for breast cancer were significantly associated with prognosis, irrespective of treatment (Cox proportional hazards, P = 3.9 × 10-3 and 1.9 × 10-9, respectively). After building a multivariable model with standard clinical and pathological features, the addition of miR-923 and CA 15-3 information into the model resulted in a significantly better predictor of disease recurrence in patients, irrespective of treatment, compared with the use of clinicopathological data alone (area under the curve at 3 years, 0.858 vs. 0.770 with clinicopathological markers only; P = .017). CONCLUSION We propose that the plasma levels of miR-923 and CA 15-3, combined with standard clinicopathological predictors, could be used as a preoperative, noninvasive estimate of patient prognosis to identify which women might need more aggressive treatment or closer surveillance after surgery for breast cancer.
Collapse
|
43
|
Strijker M, Soer EC, de Pastena M, Creemers A, Balduzzi A, Beagan JJ, Busch OR, van Delden OM, Halfwerk H, van Hooft JE, van Lienden KP, Marchegiani G, Meijer SL, van Noesel CJ, Reinten RJ, Roos E, Schokker S, Verheij J, van de Vijver MJ, Waasdorp C, Wilmink JW, Ylstra B, Besselink MG, Bijlsma MF, Dijk F, van Laarhoven HW. Circulating tumor DNA quantity is related to tumor volume and both predict survival in metastatic pancreatic ductal adenocarcinoma. Int J Cancer 2019; 146:1445-1456. [PMID: 31340061 PMCID: PMC7004068 DOI: 10.1002/ijc.32586] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 01/10/2023]
Abstract
Circulating tumor DNA (ctDNA) is assumed to reflect tumor burden and has been suggested as a tool for prognostication and follow‐up in patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). However, the prognostic value of ctDNA and its relation with tumor burden has yet to be substantiated, especially in mPDAC. In this retrospective analysis of prospectively collected samples, cell‐free DNA from plasma samples of 58 treatment‐naive mPDAC patients was isolated and sequenced using a custom‐made pancreatobiliary NGS panel. Pathogenic mutations were detected in 26/58 (44.8%) samples. Cross‐check with droplet digital PCR showed good agreement in Bland–Altman analysis (p = 0.217, nonsignificance indicating good agreement). In patients with liver metastases, ctDNA was more frequently detected (24/37, p < 0.001). Tumor volume (3D reconstructions from imaging) and ctDNA variant allele frequency (VAF) were correlated (Spearman's ρ = 0.544, p < 0.001). Median overall survival (OS) was 3.2 (95% confidence interval [CI] 1.6–4.9) versus 8.4 (95% CI 1.6–15.1) months in patients with detectable versus undetectable ctDNA (p = 0.005). Both ctDNA VAF and tumor volume independently predicted OS after adjustment for carbohydrate antigen 19.9 and treatment regimen (hazard ratio [HR] 1.05, 95% CI 1.01–1.09, p = 0.005; HR 1.00, 95% CI 1.01–1.05, p = 0.003). In conclusion, our study showed that ctDNA detection rates are higher in patients with larger tumor volume and liver metastases. Nevertheless, measurements may diverge and, thus, can provide complementary information. Both ctDNA VAF and tumor volume were strong predictors of OS. What's new? Circulating tumor DNA (ctDNA) attracts much interest as a possible prognostic tool for cancer. Here, the authors showed that the quantity of ctDNA correlated strongly with tumor volume in metastatic pancreatic ductal adenocarcinoma (mPDAC). They conducted a retrospective analysis using samples collected from 58 untreated mPDAC patients. For this study, the authors designed a pancreatobiliary NGS panel, which they used to test the patients’ cell‐free DNA, along with droplet digital PCR. Both ctDNA variant allele frequency and tumor volume predicted overall survival, they found.
Collapse
Affiliation(s)
- Marin Strijker
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eline C Soer
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Matteo de Pastena
- Department of General and Pancreatic Surgery, The Pancreas Institute, University of Verona Hospital Trust, Verona, Italy
| | - Aafke Creemers
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alberto Balduzzi
- Department of General and Pancreatic Surgery, The Pancreas Institute, University of Verona Hospital Trust, Verona, Italy
| | - Jamie J Beagan
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Amsterdam, Amsterdam, The Netherlands
| | - Olivier R Busch
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Otto M van Delden
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanin E van Hooft
- Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Krijn P van Lienden
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giovanni Marchegiani
- Department of General and Pancreatic Surgery, The Pancreas Institute, University of Verona Hospital Trust, Verona, Italy
| | - Sybren L Meijer
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Carel J van Noesel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Roy J Reinten
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eva Roos
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sandor Schokker
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc J van de Vijver
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Amsterdam, Amsterdam, The Netherlands
| | - Cynthia Waasdorp
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Johanna W Wilmink
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University Amsterdam, Amsterdam, The Netherlands
| | - Marc G Besselink
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Frederike Dijk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Hanneke W van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
44
|
Hanibuchi M, Kanoh A, Kuramoto T, Saito T, Tobiume M, Saijo A, Kozai H, Kondo M, Morizumi S, Yoneda H, Kagawa K, Ogino H, Sato S, Kawano H, Otsuka K, Toyoda Y, Nokihara H, Goto H, Nishioka Y. Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA. Oncotarget 2019; 10:3654-3666. [PMID: 31217900 PMCID: PMC6557207 DOI: 10.18632/oncotarget.26951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
The feasibility and required sensitivity of circulating free DNA (cfDNA)-based detection methods in second-line epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment are not well elucidated. We examined T790M and other activating mutations of EGFR by cfDNA to assess the clinical usability. In 45 non-small cell lung cancer (NSCLC) patients harboring activating EGFR mutations, cfDNAs were prepared from the plasma samples. EGFR mutations in cfDNA were detected using highly sensitive methods and originally developed assays and these results were compared to tissue-based definitive diagnoses. The specificity of each cfDNA-based method ranged 96–100% whereas the sensitivity ranged 56–67%, indicating its low pseudo-positive rate. In EGFR-TKI failure cohort, 41–46% samples were positive for T790M by each cfDNA-based method, which was comparable to re-biopsy tissue-based T790M positive rates in literature. The concordance of the results for each EGFR mutation ranged from 83–95%. In eight patients, the results of the cfDNA-based assays and re-biopsy-derived tissue-based test were compared. The observed overall agreement ranged in 50–63% in T790M, and in 63–100% in activating EGFR mutations. In this study, we have newly developed three types of assay which have enough sensitivity to detect cfDNA. We also detected T790M in 44% of patients who failed prior EGFR-TKI treatment, indicating that cfDNA-based assay has clinical relevance for detecting acquired mutations of EGFR.
Collapse
Affiliation(s)
- Masaki Hanibuchi
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan.,Department of Internal Medicine, Shikoku Central Hospital of the Mutual Aid Association of Public School Teachers, Shikoku-Chuo, 799-0193, Japan
| | - Akira Kanoh
- Biomarker Research, Early Development Strategy and Planning, Taiho Pharmaceutical Co., Ltd., Tsukuba, 300-2611, Japan
| | - Takuya Kuramoto
- Biomarker Research, Early Development Strategy and Planning, Taiho Pharmaceutical Co., Ltd., Tsukuba, 300-2611, Japan
| | - Tatsuro Saito
- Riken Genesis Co., Ltd., Shinagawa-ku, Tokyo, 141-0032, Japan
| | - Makoto Tobiume
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Atsuro Saijo
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroyuki Kozai
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Mayo Kondo
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Shun Morizumi
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroto Yoneda
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Kozo Kagawa
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hirokazu Ogino
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Seidai Sato
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroshi Kawano
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Kenji Otsuka
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Yuko Toyoda
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hiroshi Nokihara
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Hisatsugu Goto
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Yasuhiko Nishioka
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| |
Collapse
|
45
|
Tian J, Geng Y, Lv D, Li P, Cordova M, Liao Y, Tian X, Zhang X, Zhang Q, Zou K, Zhang Y, Zhang X, Li Y, Zhang J, Ma Z, Shao Y, Song L, Owen GI, Li T, Liu R, Liu Q, Zou L, Zhang Z, Li Z. Using plasma cell-free DNA to monitor the chemoradiotherapy course of cervical cancer. Int J Cancer 2019; 145:2547-2557. [PMID: 30919951 DOI: 10.1002/ijc.32295] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/10/2019] [Accepted: 03/12/2019] [Indexed: 12/16/2022]
Abstract
The liquid biopsy is being integrated into cancer diagnostics and surveillance. However, critical questions still remain, such as how to precisely evaluate cancer mutation burden and interpret the corresponding clinical implications. Herein, we evaluated the role of peripheral blood cell-free DNA (cfDNA) in characterizing the dynamic mutation alterations of 48 cancer driver genes from cervical cancer patients. We performed targeted deep sequencing on 93 plasma cfDNA from 57 cervical cancer patients and from this developed an algorithm, allele fraction deviation (AFD), to monitor in an unbiased manner the dynamic changes of genomic aberrations. Differing treatments, including chemotherapy (n = 22), radiotherapy (n = 14) and surgery (n = 15), led to a significant decrease in AFD values (Wilcoxon, p = 0.029). The decrease of cfDNA AFD values was accompanied by shrinkage in the size of the tumor in most patients. However, in a subgroup of patients where cfDNA AFD values did not reflect a reduction in tumor size, there was a detection of progressive disease (metastasis). Furthermore, a low AFD value at diagnosis followed a later increase of AFD value also successfully predicted relapse. These results show that plasma cfDNA, together with targeted deep sequencing, may help predict treatment response and disease development in cervical cancer.
Collapse
Affiliation(s)
- Jichao Tian
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yan Geng
- Department of Radiotherapy, Ansteel Group Hospital, Anshan, Liaoning, China
| | - Dekang Lv
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Peiying Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Miguel Cordova
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Yuwei Liao
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Xiaoyuan Tian
- The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xiaolong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Qingzheng Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Kun Zou
- The first affiliated hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yu Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Xia Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yulong Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Jian Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Zhaokui Ma
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yanyan Shao
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Luyao Song
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Gareth I Owen
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tingting Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Ruimei Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Quentin Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Lijuan Zou
- The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhuo Zhang
- The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhiguang Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| |
Collapse
|
46
|
Rohanizadegan M. Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. Cancer Genet 2018; 228-229:159-168. [PMID: 29572011 PMCID: PMC6108954 DOI: 10.1016/j.cancergen.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation. This review summarizes the existing evidence on the use of ctDNA specifically in breast cancer, including detection methods, diagnostic accuracy, role in genetics and epigenetics evaluation of the tumor, and comparison with other biomarkers. Current evidence suggests that increasing levels of ctDNA in breast cancer can be of significant diagnostic value for early detection of breast cancer although the sensitivity and specificity of the methods is still suboptimal. Additionally, ctDNA allows for characterizing the tumor in a non-invasive way and monitor the response to therapy, although discordance of ctDNA results with direct biopsy (i.e. due to tumor heterogeneity) is still considered a notable limitation.
Collapse
Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
47
|
Fettke H, Kwan EM, Azad AA. Cell-free DNA in cancer: current insights. Cell Oncol (Dordr) 2018; 42:13-28. [PMID: 30367445 DOI: 10.1007/s13402-018-0413-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The field of liquid biopsies in oncology is rapidly expanding, with the application of cell-free circulating tumour DNA (ctDNA) showing promise in this era of precision medicine. Compared with traditional clinical and radiographic tumour monitoring methods, the analysis of ctDNA provides a minimally-invasive and technically feasible approach to assess temporal and spatial molecular evolutions of the tumour landscape. The constantly advancing technological platforms available for ctDNA extraction and analysis allow greater analytical sensitivities than ever before. The potential translational impact of ctDNA as a blood-based biomarker for the identification, characterization and monitoring of cancer has been demonstrated in numerous proof-of-concept studies, with ctDNA analysis beginning to be applied clinically across multiple facets of oncology. CONCLUSIONS In this review we discuss the biology, recent advancements, technical considerations and clinical implications of ctDNA in the context of cancer, and highlight important challenges and future directions for the integration of ctDNA into standardised patient care.
Collapse
Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.,Department of Medical Oncology, Monash Health, Melbourne, Australia
| |
Collapse
|
48
|
Lee Y, Park S, Kim WS, Lee JC, Jang SJ, Choi J, Choi C. Correlation between progression-free survival, tumor burden, and circulating tumor DNA in the initial diagnosis of advanced-stage EGFR-mutated non-small cell lung cancer. Thorac Cancer 2018; 9:1104-1110. [PMID: 29989342 PMCID: PMC6119619 DOI: 10.1111/1759-7714.12793] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND This study was conducted to identify whether the presence of circulating tumor DNA (ctDNA) in plasma before treatment with EGFR-tyrosine kinase inhibitors (TKIs) is associated with clinical outcomes. METHODS Fifty-seven pairs of tissues and plasma samples were obtained from patients with NSCLC adenocarcinoma harboring activating EGFR mutations before the administration of EGFR-TKI treatment. ctDNA mutation was identified using the PANAMutyper EGFR mutation kit. Both qualitative and quantitative analyzes of the data were performed. RESULTS Concordance rates with tissue biopsy were 40.4% and 59.6% for the qualitative and quantitative methods, respectively. Bone metastasis showed a statistically significant correlation with ctDNA detection (odds ratio 3.985, 95% confidence interval [CI] 1.027-15.457; P = 0.046). Progression-free survival (PFS) was significantly shorter in the group detected with ctDNA than in the undetected ctDNA group (median PFS 9.8 vs. 20.7 months; hazard ratio [HR] 2.30, 95% CI 1.202-4.385; P = 0.012). Detection of ctDNA before treatment with EGFR-TKIs (HR 2.388, 95% CI 1.138-5.014; P = 0.021) and extra-thoracic lymph node metastasis (HR 13.533, 95% CI 2.474-68.747; P = 0.002) were independently associated with PFS. Six of 11 patients (45.5%) monitored by serial sampling showed a dynamic change in ctDNA prior to disease progression. CONCLUSION Quantitative testing can increase the sensitivity of the ctDNA detection test. Patients with detectable ctDNA had significantly shorter PFS after receiving EGFR-TKIs than those with undetectable ctDNA. Tumor burden may be associated with plasma ctDNA detection. A shorter PFS was associated with detection of ctDNA and extra-thoracic lymph node metastasis. Dynamic changes in the ctDNA level may help predict clinical outcomes.
Collapse
Affiliation(s)
- Yunkyoung Lee
- Department of Pulmonary and Critical Care MedicineChungnam National University HospitalDaejeonSouth Korea
| | - Sojung Park
- Department of Pulmonary and Critical Care Medicine, Hallym University Medical CenterUniversity of Hallym College of MedicineKangwonKorea
| | - Woo Sung Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Se Jin Jang
- Department of Pathology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Jene Choi
- Department of Pathology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| | - Chang‐Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
- Department of Oncology, Asan Medical CenterUniversity of Ulsan, College of MedicineSeoulKorea
| |
Collapse
|
49
|
Li H, Xu Y, Zhao F, Song G, Rugo HS, Zhang Y, Yang L, Liu X, Shao B, Yang L, Liu Y, Ran R, Zhang R, Guan Y, Chang L, Yi X. Plasma PIK3CA ctDNA specific mutation detected by next generation sequencing is associated with clinical outcome in advanced breast cancer. Am J Cancer Res 2018; 8:1873-1886. [PMID: 30323979 PMCID: PMC6176180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023] Open
Abstract
Through next generation sequencing, this study evaluated the circulating tumor DNA (ctDNA) of advanced breast cancer patients to prospectively explore the relationship between specific DNA mutations and prognosis as well as therapeutic decision making. The target region covered 1021 gene totally. Clinical characteristics, treatment and outcome data were collected. We analyzed progression-free survival (PFS) from first-line therapy and overall survival (OS), and found that their endpoints were correlated with observed gene mutations. We enrolled 54 patients, with a median follow-up time of 8 years. Mutations were found in TP53, PIK3CA, and ERBB family, at 40.7%, 35.2%, and 25.9%, respectively. PIK3CA more frequently occurred in the site of 3140 A>G (p.H1047R) for 20.4% and HER2+ diseases, and it was associated with shorter median PFS and worse OS among HER2+ patients [mutant vs. wild type: 4 (range 2-9) vs. 8 (range 2-22) months, P=0.006], and [mutant vs. wild type: 29 (range 12-74) vs. 64 (range 20-96) months, P=0.043], respectively. The patients with mutations in TP53 had shorter OS (median 64 vs. 121 months, P=0.006). Multivariate analysis for HER2+ disease demonstrated that the PIK3CA p.H1047R mutation was the only factor associated with shorter PFS (P=0.025); while the receiver operating characteristic (ROC) analysis produces an area under the curve (AUC) of 0.789. The ctDNA analysis, found PIK3CA p.H1047R mutation was more frequent in HER2+ disease and associated with worse OS. It was also the only mutation associated with shorter PFS through a multivariate analysis of HER2+ patients who were treated with trastuzumab, suggesting trastuzumab had lower activity in these patients. The presence of a TP53 mutation was associated with worse OS.
Collapse
Affiliation(s)
- Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | - Yaping Xu
- Geneplus-BeijingBeijing 102206, China
| | - Fangyuan Zhao
- University of Chicago, Division of The Social Sciences1130E, 59th Street, Chicago 60637, IL, USA
| | - Guohong Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | - Hope S Rugo
- Department of Medicine, University of California at San Francisco, Helen Diller Family Comprehensive Cancer CenterSan Francisco, USA
| | - Yan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Branch of Medical Statistics, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | - Ling Yang
- Geneplus-BeijingBeijing 102206, China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | - Bin Shao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | | | - Yaxin Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | - Ran Ran
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | - Ruyan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute52 Fucheng Rd, Beijing 100142, China
| | | | | | - Xin Yi
- Geneplus-BeijingBeijing 102206, China
| |
Collapse
|
50
|
Kodahl AR, Ehmsen S, Pallisgaard N, Jylling AMB, Jensen JD, Lænkholm A, Knoop AS, Ditzel HJ. Correlation between circulating cell-free PIK3CA tumor DNA levels and treatment response in patients with PIK3CA-mutated metastatic breast cancer. Mol Oncol 2018; 12:925-935. [PMID: 29689598 PMCID: PMC5983134 DOI: 10.1002/1878-0261.12305] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/31/2018] [Accepted: 04/06/2018] [Indexed: 01/14/2023] Open
Abstract
Liquid biopsies focusing on the analysis of cell-free circulating tumor DNA (ctDNA) may have important clinical implications for personalized medicine, including early detection of cancer, therapeutic guidance, and monitoring of recurrence. Mutations in the oncogene, PIK3CA, are frequently observed in breast cancer and have been suggested as a predictive biomarker for PI3K-selective inhibitor treatment. In this study, we analyzed the presence of PIK3CA mutations in formalin-fixed, paraffin-embedded, metastatic tissue and corresponding ctDNA from serum of patients with advanced breast cancer using a highly sensitive, optimized droplet digital PCR (ddPCR) assay. We found 83% of patients with PIK3CA mutation in the metastatic tumor tissue also had detectable PIK3CA mutations in serum ctDNA. Patients lacking the PIK3CA mutation in corresponding serum ctDNA all had nonvisceral metastatic disease. Four patients with detectable PIK3CA-mutated ctDNA were followed with an additional serum sample during oncological treatment. In all cases, changes in PIK3CA ctDNA level correlated with treatment response. Our results showed high concordance between detection of PIK3CA mutations in tumor tissue and in corresponding serum ctDNA and suggest that serum samples from patients with advanced breast cancer and ddPCR may be used for PIK3CA mutation status assessment to complement imaging techniques as an early marker of treatment response.
Collapse
Affiliation(s)
| | - Sidse Ehmsen
- Department of Cancer and InflammationInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | | | | | | | | | - Ann S. Knoop
- Department of OncologyRigshospitaletCopenhagenDenmark
| | - Henrik J. Ditzel
- Department of OncologyOdense University HospitalDenmark
- Department of Cancer and InflammationInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Academy of Geriatric Cancer Research (AgeCare)Odense University HospitalDenmark
| |
Collapse
|