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Takahashi N, Pongor L, Agrawal SP, Shtumpf M, Rajapakse VN, Shafiei A, Schultz CW, Kim S, Roame D, Carter P, Vilimas R, Nichols S, Desai P, Figg WD, Bagheri M, Teif VB, Thomas A. Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597054. [PMID: 38895436 PMCID: PMC11185519 DOI: 10.1101/2024.06.02.597054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Profiling circulating cell-free DNA (cfDNA) has become a fundamental practice in cancer medicine, but the effectiveness of cfDNA at elucidating tumor-derived molecular features has not been systematically compared to standard single-lesion tumor biopsies in prospective cohorts of patients. The use of plasma instead of tissue to guide therapy is particularly attractive for patients with small cell lung cancer (SCLC), a cancer whose aggressive clinical course making it exceedingly challenging to obtain tumor biopsies. Methods Here, a prospective cohort of 49 plasma samples obtained before, during, and after treatment from 20 patients with recurrent SCLC, we study cfDNA low pass whole genome (0.1X coverage) and exome (130X) sequencing in comparison with time-point matched tumor, characterized using exome and transcriptome sequencing. Results Direct comparison of cfDNA versus tumor biopsy reveals that cfDNA not only mirrors the mutation and copy number landscape of the corresponding tumor but also identifies clinically relevant resistance mechanisms and cancer driver alterations not found in matched tumor biopsies. Longitudinal cfDNA analysis reliably tracks tumor response, progression, and clonal evolution. Genomic sequencing coverage of plasma DNA fragments around transcription start sites shows distinct treatment-related changes and captures the expression of key transcription factors such as NEUROD1 and REST in the corresponding SCLC tumors, allowing prediction of SCLC neuroendocrine phenotypes and treatment responses. Conclusions These findings have important implications for non-invasive stratification and subtype-specific therapies for patients with SCLC, now treated as a single disease.
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Affiliation(s)
- Nobuyuki Takahashi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
- Medical Oncology Branch, Center Hospital, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Medical Oncology, National Cancer Center East Hospital, Kashiwa, Japan
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | | | - Mariya Shtumpf
- School of Life Sciences, University of Essex, Colchester, UK
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Ahmad Shafiei
- Department of Radiology and Imaging Sciences, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Christopher W Schultz
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Sehyun Kim
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Diana Roame
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Paula Carter
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Rasa Vilimas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Samantha Nichols
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Parth Desai
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - William Douglas Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Mohammad Bagheri
- Department of Radiology and Imaging Sciences, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Colchester, UK
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, USA
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Fűr GM, Nemes K, Magó É, Benő AÁ, Topolcsányi P, Moldvay J, Pongor LS. Applied models and molecular characteristics of small cell lung cancer. Pathol Oncol Res 2024; 30:1611743. [PMID: 38711976 PMCID: PMC11070512 DOI: 10.3389/pore.2024.1611743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024]
Abstract
Small cell lung cancer (SCLC) is a highly aggressive type of cancer frequently diagnosed with metastatic spread, rendering it surgically unresectable for the majority of patients. Although initial responses to platinum-based therapies are often observed, SCLC invariably relapses within months, frequently developing drug-resistance ultimately contributing to short overall survival rates. Recently, SCLC research aimed to elucidate the dynamic changes in the genetic and epigenetic landscape. These have revealed distinct subtypes of SCLC, each characterized by unique molecular signatures. The recent understanding of the molecular heterogeneity of SCLC has opened up potential avenues for precision medicine, enabling the development of targeted therapeutic strategies. In this review, we delve into the applied models and computational approaches that have been instrumental in the identification of promising drug candidates. We also explore the emerging molecular diagnostic tools that hold the potential to transform clinical practice and patient care.
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Affiliation(s)
- Gabriella Mihalekné Fűr
- Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
| | - Kolos Nemes
- Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
| | - Éva Magó
- Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
- Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
| | - Alexandra Á. Benő
- Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
| | - Petronella Topolcsányi
- Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
| | - Judit Moldvay
- Department of Pulmonology, Szeged University Szent-Gyorgyi Albert Medical School, Szeged, Hungary
- 1st Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Lőrinc S. Pongor
- Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, Hungary
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Park S, Kang JK, Lee N, Lee SH, Kim HP, Kim SY, Kim TY, Kim H, Jung HA, Sun JM, Ahn JS, Ahn MJ, Park K. Predicting disease recurrence in limited disease small cell lung cancer using cell-free DNA-based mutation and fragmentome analyses. Transl Lung Cancer Res 2024; 13:280-291. [PMID: 38496698 PMCID: PMC10938094 DOI: 10.21037/tlcr-23-479] [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: 07/25/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024]
Abstract
Background Limited disease (LD) small cell lung cancer (SCLC) treated with definitive concurrent chemoradiotherapy (CCRT) potentially experience disease recurrence. We investigated the feasibility of circulating-tumor DNA (ctDNA)-based genomic and fragmentome analyses to assess the risk of recurrence. Methods Targeted sequencing was conducted using pre-treatment and on-treatment blood samples from definitive CCRT-treated patients with LD-SCLC (n=50). Based on 12-month recurrence-free survival (RFS), patients were categorized into persistent-response (PeR, n=29) and non-PeR (n=21) groups. Fragmentome analysis was conducted using ctDNA fragments of different lengths: P1 (100-155 bp) and P2 (160-180 bp). Results Patients with TP53 (n=15) and RB1 (n=11) mutation in on-treatment samples demonstrated significantly shorter RFS than patients with wild-type (WT) (P=0.05, P=0.0014, respectively). Fragmentome analysis of all available on-treatment samples (n=26) revealed that the non-PeR group (n=10) had a significantly higher P1 range (P=0.003) and lower P2 range (P=0.002). The areas under the curves for P1, P2, and the fragmentation ratio (P1/P2) in distinguishing the PeR and non-PeR were 0.850, 0.725, and 0.900, respectively. Using optimal cut-off, longer RFSs were found with the low-fragmentation-ratio group than with the high-fragmentation-ratio group (not reached vs. 7.6 months, P=0.002). Patients with both WT RB1 and a low-fragmentation-ratio (n=10) showed better outcomes than patients with both mutated RB1 and a high-fragmentation-ratio (n=10; hazard ratio, 7.55; 95% confidence interval: 2.14-26.6; P=0.002). Conclusions RB1 mutations and high fragmentation ratios correlated with early disease recurrence. Analyzing ctDNA could help in predicting early treatment failure and making clinical decisions for high-risk patients.
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Affiliation(s)
- Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | - Naeun Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | | | | | | | - Hyemin Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyun Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Mu Sun
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Keunchil Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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5
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Mierke CT. Phenotypic Heterogeneity, Bidirectionality, Universal Cues, Plasticity, Mechanics, and the Tumor Microenvironment Drive Cancer Metastasis. Biomolecules 2024; 14:184. [PMID: 38397421 PMCID: PMC10887446 DOI: 10.3390/biom14020184] [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: 12/25/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Tumor diseases become a huge problem when they embark on a path that advances to malignancy, such as the process of metastasis. Cancer metastasis has been thoroughly investigated from a biological perspective in the past, whereas it has still been less explored from a physical perspective. Until now, the intraluminal pathway of cancer metastasis has received the most attention, while the interaction of cancer cells with macrophages has received little attention. Apart from the biochemical characteristics, tumor treatments also rely on the tumor microenvironment, which is recognized to be immunosuppressive and, as has recently been found, mechanically stimulates cancer cells and thus alters their functions. The review article highlights the interaction of cancer cells with other cells in the vascular metastatic route and discusses the impact of this intercellular interplay on the mechanical characteristics and subsequently on the functionality of cancer cells. For instance, macrophages can guide cancer cells on their intravascular route of cancer metastasis, whereby they can help to circumvent the adverse conditions within blood or lymphatic vessels. Macrophages induce microchannel tunneling that can possibly avoid mechanical forces during extra- and intravasation and reduce the forces within the vascular lumen due to vascular flow. The review article highlights the vascular route of cancer metastasis and discusses the key players in this traditional route. Moreover, the effects of flows during the process of metastasis are presented, and the effects of the microenvironment, such as mechanical influences, are characterized. Finally, the increased knowledge of cancer metastasis opens up new perspectives for cancer treatment.
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Affiliation(s)
- Claudia Tanja Mierke
- Faculty of Physics and Earth System Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, Leipzig University, 04103 Leipzig, Germany
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6
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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Li J, Wang L, Dong Z, Song Q, Wang Z. A meta-analysis of circulating tumor DNA as a survival indicator in small cell lung cancer patients. Clin Exp Med 2023; 23:3935-3945. [PMID: 37027065 DOI: 10.1007/s10238-023-01052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/17/2023] [Indexed: 04/08/2023]
Abstract
A high level of circulating tumor DNA (ctDNA) has been linked to poor survival in patients with certain solid tumors. In spite of this, it is still unclear whether ctDNA is associated with poor survival in small cell lung cancer (SCLC). To investigate the above association, we conducted a systematic review and meta-analysis. PubMed, Web of Science, Cochrane's Library, and Embase were searched for relevant cohort studies from the inception of the databases to November 28, 2022. Data collection, literature search, and statistical analysis were carried out independently by two authors. To account for heterogeneity, we used a random-effects model. In this meta-analysis, 391 patients with SCLC were identified, and the data were pooled from nine observational studies and followed for 11.4 to 25.0 months. A high ctDNA was associated with worse overall survival (OS, risk ratio [RR] 2.50, 95% confidence interval [CI]1.85 to 3.38, p < 0.001; I2 = 25%) and progression-free survival (PFS, RR 2.33, 95% CI 1.48 to 3.64, p < 0.001, I2 = 42%). Subgroup analyses retrieved consistent results in prospective and retrospective studies, in studies with ctDNA measured with polymerase chain reaction or next-generation sequencing, and in studies analyzed with univariate or multivariate regression models. Studies suggest that ctDNA may be an important factor in predicting poor OS and PFS in SCLC patients.
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Affiliation(s)
- Jie Li
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Liqun Wang
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhouhuan Dong
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Qi Song
- Department of Oncology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Zhanbo Wang
- Department of Pathology, The First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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Kwon HJ, Park UH, Goh CJ, Park D, Lim YG, Lee IK, Do WJ, Lee KJ, Kim H, Yun SY, Joo J, Min NY, Lee S, Um SW, Lee MS. Enhancing Lung Cancer Classification through Integration of Liquid Biopsy Multi-Omics Data with Machine Learning Techniques. Cancers (Basel) 2023; 15:4556. [PMID: 37760525 PMCID: PMC10526503 DOI: 10.3390/cancers15184556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Early detection of lung cancer is crucial for patient survival and treatment. Recent advancements in next-generation sequencing (NGS) analysis enable cell-free DNA (cfDNA) liquid biopsy to detect changes, like chromosomal rearrangements, somatic mutations, and copy number variations (CNVs), in cancer. Machine learning (ML) analysis using cancer markers is a highly promising tool for identifying patterns and anomalies in cancers, making the development of ML-based analysis methods essential. We collected blood samples from 92 lung cancer patients and 80 healthy individuals to analyze the distinction between them. The detection of lung cancer markers Cyfra21 and carcinoembryonic antigen (CEA) in blood revealed significant differences between patients and controls. We performed machine learning analysis to obtain AUC values via Adaptive Boosting (AdaBoost), Multi-Layer Perceptron (MLP), and Logistic Regression (LR) using cancer markers, cfDNA concentrations, and CNV screening. Furthermore, combining the analysis of all multi-omics data for ML showed higher AUC values compared with analyzing each element separately, suggesting the potential for a highly accurate diagnosis of cancer. Overall, our results from ML analysis using multi-omics data obtained from blood demonstrate a remarkable ability of the model to distinguish between lung cancer and healthy individuals, highlighting the potential for a diagnostic model against lung cancer.
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Affiliation(s)
- Hyuk-Jung Kwon
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
| | - Ui-Hyun Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Chul Jun Goh
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Dabin Park
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Yu Gyeong Lim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Isaac Kise Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
- Department of Computer Science and Engineering, Incheon National University (INU), Incheon 22012, Republic of Korea
- NGENI Foundation, San Diego, CA 92123, USA
| | - Woo-Jung Do
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Kyoung Joo Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Hyojung Kim
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Seon-Young Yun
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Joungsu Joo
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Na Young Min
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Sunghoon Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea;
| | - Min-Seob Lee
- Eone-Diagnomics Genome Center, Inc., 143, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea; (H.-J.K.); (U.-H.P.); (C.J.G.); (D.P.); (Y.G.L.); (I.K.L.); (W.-J.D.); (K.J.L.); (H.K.); (N.Y.M.)
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA 92123, USA
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9
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Ng AS, Chan DKH. Commonalities and differences in the mutational signature and somatic driver mutation landscape across solid and hollow viscus organs. Oncogene 2023; 42:2713-2724. [PMID: 37573406 PMCID: PMC10491491 DOI: 10.1038/s41388-023-02802-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Advances in sequencing have revealed a highly variegated landscape of mutational signatures and somatic driver mutations in a range of normal tissues. Normal tissues accumulate mutations at varying rates ranging from 11 per cell per year in the liver, to 1879 per cell per year in the bladder. In addition, some normal tissues are also comprised of a large proportion of cells which possess driver mutations while appearing phenotypically normal, as in the oesophagus where a majority of cells harbour driver mutations. Individual tissue proliferation and mutation rate, unique mutagenic stimuli, and local tissue architecture contribute to this highly variegated landscape which confounds the functional characterization of driver mutations found in normal tissue. In particular, our understanding of the relationship between normal tissue somatic mutations and tumour initiation or future cancer risk remains poor. Here, we describe the mutational signatures and somatic driver mutations in solid and hollow viscus organs, highlighting unique characteristics in a tissue-specific manner, while simultaneously seeking to describe commonalities which can bring forward a basic unified theory on the role of these driver mutations in tumour initiation. We discuss novel findings which can be used to inform future research in this field.
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Affiliation(s)
- Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Dedrick Kok Hong Chan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Division of Colorectal Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
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10
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Zhang C, Zhang C, Wang K, Wang H. Orchestrating smart therapeutics to achieve optimal treatment in small cell lung cancer: recent progress and future directions. J Transl Med 2023; 21:468. [PMID: 37452395 PMCID: PMC10349514 DOI: 10.1186/s12967-023-04338-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Small cell lung cancer (SCLC) is a recalcitrant malignancy with elusive mechanism of pathogenesis and dismal prognosis. Over the past decades, platinum-based chemotherapy has been the backbone treatment for SCLC. However, subsequent chemoresistance after initial effectiveness urges researchers to explore novel therapeutic targets of SCLC. Recent years have witnessed significant improvements in targeted therapy in SCLC. New molecular candidates such as Ataxia telangiectasia and RAD3-related protein (ATR), WEE1, checkpoint kinase 1 (CHK1) and poly-ADP-ribose polymerase (PARP) have shown promising therapeutic utility in SCLC. While immune checkpoint inhibitor (ICI) has emerged as an indispensable treatment modality for SCLC, approaches to boost efficacy and reduce toxicity as well as selection of reliable biomarkers for ICI in SCLC have remained elusive and warrants our further investigation. Given the increasing importance of precision medicine in SCLC, optimal subtyping of SCLC using multi-omics have gradually applied into clinical practice, which may identify more drug targets and better tailor treatment strategies to each individual patient. The present review summarizes recent progress and future directions in SCLC. In addition to the emerging new therapeutics, we also focus on the establishment of predictive model for early detection of SCLC. More importantly, we also propose a multi-dimensional model in the prognosis of SCLC to ultimately attain the goal of accurate treatment of SCLC.
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Affiliation(s)
- Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Chenxing Zhang
- Department of Nephrology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Number 440, Ji Yan Road, Jinan, China.
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11
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Sivapalan L, Iams WT, Belcaid Z, Scott SC, Niknafs N, Balan A, White JR, Kopparapu P, Cann C, Landon BV, Pereira G, Velculescu VE, Hann CL, Lovly CM, Anagnostou V. Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer. Clin Cancer Res 2023; 29:2310-2323. [PMID: 37071497 PMCID: PMC10261918 DOI: 10.1158/1078-0432.ccr-22-2242] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/27/2022] [Accepted: 02/03/2023] [Indexed: 04/19/2023]
Abstract
PURPOSE Patients with small-cell lung cancer (SCLC) have an exceptionally poor prognosis, calling for improved real-time noninvasive biomarkers of therapeutic response. EXPERIMENTAL DESIGN We performed targeted error-correction sequencing on 171 serial plasmas and matched white blood cell (WBC) DNA from 33 patients with metastatic SCLC who received treatment with chemotherapy (n = 16) or immunotherapy-containing (n = 17) regimens. Tumor-derived sequence alterations and plasma aneuploidy were evaluated serially and combined to assess changes in total cell-free tumor load (cfTL). Longitudinal dynamic changes in cfTL were monitored to determine circulating cell-free tumor DNA (ctDNA) molecular response during therapy. RESULTS Combined tiered analyses of tumor-derived sequence alterations and plasma aneuploidy allowed for the assessment of ctDNA molecular response in all patients. Patients classified as molecular responders (n = 9) displayed sustained elimination of cfTL to undetectable levels. For 14 patients, we observed initial molecular responses, followed by ctDNA recrudescence. A subset of patients (n = 10) displayed a clear pattern of molecular progression, with persistence of cfTL across all time points. Molecular responses captured the therapeutic effect and long-term clinical outcomes in a more accurate and rapid manner compared with radiographic imaging. Patients with sustained molecular responses had longer overall (log-rank P = 0.0006) and progression-free (log-rank P < 0.0001) survival, with molecular responses detected on average 4 weeks earlier than imaging. CONCLUSIONS ctDNA analyses provide a precise approach for the assessment of early on-therapy molecular responses and have important implications for the management of patients with SCLC, including the development of improved strategies for real-time tumor burden monitoring. See related commentary by Pellini and Chaudhuri, p. 2176.
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Affiliation(s)
- Lavanya Sivapalan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wade T. Iams
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Zineb Belcaid
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan C. Scott
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R. White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Prasad Kopparapu
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Christopher Cann
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Blair V. Landon
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Gavin Pereira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victor E. Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine L. Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine M. Lovly
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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12
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Assi T, Khoury R, Ibrahim R, Baz M, Ibrahim T, LE Cesne A. Overview of the role of liquid biopsy in cancer management. Transl Oncol 2023; 34:101702. [PMID: 37267803 DOI: 10.1016/j.tranon.2023.101702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
With the emergence of novel targeted therapeutic options in early-stage and advanced-stage malignancies, researchers have shifted their focus on developing personalized treatment plans through molecular profiling. Circulating tumor DNA (ctDNA) is a cell-free DNA (ctDNA) fragment, originating from tumor cells, and circulating in the bloodstream as well as biological fluids. Over the past decade, many techniques were developed for liquid biopsies through next-generation sequencing. This alternative non-invasive biopsy offers several advantages in various types of tumors over traditional tissue biopsy. The process of liquid biopsy is considered minimally invasive and therefore easily repeatable when needed, providing a more dynamic analysis of the tumor cells. Moreover, it has an advantage in patients with tumors that are not candidates for tissue sampling. Besides, it offers a deeper understanding of tumor burden as well as treatment response, thereby enhancing the detection of minimal residual disease and therapeutic guidance for personalized medicine. Despite its many advantages, ctDNA and liquid biopsy do have some limitations. This paper discusses the basis of ctDNA and the current data available on the subject, as well as its clinical utility. We also reflect on the limitations of using ctDNA in addition to its future perspectives in clinical oncology and precision medicine.
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Affiliation(s)
- Tarek Assi
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Rita Khoury
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Rebecca Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Maria Baz
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Tony Ibrahim
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
| | - Axel LE Cesne
- Division of International Patients Care, Gustave Roussy Cancer Campus, Villejuif, France
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13
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Khan SR, Scheffler M, Soomar SM, Rashid YA, Moosajee M, Ahmad A, Raza A, Uddin S. Role of circulating-tumor DNA in the early-stage non-small cell lung carcinoma as a predictive biomarker. Pathol Res Pract 2023; 245:154455. [PMID: 37054576 DOI: 10.1016/j.prp.2023.154455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
Lung cancer is one of the most common solid malignancies. Tissue biopsy is the standard method for accurately diagnosing lung and many other malignancies over decades. However, molecular profiling of tumors leads to establishing a new horizon in the field of precision medicine, which has now entered the mainstream in clinical practice. In this context, a minimally invasive complementary method has been proposed as a liquid biopsy (LB) which is a blood-based test that is gaining popularity as it provides the opportunity to test genotypes in a unique, less invasive manner. Circulating tumor cells (CTC) captivating the Circulating-tumor DNA (Ct-DNA) are often present in the blood of lung cancer patients and are the fundamental concept behind LB. There are multiple clinical uses of Ct-DNA, including its role in prognostic and therapeutic purposes. The treatment of lung cancer has drastically evolved over time. Therefore, this review article mainly focuses on the current literature on circulating tumor DNA and its clinical implications and future goals in non-small cell lung cancer.
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Affiliation(s)
- Saqib Raza Khan
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan.
| | - Matthias Scheffler
- Internal Medicine Department, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Yasmin Abdul Rashid
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Munira Moosajee
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Aamir Ahmad
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar.
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14
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Kanesvaran R, Chia PL, Chiong E, Chua MLK, Ngo NT, Ow S, Sim HG, Tan MH, Tay KH, Wong ASC, Wong SW, Tan PH. An approach to genetic testing in patients with metastatic castration-resistant prostate cancer in Singapore. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2023; 52:135-148. [PMID: 38904491 DOI: 10.47102/annals-acadmedsg.2022372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Introduction There has been a rapid evolution in the treatment strategies for metastatic castration-resistant prostate cancer (mCRPC) following the identification of targetable mutations, making genetic testing essential for patient selection. Although several international guidelines recommend genetic testing for patients with mCRPC, there is a lack of locally endorsed clinical practice guidelines in Singapore. Method A multidisciplinary specialist panel with representation from medical and radiation oncology, urology, pathology, interventional radiology, and medical genetics discussed the challenges associated with patient selection, genetic counselling and sample processing in mCRPC. Results A clinical model for incorporating genetic testing into routine clinical practice in Singapore was formulated. Tumour testing with an assay that is able to detect both somatic and germline mutations should be utilised. The panel also recommended the "mainstreaming" approach for genetic counselling in which pre-test counselling is conducted by the managing clinician and post-test discussion with a genetic counsellor, to alleviate the bottlenecks at genetic counselling stage in Singapore. The need for training of clinicians to provide pre-test genetic counselling and educating the laboratory personnel for appropriate sample processing that facilitates downstream genetic testing was recognised. Molecular tumour boards and multidisciplinary discussions are recommended to guide therapeutic decisions in mCRPC. The panel also highlighted the issue of reimbursement for genetic testing to reduce patient-borne costs and increase the reach of genetic testing among this patient population. Conclusion This article aims to provide strategic and implementable recommendations to overcome the challenges in genetic testing for patients with mCRPC in Singapore.
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Affiliation(s)
| | - Puey Ling Chia
- Department of Medical Oncology, Tan Tock Seng Hospital, Singapore
| | - Edmund Chiong
- Department of Urology, National University Hospital, Singapore
- Department of Surgery, National University of Singapore, Singapore
| | | | - Nye Thane Ngo
- Division of Pathology, Singapore General Hospital, Singapore
| | - Samuel Ow
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - Hong Gee Sim
- Ravenna Urology Clinic, Gleneagles Medical Centre, Singapore
| | | | - Kiang Hiong Tay
- Department of Vascular and Interventional Radiation, Singapore General Hospital, Singapore
| | | | | | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
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15
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A nucleolin-activated polyvalent aptamer nanoprobe for the detection of cancer cells. Anal Bioanal Chem 2023; 415:2217-2226. [PMID: 36864310 DOI: 10.1007/s00216-023-04629-3] [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: 01/07/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Sensitive detection of cancer cells plays a critical role in early cancer diagnosis. Nucleolin, overexpressed on the surface of cancer cells, is regarded as a candidate biomarker for cancer diagnosis. Thus, cancer cells can be detected through the detection of membrane nucleolin. Herein, we designed a nucleolin-activated polyvalent aptamer nanoprobe (PAN) to detect cancer cells. In brief, a long single-stranded DNA with many repeated sequences was synthesized through rolling circle amplification (RCA). Then the RCA product acted as a scaffold chain to combine with multiple AS1411 sequences, which was doubly modified with fluorophore and quenching group, respectively. The fluorescence of PAN was initially quenched. Upon binding to target protein, the conformation of PAN changed, leading to the recovery of fluorescence. The fluorescence signal of cancer cells treated with PAN was much brighter compared with that of monovalent aptamer nanoprobes (MAN) at the same concentration. Furthermore, the binding affinity of PAN to B16 cells was proved to be 30 times higher than that of MAN by calculating the dissociation constants. The results indicated that PAN could specifically detect target cells, and this design concept has potential to become promising in cancer diagnosis.
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16
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Lawrence P, Chabane M, Abrouk L, Thiesson A, Berthé D, Diarra AB, Bengaly K, Traoré B, Kassogué D, Durand G, Voegele C, Le Calvez-Kelm F, Steenkeste N, Hainaut P, Kouriba B, Gormally E. First Molecular Characterization of Chronic Hepatitis B Carriers in Timbuktu, Mali. Diagnostics (Basel) 2023; 13:375. [PMID: 36766478 PMCID: PMC9913942 DOI: 10.3390/diagnostics13030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
In Mali, hepatocellular carcinoma (HCC) is the third and sixth most common cancer in men and women, respectively. Mali comprises several distinct climato-ecological zones. Most studies to date have been conducted in the sub-Sahelian zone of southern Mali, including the capital city Bamako. In this part of the country, the main risk factors for HCC are chronic hepatitis B virus (HBV) carriage and dietary exposure to aflatoxins, a well-known hepatocarcinogen. Data are scarce for other ecological zones, but our preliminary data from 721 blood donors in the area of Timbuktu, presented in this study, suggest that chronic HBV carriage is also endemic in the northern Saharan zone of Mali. For further study, 29 healthy HBV chronic carrier volunteers were recruited from the blood transfusion center in Timbuktu. Successful viral genotyping in 20 volunteers revealed HBV genotype E in 13 cases and D in 7 cases, suggesting that this geographical and anthropological transition zone may also represent a transition zone between HBV genotypes that dominate sub-Saharan and northern Africa, respectively. Sequencing of circulating cell-free plasma DNA (cfDNA) from donors did not reveal the presence of the TP53 R249S mutation in these donors, a marker of dietary exposure to aflatoxins in sub-Saharan Africa. These results suggest that the geo-epidemiological distribution of the risk factors for HCC is not uniform across Mali, but is dependent upon climatic, socioeconomic and anthropological factors that might have an impact on patterns of chronic liver disease and cancer.
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Affiliation(s)
- Philip Lawrence
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
| | | | - Lucie Abrouk
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
| | - Adrien Thiesson
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
| | | | - Amadou B. Diarra
- Centre National de Transfusion Sanguine (CNTS, National Blood Bank), Bamako BPE1520, Mali
| | - Karim Bengaly
- Centre d’Infectiologie Charles Mérieux, Bamako BPE2283, Mali
| | - Brehima Traoré
- Centre d’Infectiologie Charles Mérieux, Bamako BPE2283, Mali
| | | | - Geoffroy Durand
- International Agency for Research on Cancer, 69008 Lyon, France
| | | | | | | | - Pierre Hainaut
- Institute of Advanced Biosciences, INSERM U1209, CNRS UMR 5309, Université Grenoble Alpes, 38700 La Tronche, France
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux, Bamako BPE2283, Mali
| | - Emmanuelle Gormally
- CONFLUENCE: Sciences et Humanités Confluence (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
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17
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Lastwika KJ, Kunihiro A, Solan JL, Zhang Y, Taverne LR, Shelley D, Rho JH, Randolph TW, Li CI, Grogan EL, Massion PP, Fitzpatrick AL, MacPherson D, Houghton AM, Lampe PD. Posttranslational modifications induce autoantibodies with risk prediction capability in patients with small cell lung cancer. Sci Transl Med 2023; 15:eadd8469. [PMID: 36630482 PMCID: PMC10117289 DOI: 10.1126/scitranslmed.add8469] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Small cell lung cancer (SCLC) elicits the generation of autoantibodies that result in unique paraneoplastic neurological syndromes. The mechanistic basis for the formation of such autoantibodies is largely unknown but is key to understanding their etiology. We developed a high-dimensional technique that enables detection of autoantibodies in complex with native antigens directly from patient plasma. Here, we used our platform to screen 1009 human plasma samples for 3600 autoantibody-antigen complexes, finding that plasma from patients with SCLC harbors, on average, fourfold higher disease-specific autoantibody signals compared with plasma from patients with other cancers. Across three independent SCLC cohorts, we identified a set of common but previously unknown autoantibodies that are produced in response to both intracellular and extracellular tumor antigens. We further characterized several disease-specific posttranslational modifications within extracellular proteins targeted by these autoantibodies, including citrullination, isoaspartylation, and cancer-specific glycosylation. Because most patients with SCLC have metastatic disease at diagnosis, we queried whether these autoantibodies could be used for SCLC early detection. We created a risk prediction model using five autoantibodies with an average area under the curve of 0.84 for the three cohorts that improved to 0.96 by incorporating cigarette smoke consumption in pack years. Together, our findings provide an innovative approach to identify circulating autoantibodies in SCLC with mechanistic insight into disease-specific immunogenicity and clinical utility.
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Affiliation(s)
- Kristin J Lastwika
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew Kunihiro
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Joell L Solan
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yuzheng Zhang
- Department of Biostatistics, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lydia R Taverne
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Shelley
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jung-Hyun Rho
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy W Randolph
- Department of Biostatistics, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Christopher I Li
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Eric L Grogan
- Departments of Surgery, Medicine Radiology, and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Pierre P Massion
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA
| | - Annette L Fitzpatrick
- Department of Family Medicine, University of Washington, Seattle, WA 98195, USA
- Departments of Family Medicine, Epidemiology, and Global Health, University of Washington, Seattle, WA 98195, USA
| | - David MacPherson
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - A McGarry Houghton
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Paul D Lampe
- Translational Research Program, Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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18
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Pisareva E, Roch B, Sanchez C, Pastor B, Mirandola A, Diab-Assaf M, Mazard T, Prévostel C, Al Amir Dache Z, Thierry AR. Comparison of the structures and topologies of plasma extracted circulating nuclear and mitochondrial cell-free DNA. Front Genet 2023; 14:1104732. [PMID: 37152979 PMCID: PMC10158822 DOI: 10.3389/fgene.2023.1104732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: The function, origin and structural features of circulating nuclear DNA (cir-nDNA) and mitochondrial DNA (cir-mtDNA) are poorly known, even though they have been investigated in numerous clinical studies, and are involved in a number of routine clinical applications. Based on our previous report disproving the conventional plasma isolation used for cirDNA analysis, this work enables a direct topological comparison of the circulating structures associated with nuclear DNA and mitochondrial cell-free DNA. Materials and methods: We used a Q-PCR and low-pass whole genome sequencing (LP-WGS) combination approach of cir-nDNA and cir-mtDNA, extracted using a procedure that eliminates platelet activation during the plasma isolation process to prevent mitochondria release in the extracellular milieu. Various physical procedures, such as filtration and differential centrifugation, were employed to infer their circulating structures. Results: DSP-S cir-mtDNA mean size profiles distributed on a slightly shorter range than SSP-S. SSP-S detected 40-fold more low-sized cir-mtDNA fragments (<90 bp/nt) and three-fold less long-sized fragments (>200 bp/nt) than DSP-S. The ratio of the fragment number below 90 bp over the fragment number above 200 bp was very homogenous among both DSP-S and SSP-S profiles, being 134-fold lower with DSP-S than with SSP-S. Cir-mtDNA and cir-nDNA DSP-S and SSP-S mean size profiles of healthy individuals ranged in different intervals with periodic sub-peaks only detectable with cir-nDNA. The very low amount of cir-mtDNA fragments of short size observed suggested that most of the cir-mtDNA is poorly fragmented and appearing longer than ∼1,000 bp, the readout limit of this LP-WGS method. Data suggested that cir-nDNA is, among DNA extracted in plasma, associated with ∼8.6% of large structures (apoptotic bodies, large extracellular vesicles (EVs), cell debris…), ∼27.7% in chromatin and small EVs and ∼63.7% mainly in oligo- and mono-nucleosomes. By contrast, cir-mtDNA appeared to be preponderantly (75.7%) associated with extracellular mitochondria, either in its free form or with large EVs; to a lesser extent, it was also associated with other structures: small EVs (∼18.4%), and exosomes or protein complexes (∼5.9%). Conclusion: This is the first study to directly compare the structural features of cir-nDNA and cir-mtDNA. The significant differences revealed between both are due to the DNA topological structure contained in the nucleus (chromatin) and in the mitochondria (plasmid) that determine their biological stability in blood. Although cir-nDNA and cir-mtDNA are principally associated with mono-nucleosomes and cell-free mitochondria, our study highlights the diversity of the circulating structures associated with cell-free DNA. They consequently have different pharmacokinetics as well as physiological functions. Thus, any accurate evaluation of their biological or diagnostic individual properties must relies on appropriate pre-analytics, and optimally on the isolation or enrichment of one category of their cirDNA associated structures.
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Affiliation(s)
- Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Benoit Roch
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
- Thoracic Oncology Unit, Arnaud De Villeneuve Hospital, University Hospital of Montpellier, Montpellier, France
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Alexia Mirandola
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Mona Diab-Assaf
- Faculty of Sciences II, Lebanese University Fanar, Beirut, Lebanon
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Corinne Prévostel
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Alain R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, France
- *Correspondence: Alain R. Thierry,
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19
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Wang Q, Gümüş ZH, Colarossi C, Memeo L, Wang X, Kong CY, Boffetta P. SCLC: Epidemiology, Risk Factors, Genetic Susceptibility, Molecular Pathology, Screening, and Early Detection. J Thorac Oncol 2023; 18:31-46. [PMID: 36243387 PMCID: PMC10797993 DOI: 10.1016/j.jtho.2022.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022]
Abstract
We review research regarding the epidemiology, risk factors, genetic susceptibility, molecular pathology, and early detection of SCLC, a deadly tumor that accounts for 14% of lung cancers. We first summarize the changing incidences of SCLC globally and in the United States among males and females. We then review the established risk factor (i.e., tobacco smoking) and suspected nonsmoking-related risk factors for SCLC, and emphasize the importance of continued effort in tobacco control worldwide. Review of genetic susceptibility and molecular pathology suggests different molecular pathways in SCLC development compared with other types of lung cancer. Last, we comment on the limited utility of low-dose computed tomography screening in SCLC and on several promising blood-based molecular biomarkers as potential tools in SCLC early detection.
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Affiliation(s)
- Qian Wang
- University Hospitals Seidman Cancer Center, Cleveland, Ohio.
| | - Zeynep H Gümüş
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Thoracic Oncology, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Cristina Colarossi
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, Catania, Italy
| | - Lorenzo Memeo
- Pathology Unit, Department of Experimental Oncology, Mediterranean Institute of Oncology, Catania, Italy
| | - Xintong Wang
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chung Yin Kong
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paolo Boffetta
- Department of Family, Population & Preventive Medicine, Stony Brook University, Stony Brook, New York; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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20
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Vishwakarma SK, Fathima N, Tiwari SK, Khan AA. Simultaneous extraction and quantification of circulating mitochondrial and nuclear DNA using a single plasma sample to predict specific molecular diagnostic implications. Mitochondrion 2023; 68:114-124. [PMID: 36509340 DOI: 10.1016/j.mito.2022.12.003] [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: 01/24/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The magnitude of variations in the level of circulating mitochondrial (cir-mtDNA) and nuclear DNA (cir-ncDNA) in different diseases has indicated the need for investigating a discriminative approach for evaluating their diagnostic significance. This study reports a typical in-house process for extracting both types of cir-DNAs from a single plasma sample and assessed their usefulness in discriminating type 2 diabetes mellitus patients from healthy individuals to eliminate the prevailing dispute about their discriminative role and improve their diagnostic value. This approach offers a more precise and valuable tool for distinguishing the impact of cir-mtDNA from cir-ncDNA in diagnostic implications.
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Affiliation(s)
- Sandeep Kumar Vishwakarma
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Kanchanbagh, Hyderabad, Telangana, India.
| | - Nusrath Fathima
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Kanchanbagh, Hyderabad, Telangana, India
| | - Santosh K Tiwari
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Kanchanbagh, Hyderabad, Telangana, India
| | - Aleem Ahmed Khan
- Central Laboratory for Stem Cell Research and Translational Medicine, Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences, Kanchanbagh, Hyderabad, Telangana, India
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21
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Somatic variation in normal tissues: friend or foe of cancer early detection? Ann Oncol 2022; 33:1239-1249. [PMID: 36162751 DOI: 10.1016/j.annonc.2022.09.156] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/03/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Seemingly normal tissues progressively become populated by mutant clones over time. Most of these clones bear mutations in well-known cancer genes but only rarely do they transform into cancer. This poses questions on what triggers cancer initiation and what implications somatic variation has for cancer early detection. DESIGN We analysed recent mutational screens of healthy and cancer-free diseased tissues to compare somatic drivers and the causes of somatic variation across tissues. We then reviewed the mechanisms of clonal expansion and their relationships with age and diseases other than cancer. We finally discussed the relevance of somatic variation for cancer initiation and how it can help or hinder cancer detection and prevention. RESULTS The extent of somatic variation is highly variable across tissues and depends on intrinsic features, such as tissue architecture and turnover, as well as the exposure to endogenous and exogenous insults. Most somatic mutations driving clonal expansion are tissue-specific and inactivate tumor suppressor genes involved in chromatin modification and cell growth signaling. Some of these genes are more frequently mutated in normal tissues than cancer, indicating a context-dependent cancer promoting or protective role. Mutant clones can persist over a long time or disappear rapidly, suggesting that their fitness depends on the dynamic equilibrium with the environment. The disruption of this equilibrium is likely responsible for their transformation into malignant clones and knowing what triggers this process is key for cancer prevention and early detection. Somatic variation should be considered in liquid biopsy, where it may contribute cancer-independent mutations, and in the identification of cancer drivers, since not all mutated genes favoring clonal expansion also drive tumorigenesis. CONCLUSIONS Somatic variation and the factors governing homeostasis of normal tissues should be taken into account when devising strategies for cancer prevention and early detection.
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22
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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[Research Progress on the Application of Liquid Biopsy in the Diagnosis
and Treatment of Small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:609-614. [PMID: 36002198 PMCID: PMC9411954 DOI: 10.3779/j.issn.1009-3419.2022.101.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Small cell lung cancer (SCLC) is a malignant tumor with strong invasiveness and high mortality. It has the characteristics of easy metastasis, fast growth, high degree of malignancy and strong invasiveness. The prognosis of patients is generally poor. The current clinical diagnosis of SCLC is mainly based on tissue biopsy, which is invasive, long cycle time and high cost. In recent years, liquid biopsy has been gradually applied because of its non-invasive, comprehensive and real-time characteristics that traditional tissue biopsy does not have. The main detection objects of liquid biopsy include circulating tumor DNA (ctDNA), circulating tumor cells (CTCs) and exosomes in peripheral blood. The application of liquid biopsy in the clinical treatment of SCLC will help clinicians to improve the detailed diagnosis of SCLC patients, as well as the timely control and response to the treatment response of patients.
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24
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Agnoletto C, Volinia S. Mitochondria dysfunction in circulating tumor cells. Front Oncol 2022; 12:947479. [PMID: 35992829 PMCID: PMC9386562 DOI: 10.3389/fonc.2022.947479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/11/2022] [Indexed: 12/16/2022] Open
Abstract
Circulating tumor cells (CTCs) represent a subset of heterogeneous cells, which, once released from a tumor site, have the potential to give rise to metastasis in secondary sites. Recent research focused on the attempt to detect and characterize these rare cells in the circulation, and advancements in defining their molecular profile have been reported in diverse tumor species, with potential implications for clinical applications. Of note, metabolic alterations, involving mitochondria, have been implicated in the metastatic process, as key determinants in the transition of tumor cells to a mesenchymal or stemness-like phenotype, in drug resistance, and in induction of apoptosis. This review aimed to briefly analyse the most recent knowledge relative to mitochondria dysfunction in CTCs, and to envision implications of altered mitochondria in CTCs for a potential utility in clinics.
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Affiliation(s)
- Chiara Agnoletto
- Rete Oncologica Veneta (ROV), Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Stefano Volinia
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Biological and Chemical Research Centre (CNBCh UW), University of Warsaw, Warsaw, Poland
- Center of New Technologies, University of Warsaw, Warsaw, Poland
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25
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Padinharayil H, Varghese J, John MC, Rajanikant GK, Wilson CM, Al-Yozbaki M, Renu K, Dewanjee S, Sanyal R, Dey A, Mukherjee AG, Wanjari UR, Gopalakrishnan AV, George A. Non-small cell lung carcinoma (NSCLC): Implications on molecular pathology and advances in early diagnostics and therapeutics. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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26
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Tsumura T, Doi K, Marusawa H. Precision Medicine of Hepatobiliary and Pancreatic Cancers: Focusing on Clinical Trial Outcomes. Cancers (Basel) 2022; 14:cancers14153674. [PMID: 35954337 PMCID: PMC9367472 DOI: 10.3390/cancers14153674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 02/04/2023] Open
Abstract
Tumor-agnostic precision medicine employing comprehensive genome profiling (CGP) and using next-generation sequencing (NGS) has been progressing recently. This review focuses on precision medicine for advanced unresectable hepatobiliary and pancreatic cancers. In this paper, for biliary tract cancer (BTC), therapies that target several regulators of cancer cell growth, including isocitrate dehydrogenase 1 (IDH1), fibroblast growth factor receptor 2 (FGFR2) fusion, proto-oncogene B-Raf (BRAF), and human epidermal growth factor receptor 2 (HER2) alterations, are reviewed. For pancreatic ductal adenocarcinoma (PDAC), therapies for Kirsten rat sarcoma virus (KRAS) gene mutation G12C, neuregulin (NRG)1, and breast cancer type 1 and 2 susceptibility (BRCA1/2), gene alterations are summarized. On the other hand, precision medicine targets were not established for hepatocellular carcinoma (HCC), although telomerase reverse transcriptase (TERT), tumor protein P53 (TP53), and Wnt/β catenin signaling alterations have been recognized as HCC driver oncogenes. Tumor-agnostic therapies for microsatellite instability-high (MSI-H) and neurotropic tyrosine receptor kinase (NTRK) fusion cancers effectively treat biliary and pancreatic cancers. Precision medicine methods developed using NGS of circulating tumor DNA (ctDNA) and utilizing a liquid biopsy technique are discussed.
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Affiliation(s)
- Takehiko Tsumura
- Department of Medical Oncology, Osaka Red Cross Hospital, Osaka 543-8555, Japan;
- Department of Gastroenterology, Osaka Red Cross Hospital, Osaka 543-8555, Japan;
- Correspondence: ; Tel.: +81-6-6774-5111; Fax: +81-6-6774-5131
| | - Keitaro Doi
- Department of Medical Oncology, Osaka Red Cross Hospital, Osaka 543-8555, Japan;
| | - Hiroyuki Marusawa
- Department of Gastroenterology, Osaka Red Cross Hospital, Osaka 543-8555, Japan;
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27
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Lodrini M, Graef J, Thole-Kliesch TM, Astrahantseff K, Sprüssel A, Grimaldi M, Peitz C, Linke RB, Hollander JF, Lankes E, Künkele A, Oevermann L, Schwabe G, Fuchs J, Szymansky A, Schulte JH, Hundsdörfer P, Eckert C, Amthauer H, Eggert A, Deubzer HE. Targeted Analysis of Cell-free Circulating Tumor DNA is Suitable for Early Relapse and Actionable Target Detection in Patients with Neuroblastoma. Clin Cancer Res 2022; 28:1809-1820. [PMID: 35247920 DOI: 10.1158/1078-0432.ccr-21-3716] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/12/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Treating refractory or relapsed neuroblastoma remains challenging. Monitoring body fluids for tumor-derived molecular information indicating minimal residual disease supports more frequent diagnostic surveillance and may have the power to detect resistant subclones before they give rise to relapses. If actionable targets are identified from liquid biopsies, targeted treatment options can be considered earlier. EXPERIMENTAL DESIGN Droplet digital PCR assays assessing MYCN and ALK copy numbers and allelic frequencies of ALK p.F1174L and ALK p.R1275Q mutations were applied to longitudinally collected liquid biopsies and matched tumor tissue samples from 31 patients with high-risk neuroblastoma. Total cell-free DNA (cfDNA) levels and marker detection were compared with data from routine clinical diagnostics. RESULTS Total cfDNA concentrations in blood plasma from patients with high-risk neuroblastoma were higher than in healthy controls and consistently correlated with neuron-specific enolase levels and lactate dehydrogenase activity but not with 123I-meta-iodobenzylguanidine scores at relapse diagnosis. Targeted cfDNA diagnostics proved superior for early relapse detection to all current diagnostics in 2 patients. Marker analysis in cfDNA indicated intratumor heterogeneity for cell clones harboring MYCN amplifications and druggable ALK alterations that were not detectable in matched tumor tissue samples in 17 patients from our cohort. Proof of concept is provided for molecular target detection in cerebrospinal fluid from patients with isolated central nervous system relapses. CONCLUSIONS Tumor-specific alterations can be identified and monitored during disease course in liquid biopsies from pediatric patients with high-risk neuroblastoma. This approach to cfDNA surveillance warrants further prospective validation and exploitation for diagnostic purposes and to guide therapeutic decisions.
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Affiliation(s)
- Marco Lodrini
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Josefine Graef
- Department of Nuclear Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa M Thole-Kliesch
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Sprüssel
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Maddalena Grimaldi
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Constantin Peitz
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Rasmus B Linke
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Jan F Hollander
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Erwin Lankes
- Department of Pediatric Endocrinology and Diabetes, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Lena Oevermann
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Georg Schwabe
- Children's Hospital, Carl-Thiem-Klinikum, Cottbus, Germany
| | - Jörg Fuchs
- Department of Pediatric Surgery and Pediatric Urology, University Children's Hospital, Eberhard-Karls-University Tuebingen, Tuebingen, Germany
| | - Annabell Szymansky
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Oncology, Helios Klinikum Berlin Buch, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Holger Amthauer
- Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hedwig E Deubzer
- Department of Pediatric Hematology and Oncology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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28
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Kapeleris J, Ebrahimi Warkiani M, Kulasinghe A, Vela I, Kenny L, Ladwa R, O'Byrne K, Punyadeera C. Clinical Applications of Circulating Tumour Cells and Circulating Tumour DNA in Non-Small Cell Lung Cancer-An Update. Front Oncol 2022; 12:859152. [PMID: 35372000 PMCID: PMC8965052 DOI: 10.3389/fonc.2022.859152] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Despite efforts to improve earlier diagnosis of non-small cell lung cancer (NSCLC), most patients present with advanced stage disease, which is often associated with poor survival outcomes with only 15% surviving for 5 years from their diagnosis. Tumour tissue biopsy is the current mainstream for cancer diagnosis and prognosis in many parts of the world. However, due to tumour heterogeneity and accessibility issues, liquid biopsy is emerging as a game changer for both cancer diagnosis and prognosis. Liquid biopsy is the analysis of tumour-derived biomarkers in body fluids, which has remarkable advantages over the use of traditional tumour biopsy. Circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA) are two main derivatives of liquid biopsy. CTC enumeration and molecular analysis enable monitoring of cancer progression, recurrence, and treatment response earlier than traditional biopsy through a minimally invasive liquid biopsy approach. CTC-derived ex-vivo cultures are essential to understanding CTC biology and their role in metastasis, provide a means for personalized drug testing, and guide treatment selection. Just like CTCs, ctDNA provides opportunity for screening, monitoring, treatment evaluation, and disease surveillance. We present an updated review highlighting the prognostic and therapeutic significance of CTCs and ctDNA in NSCLC.
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Affiliation(s)
- Joanna Kapeleris
- Saliva and Liquid Biopsy Translational Laboratory, The Centre for Biomedical Technologies, The School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
| | | | - Arutha Kulasinghe
- Translational Research Institute, Brisbane, QLD, Australia.,The School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ian Vela
- The School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre, Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Princess Alexandra Hospital, Translational Research Institute, Brisbane, QLD, Australia.,Department of Urology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Liz Kenny
- School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Central Integrated Regional Cancer Service, Queensland Health, Brisbane, QLD, Australia
| | - Rahul Ladwa
- Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia.,School of Medicine, University of Queensland, Herston, QLD, Australia
| | - Kenneth O'Byrne
- Translational Research Institute, Brisbane, QLD, Australia.,Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, The Centre for Biomedical Technologies, The School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery and Menzies Health Institute Queensland, Griffith University, Nathan, QLD, Australia
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29
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Prognostic Value of Circulating Tumour DNA in Asian Patients with Hepatocellular Carcinoma: A Systematic Review and Meta-Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:8019652. [PMID: 35251214 PMCID: PMC8893997 DOI: 10.1155/2022/8019652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/16/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Circulating tumour DNA (ctDNA) is a noninvasive method of detecting tumours, and its prognostic significance in hepatocellular carcinoma (HCC) patients is controversial. We conducted a systematic review of published research data to evaluate the prognostic value of ctDNA in HCC patients. METHODS The PubMed, Embase, Web of Science, Cochrane Library, and Scopus databases were searched to identify eligible studies reporting disease-free survival (DFS) and overall survival (OS) stratified by ctDNA prior to January 2022. We evaluated the quality and design of these studies. The hazard ratio (HR) was used to combine the survivorship curve and univariate and multivariate results of the included studies. RESULTS In total, 8 articles were included, encompassing 577 HCC patients. The results of survival curve analysis showed that ctDNA was related to poor OS and DFS, and the effect sizes were HR = 2.44, 95% CI (1.42, 4.20), P=0.001; HR = 2.63, 95% CI (1.96, 3.53), P < 0.001. The univariate analysis results showed that ctDNA was related to poor OS (HR = 4.48, 95% CI (1.17, 13.70), P=0.003). The combined results of multivariate analysis showed that ctDNA was related to a shorter risk of OS (HR = 3.74, 95% CI (1.45, 9.65), P=0.006). The univariate and multivariate descriptive analysis results showed that ctDNA was related to shorter DFS, and the effect sizes were HR = 3.28, 95% CI (1.23, 11.30), P=0.011; HR = 3.01, 95% CI (1.11, 10.5), P < 0.001. CONCLUSION The evidence provided by this analysis suggests that ctDNA may be a prognostic biomarker and is negatively correlated with the survival of HCC patients. Mutations in the TERT and SOCS3 promoters in ctDNA are associated with poor prognosis and are expected to become good targets for liquid biopsy and to help select treatment strategies.
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30
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Stadler JC, Belloum Y, Deitert B, Sementsov M, Heidrich I, Gebhardt C, Keller L, Pantel K. Current and Future Clinical Applications of ctDNA in Immuno-Oncology. Cancer Res 2022; 82:349-358. [PMID: 34815256 PMCID: PMC9397642 DOI: 10.1158/0008-5472.can-21-1718] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/06/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Testing peripheral blood for circulating tumor DNA (ctDNA) offers a minimally invasive opportunity to diagnose, characterize, and monitor the disease in individual cancer patients. ctDNA can reflect the actual tumor burden and specific genomic state of disease and thus might serve as a prognostic and predictive biomarker for immune checkpoint inhibitor (ICI) therapy. Recent studies in various cancer entities (e.g., melanoma, non-small cell lung cancer, colon cancer, and urothelial cancer) have shown that sequential ctDNA analyses allow for the identification of responders to ICI therapy, with a significant lead time to imaging. ctDNA assessment may also help distinguish pseudoprogression under ICI therapy from real progression. Developing dynamic changes in ctDNA concentrations as a potential surrogate endpoint of clinical efficacy in patients undergoing adjuvant immunotherapy is ongoing. Besides overall ctDNA burden, further ctDNA characterization can help uncover tumor-specific determinants (e.g., tumor mutational burden and microsatellite instability) of responses or resistance to immunotherapy. In future studies, standardized ctDNA assessments need to be included in interventional clinical trials across cancer entities to demonstrate the clinical utility of ctDNA as a biomarker for personalized cancer immunotherapy.
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Affiliation(s)
- Julia-Christina Stadler
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yassine Belloum
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Deitert
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark Sementsov
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Isabel Heidrich
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoffer Gebhardt
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Keller
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Corresponding Authors: Klaus Pantel, Institute for Tumor Biologie, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Hamburg, 20246, Germany. E-mail: ; and Laura Keller, E-mail:
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Corresponding Authors: Klaus Pantel, Institute for Tumor Biologie, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Hamburg, 20246, Germany. E-mail: ; and Laura Keller, E-mail:
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Croitoru VM, Cazacu IM, Popescu I, Paul D, Dima SO, Croitoru AE, Tanase AD. Clonal Hematopoiesis and Liquid Biopsy in Gastrointestinal Cancers. Front Med (Lausanne) 2022; 8:772166. [PMID: 35127745 PMCID: PMC8814311 DOI: 10.3389/fmed.2021.772166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/02/2021] [Indexed: 02/03/2023] Open
Abstract
The use of blood liquid biopsy is increasingly being incorporated into the clinical setting of gastrointestinal cancers care. Clonal hematopoiesis (CH) occurs naturally as a result of the accumulation of somatic mutations and the clonal proliferation of hematopoietic stem cells with normal aging. The identification of CH-mutations has been described as a source of biological noise in blood liquid biopsy. Incorrect interpretation of CH events as cancer related can have a direct impact on cancer diagnosis and treatment. This review summarizes the current understanding of CH as a form of biological noise in blood liquid biopsy and the reported clinical significance of CH in patients with GI cancers.
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Affiliation(s)
- Vlad M. Croitoru
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
- Department of Medical Oncology, Fundeni Clinical Institute, Bucharest, Romania
| | - Irina M. Cazacu
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
- Department of Medical Oncology, Fundeni Clinical Institute, Bucharest, Romania
| | - Ionut Popescu
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
| | - Doru Paul
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine/New York-Presbyterian, New York, NY, United States
| | - Simona Olimpia Dima
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Adina Emilia Croitoru
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
- Department of Medical Oncology, Fundeni Clinical Institute, Bucharest, Romania
- *Correspondence: Adina Emilia Croitoru
| | - Alina Daniela Tanase
- Faculty of Medicine, Titu Maiorescu University, Bucharest, Romania
- Bone Marrow Transplant Unit, Fundeni Clinical Institute, Bucharest, Romania
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32
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Xia L, Mei J, Kang R, Deng S, Chen Y, Yang Y, Feng G, Deng Y, Gan F, Lin Y, Pu Q, Ma L, Lin F, Yuan Y, Hu Y, Guo C, Liao H, Liu C, Zhu Y, Wang W, Liu Z, Xu Y, Li K, Li C, Li Q, He J, Chen W, Zhang X, Kou Y, Wang Y, Wu Z, Che G, Chen L, Liu L. Perioperative ctDNA-based Molecular Residual Disease Detection for Non-Small Cell Lung Cancer: A Prospective Multicenter Cohort Study (LUNGCA-1). Clin Cancer Res 2021; 28:3308-3317. [PMID: 34844976 DOI: 10.1158/1078-0432.ccr-21-3044] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/02/2021] [Accepted: 11/19/2021] [Indexed: 02/05/2023]
Abstract
PURPOSE We assessed whether perioperative circulating tumor DNA (ctDNA) could be a biomarker for early detection of molecular residual disease (MRD) and prediction of postoperative relapse in resected non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN Based on our prospective, multicenter cohort on dynamic monitoring of ctDNA in lung cancer surgery patients (LUNGCA), we enrolled 950 plasma samples obtained at three perioperative time points (before surgery, 3-day and 1-month after surgery) of 330 stage I-III NSCLC patients (LUNGCA-1), as a part of LUNGCA cohort. Using a customized 769-gene panel, somatic mutations in tumor tissues and plasma samples were identified with next-generation sequencing and utilized for ctDNA-based MRD analysis. RESULTS Preoperative ctDNA positivity was associated with lower recurrence-free survival (RFS) (HR=4.2; P<0.001). The presence of MRD (ctDNA positivity at postoperative 3-day and/or 1-month) was a strong predictor for disease relapse (HR=11.1; P<0.001). ctDNA-based MRD had a higher relative contribution to RFS prediction than all clinicopathological variables such as the TNM stage. Furthermore, MRD-positive patients who received adjuvant therapies had improved RFS over those not receiving adjuvant therapy (HR=0.3; P=0.008), whereas MRD-negative patients receiving adjuvant therapies had lower RFS than their counterparts without adjuvant therapy (HR=3.1; P<0.001). After adjusting for clinicopathological variables, whether receiving adjuvant therapies remained an independent factor for RFS in the MRD-positive population (P=0.002) but not in the MRD-negative population (P=0.283). CONCLUSIONS Perioperative ctDNA analysis is effective in early detection of MRD and relapse risk stratification of NSCLC, and hence could benefit NSCLC patient management.
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Affiliation(s)
- Liang Xia
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Jiandong Mei
- Department of Thoracic Surgery / Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Ran Kang
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Senyi Deng
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yaohui Chen
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Ying Yang
- Genecast Precision Medicine Technology Institute, Beijing 100191
| | - Gang Feng
- Department of Thoracic Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital
| | - Yulan Deng
- The institute of thoracic cancer, Sichuan University
| | - Fanyi Gan
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yidan Lin
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Qiang Pu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Lin Ma
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Feng Lin
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yong Yuan
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yang Hu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | | | - Hu Liao
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Chengwu Liu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yunke Zhu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Wenping Wang
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Zheng Liu
- Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yuyang Xu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Kaidi Li
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Chuan Li
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | | | - Ji He
- Bioinformatics, Genecast Biotechnology Co. Ltd
| | | | - Xiaolong Zhang
- Department of Thoracic Surgery, Chengdu Shangjinnanfu Hospital
| | - Yingli Kou
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Yun Wang
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Zhu Wu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | - Guowei Che
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
| | | | - Lunxu Liu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital of Sichuan University
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Wentzensen N, Clarke MA. Liquid Biopsy for Cancer Detection: Clinical and Epidemiologic Considerations. Clin Cancer Res 2021; 27:5733-5735. [PMID: 34462288 DOI: 10.1158/1078-0432.ccr-21-2426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022]
Abstract
Detection of circulating nucleic acids, also referred to as liquid biopsy, has been evaluated for detection of cancer in a variety of settings. We describe important clinical and epidemiologic considerations for liquid biopsy applications in cancer early detection and for monitoring of cancer recurrence.See related article by Jeannot et al., p. 5869.
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Affiliation(s)
- Nicolas Wentzensen
- Clinical Epidemiology Unit, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, Maryland.
| | - Megan A Clarke
- Clinical Epidemiology Unit, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, Maryland
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Smith JT, Balar A, Lakhani DA, Kluwe C, Zhao Z, Kopparapu P, Almodovar K, Muterspaugh A, Yan Y, York S, Horn L, Antic S, Bertucci C, Shaffer T, Hodsdon L, Garg K, Hosseini SA, Lim L, Osmundson E, Massion PP, Lovly CM, Iams W. Circulating Tumor DNA as a Biomarker of Radiographic Tumor Burden in SCLC. JTO Clin Res Rep 2021; 2:100110. [PMID: 34589992 PMCID: PMC8474385 DOI: 10.1016/j.jtocrr.2020.100110] [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: 05/19/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/02/2022] Open
Abstract
Introduction Blood-based next-generation sequencing assays of circulating tumor DNA (ctDNA) have the ability to detect tumor-associated mutations in patients with SCLC. We sought to characterize the relationship between ctDNA mean variant allele frequency (VAF) and radiographic total-body tumor volume (TV) in patients with SCLC. Methods We identified matched blood draws and computed tomography (CT) or positron emission tomography (PET) scans within a prospective SCLC blood banking cohort. We sequenced plasma using our previously developed 14-gene SCLC-specific ctDNA assay. Three-dimensional TV was determined from PET and CT scans using MIM software and reviewed by radiation oncologists. Univariate association and multivariate regression analyses were performed to evaluate the association between mean VAF and total-body TV. Results We analyzed 75 matched blood draws and CT or PET scans from 25 unique patients with SCLC. Univariate analysis revealed a positive association between mean VAF and total-body TV (Spearman’s ρ = 0.292, p < 0.01), and when considering only treatment-naive and pretreatment patients (n = 11), there was an increase in the magnitude of association (ρ = 0.618, p = 0.048). The relationship remained significant when adjusting for treatment status and bone metastases (p = 0.046). In the subgroup of patients with TP53 variants, univariate analysis revealed a significant association (ρ = 0.762, p = 0.037) only when considering treatment-naive and pretreatment patients (n = 8). Conclusions We observed a positive association between mean VAF and total-body TV in patients with SCLC, suggesting mean VAF may represent a dynamic biomarker of tumor burden that could be followed to monitor disease status.
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Affiliation(s)
- Jarrod T Smith
- Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Aneri Balar
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dhairya A Lakhani
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christien Kluwe
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Zhiguo Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Prasad Kopparapu
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Karinna Almodovar
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anel Muterspaugh
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yingjun Yan
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sally York
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Leora Horn
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sanja Antic
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | | | | | | | - Lee Lim
- Resolution Bioscience, Bellevue, Washington
| | - Evan Osmundson
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christine M Lovly
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wade Iams
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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35
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Jiao XD, Ding LR, Zhang CT, Qin BD, Liu K, Jiang LP, Wang X, Lv LT, Ding H, Li DM, Yang H, Chen XQ, Zhu WY, Wu Y, Ling Y, He X, Liu J, Shao L, Wang HZ, Chen Y, Zheng JJ, Inui N, Zang YS. Serum tumor markers for the prediction of concordance between genomic profiles from liquid and tissue biopsy in patients with advanced lung adenocarcinoma. Transl Lung Cancer Res 2021; 10:3236-3250. [PMID: 34430361 PMCID: PMC8350084 DOI: 10.21037/tlcr-21-543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/22/2021] [Indexed: 12/18/2022]
Abstract
Background The concordance between mutations detected from plasma and tissue is critical for treatment choices of patients with advanced lung adenocarcinoma. Methods We prospectively analyzed the association of the serum tumor markers with the concordance between blood and tissue genomic profiles from 185 patients with advanced lung adenocarcinoma. The concordance was defined according to 3 criteria. Class 1 included all targetable driver mutations in 8 genes; class 2 included class 1 mutations plus mutations in KRAS, STK11, and TP53; class 3 included class 2 mutations plus tumor mutation burden (TMB) status. Results Collectively, 150 out of 185 patients had mutations in both tissue and plasma samples, while one patient was mutation-negative for both, resulting a concordance of 81.6%. The concordance rate for class 1 mutations was 80%, and 65% and 69% for class 2 and class 3, respectively. Carbohydrate antigen 19-9 (CA19-9) or cytokeratin 19 (CYFRA21-1) levels higher than the normal upper limit predicted the concordance of tissue and blood results in class 1 (P=0.005, P=0.011), class 2 (P=0.011, P<0.001), and class 3 (P=0.001, P=0.014). In class 1, the cutoff values of CA19-9 were 30, 36, and 284 U/mL to reach the concordance thresholds of 90%, 95%, and 100%, respectively (P=0.032, P=0.003, P=0.043). For CYFRA21-1, the cutoff values were 6, 18, and 52 µg/L (P=0.005, P=0.051, P=0.354). In class 2, the cutoff values for CYFRA21-1 were 18, 22, and 52 µg/L (P=0.001, P=0.001, P=0.052). In class 3, the cutoff values for CA19-9 were 36, 39, and 85 U/mL (P=0.003, P=0.001, P=0.008). For CYFRA21-1, the cutoff values were 22, 52, and 52 µg/L (P=0.900, P>0.99, P>0.99). When the sum score for 4 serum tumor markers was greater than 35, both class 1, class 2, and class 3 reached a predictive threshold of 90%. Conclusions Serum tumor markers can be used as easy and practical clinical predictors of concordance in mutation profiles between blood and tissue samples from patients with advanced lung adenocarcinoma.
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Affiliation(s)
- Xiao-Dong Jiao
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Li-Ren Ding
- Department of Respiratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine at Bingjiang, Hangzhou, China
| | - Chuan-Tao Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bao-Dong Qin
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ke Liu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Lian-Ping Jiang
- Department of Chemotherapy, Minhang Branch, Fudan University, Shanghai Cancer Center, Shanghai, China
| | - Xi Wang
- Department of Oncology, The 903rd Hospital of PLA, Hangzhou, China
| | - Li-Ting Lv
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hao Ding
- Division of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Dao-Ming Li
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hui Yang
- Department of Medical Oncology, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou, China
| | - Xue-Qin Chen
- Department of Oncology, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wen-Yu Zhu
- Department of Oncology, Changzhou No. 2 People's Hospital Cancer Center, Changzhou, China
| | - Ying Wu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yan Ling
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xi He
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jun Liu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Lin Shao
- Department of Data Science, Burning Rock Biotech, Guangzhou, China
| | - Hao-Zhe Wang
- Department of Data Science, Burning Rock Biotech, Guangzhou, China
| | - Yan Chen
- Department of Medicine, Burning Rock Biotech, Guangzhou, China
| | - Jing-Jing Zheng
- Department of Medicine, Burning Rock Biotech, Guangzhou, China
| | - Naoki Inui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Handayama, Hamamatsu, Japan
| | - Yuan-Sheng Zang
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
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Zeng D, Wang C, Mu C, Su M, Mao J, Huang J, Xu J, Shao L, Li B, Li H, Li B, Zhao J, Jiang J. Cell-free DNA from bronchoalveolar lavage fluid (BALF): a new liquid biopsy medium for identifying lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1080. [PMID: 34422992 PMCID: PMC8339831 DOI: 10.21037/atm-21-2579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022]
Abstract
Background Differentiating malignant lung tumors from benign pulmonary nodules is a great challenge. While the analysis of bronchoalveolar lavage fluid (BALF) is used for diagnosing infections and interstitial lung diseases, there is limited evidence to support its use for lung cancer diagnosis. This study aimed to interrogate the potential of using BALF cell-free DNA (cfDNA) to discriminate malignant lesions from benign nodules. Methods Fifty-three patients with solid pulmonary nodules (≤2 cm) were prospectively enrolled, including 21 confirmed with benign disease and 32 with malignant tumors. Mutations were profiled for 30 tumor tissues and 40 BALFs. Paired BALFs and plasma from 48 patients underwent DNA methylation profiling. A methylome-based classification model was developed for BALF and plasma separately. Results Among the 30 patients with paired tissues and BALFs, 96.7% and 70% had alterations detected from their tissues (79 alterations) and BALFs (53 alterations), respectively. Using tissues as references, BALFs revealed 14 new alterations and missed 41. BALF mutation displayed a sensitivity of 71%, specificity of 77.8%, and accuracy of 72.5% in detecting lung cancer. BALF methylation achieved an accuracy of 81.3%, with both sensitivity and specificity being 81%. Plasma methylation showed a 66.7% sensitivity, 71.4% specificity, and 68.8% accuracy. BALF methylation also demonstrated 82.4% sensitivity in stage I patients. Parallel bronchoscopy, lavage cytology, and bronchial brushing demonstrated an inferior sensitivity of 23%, 3.1%, and 9.7%, respectively, compared with BALF methylation and mutation (P<0.0001). Conclusions BALF cfDNA can serve as a liquid biopsy media for both mutation and methylation profiling, demonstrating better sensitivities in distinguishing small malignant tumors from benign nodules than conventional methods. Keywords Lung cancer diagnosis; pulmonary nodule; bronchoalveolar lavage fluid (BALF); methylation; genomic mutation
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Affiliation(s)
- Daxiong Zeng
- Department of Respiratory Medicine, Dusu Lake Hospital to Soochow University, Suzhou, China.,Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cangguo Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chuanyong Mu
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Meiqin Su
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jingyu Mao
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianan Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiayue Xu
- Burning Rock Biotech, Guangzhou, China
| | - Lin Shao
- Burning Rock Biotech, Guangzhou, China
| | - Bing Li
- Burning Rock Biotech, Guangzhou, China
| | - Haiyan Li
- Burning Rock Biotech, Guangzhou, China
| | - Bingsi Li
- Burning Rock Biotech, Guangzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Junhong Jiang
- Department of Respiratory Medicine, Dusu Lake Hospital to Soochow University, Suzhou, China.,Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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37
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Zulato E, Tosello V, Nardo G, Bonanno L, Del Bianco P, Indraccolo S. Implementation of Next Generation Sequencing-Based Liquid Biopsy for Clinical Molecular Diagnostics in Non-Small Cell Lung Cancer (NSCLC) Patients. Diagnostics (Basel) 2021; 11:diagnostics11081468. [PMID: 34441402 PMCID: PMC8394370 DOI: 10.3390/diagnostics11081468] [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: 06/29/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
Genetic screening of somatic mutations in circulating free DNA (cfDNA) opens up new opportunities for personalized medicine. In this study, we aim to illustrate the implementation of NGS-based liquid biopsy in clinical practice for the detection of somatic alterations in selected genes. Our work is particularly relevant for the diagnosis and treatment of NSCLC. Beginning in 2020, we implemented the use of Roche’s Avenio ctDNA expanded panel in our diagnostic routine. In this study, we retrospectively review NGS-based clinical genetic tests performed in our laboratory, focusing on key analytical parameters. Avenio ctDNA kits demonstrated 100% sensitivity in detecting single nucleotide variants (SNVs) at >0.5% variant allele frequency (VAF), and high consistency in reproducibility. Since 2020, we performed cfDNA genotyping test in 86 NSCLC patients, and we successfully sequenced 96.5% (83/86) of samples. We observed consistency in sequencing performance based upon sequencing depth and on-target rate. At least one gene variant was identified in 52 samples (63%), and one or more actionable variants were detected in 21 out of 83 (25%) of analysed patients. We demonstrated the feasibility of implementing an NGS-based liquid biopsy assay for routine genetic characterization of metastatic NSCLC patients.
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Affiliation(s)
- Elisabetta Zulato
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, I-35128 Padova, Italy; (E.Z.); (V.T.); (G.N.)
| | - Valeria Tosello
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, I-35128 Padova, Italy; (E.Z.); (V.T.); (G.N.)
| | - Giorgia Nardo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, I-35128 Padova, Italy; (E.Z.); (V.T.); (G.N.)
| | - Laura Bonanno
- Medical Oncology 2, Istituto Oncologico Veneto IOV IRCSS, I-35128 Padova, Italy;
| | - Paola Del Bianco
- Clinical Research Unit, Istituto Oncologico Veneto IOV IRCCS, I-35128 Padova, Italy;
| | - Stefano Indraccolo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, I-35128 Padova, Italy; (E.Z.); (V.T.); (G.N.)
- Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, I-35128 Padova, Italy
- Correspondence: ; Tel.: +39-049-821-5875
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38
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Venkatachalam A, Pikarsky E, Ben-Neriah Y. Putative homeostatic role of cancer driver mutations. Trends Cell Biol 2021; 32:8-17. [PMID: 34373150 DOI: 10.1016/j.tcb.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 11/18/2022]
Abstract
Somatic mutations have traditionally been associated with cancer, yet more recently, it was realized that they also appear in nontransformed cells beginning in early life. Remarkably, some of these mutations, commonly viewed as cancer driver mutations, are widely spread among cells of noncancerous tissues, sometimes affecting the majority of the tissue cells. This spreading process intensifies upon aging or exposure to extrinsic insults, such as UV irradiation, inhaling smoke, and inflammatory cues. Whereas classic driver mutations in normal cells are mostly viewed as a first step in the carcinogenesis process, here, we speculate that in certain states, they can play beneficial homeostatic roles while confronting stress and aging tissue repair.
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Affiliation(s)
- Avanthika Venkatachalam
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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Qvick A, Stenmark B, Carlsson J, Isaksson J, Karlsson C, Helenius G. Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer. Mol Med 2021; 27:68. [PMID: 34217228 PMCID: PMC8254966 DOI: 10.1186/s10020-021-00331-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The aim of this study was to investigate the clinical value of liquid biopsy as a primary source for variant analysis in lung cancer. In addition, we sought to characterize liquid biopsy variants and to correlate mutational load to clinical data. METHODS Circulating cell-free DNA was extracted from plasma from patients with lung cancer (n = 60) and controls with benign lung disease (n = 16). Variant analysis was performed using the AVENIO ctDNA Surveillance kit and the results were correlated to clinical and variant analysis data from tumor tissue or cytology retrieved from clinical routine diagnostics. RESULTS There were significantly more variants detected in lung cancer cases compared to controls (p = 0.011), but no difference between the histological subgroups of lung cancer was found (p = 0.465). Furthermore, significantly more variants were detected in patients with stage IIIb-IV disease compared to patients with stage I-IIIa (median 7 vs 4, p = 0.017). Plasma cfDNA mutational load was significantly associated with overall survival (p = 0.010). The association persisted when adjusted for stage and ECOG performance status (HR: 3.64, 95% CI 1.37-9.67, p = 0.009). Agreement between tumor and plasma samples significantly differed with stage; patients with stage IIIb-IV disease showed agreement in 88.2% of the cases with clinically relevant variants, compared to zero cases in stage I-IIIa (p = 0.004). Furthermore, one variant in EGFR, two in KRAS, and one in BRAF were detected in plasma but not in tumor samples. CONCLUSION This study concludes that in the vast majority of advanced NSCLC patients a reliable variant analysis can be performed using liquid biopsy from plasma. Furthermore, we found that the number of variants in plasma is associated with prognosis, possibly indicating a strategy for closer follow up on this crucial patient group.
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Affiliation(s)
- Alvida Qvick
- Dept. of Laboratory Medicine, Örebro University Hospital, Södra Grev. Roseng., 701 85 Örebro, Sweden
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bianca Stenmark
- Dept. of Laboratory Medicine, Örebro University Hospital, Södra Grev. Roseng., 701 85 Örebro, Sweden
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jessica Carlsson
- Dept. of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Johan Isaksson
- Dept. of Respiratory Medicine, Gävle Hospital, Gävle, Sweden
- Centre for Research and Development Region Gävleborg/Uppsala University, Gävle, Sweden
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Gisela Helenius
- Dept. of Laboratory Medicine, Örebro University Hospital, Södra Grev. Roseng., 701 85 Örebro, Sweden
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Nasrollahzadeh D, Roshandel G, Delhomme TM, Avogbe PH, Foll M, Saidi F, Poustchi H, Sotoudeh M, Malekzadeh R, Brennan P, Mckay J, Hainaut P, Abedi-Ardekani B. TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation. Int J Mol Sci 2021; 22:5627. [PMID: 34073316 PMCID: PMC8197963 DOI: 10.3390/ijms22115627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/17/2021] [Indexed: 12/30/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11-3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC.
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Affiliation(s)
- Dariush Nasrollahzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Gholamreza Roshandel
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan 49177-44563, Iran;
| | - Tiffany Myriam Delhomme
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Patrice Hodonou Avogbe
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Matthieu Foll
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Farrokh Saidi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - James Mckay
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm 1209 CNRS 5309 UGA, 38700 Grenoble, France;
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
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Pizzutilo EG, Pedrani M, Amatu A, Ruggieri L, Lauricella C, Veronese SM, Signorelli D, Cerea G, Giannetta L, Siena S, Sartore-Bianchi A. Liquid Biopsy for Small Cell Lung Cancer either De Novo or Transformed: Systematic Review of Different Applications and Meta-Analysis. Cancers (Basel) 2021; 13:2265. [PMID: 34066817 PMCID: PMC8125928 DOI: 10.3390/cancers13092265] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The potential added value of liquid biopsy (LB) is not well determined in the case of small cell lung cancer (SCLC), an aggressive tumor that can occur either de novo or from the histologic transformation of non-small cell lung cancer (NSCLC). METHODS A systematic review of studies adopting LB in patients with SCLC have been performed to assess the clinical utility of circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs). RESULTS After a screening of 728 records, 62 studies (32 evaluating CTCs, 27 ctDNA, and 3 both) met predetermined eligibility criteria. Only four studies evaluated LB in the diagnostic setting for SCLC, while its prognostic significance was evaluated in 38 studies and prominently supported by both ctDNA and CTCs. A meta-analysis of 11 studies as for CTCs enumeration showed an HR for overall survival of 2.63 (1.71-4.05), with a potential publication bias. The feasibility of tumor genomic profiling and the predictive role of LB in terms of response/resistance to chemotherapy was assessed in 11 and 24 studies, respectively, with greater consistency for those regarding ctDNA. Intriguingly, several case reports suggest that LB can indirectly capture the transition to SCLC in NSCLC treated with EGFR tyrosine kinase inhibitors. CONCLUSIONS While dedicated trials are needed, LB holds potential clinical roles in both de novo and transformed SCLC. CtDNA analysis appears the most valuable and practicable tool for both disease monitoring and genomic profiling.
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Affiliation(s)
- Elio Gregory Pizzutilo
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Martino Pedrani
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Lorenzo Ruggieri
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Calogero Lauricella
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Silvio Marco Veronese
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Diego Signorelli
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Giulio Cerea
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Laura Giannetta
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy; (E.G.P.); (M.P.); (A.A.); (L.R.); (C.L.); (S.M.V.); (D.S.); (G.C.); (L.G.); (S.S.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
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Freitas C, Sousa C, Machado F, Serino M, Santos V, Cruz-Martins N, Teixeira A, Cunha A, Pereira T, Oliveira HP, Costa JL, Hespanhol V. The Role of Liquid Biopsy in Early Diagnosis of Lung Cancer. Front Oncol 2021; 11:634316. [PMID: 33937034 PMCID: PMC8085425 DOI: 10.3389/fonc.2021.634316] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is an emerging technology with a potential role in the screening and early detection of lung cancer. Several liquid biopsy-derived biomarkers have been identified and are currently under ongoing investigation. In this article, we review the available data on the use of circulating biomarkers for the early detection of lung cancer, focusing on the circulating tumor cells, circulating cell-free DNA, circulating micro-RNAs, tumor-derived exosomes, and tumor-educated platelets, providing an overview of future potential applicability in the clinical practice. While several biomarkers have shown exciting results, diagnostic performance and clinical applicability is still limited. The combination of different biomarkers, as well as their combination with other diagnostic tools show great promise, although further research is still required to define and validate the role of liquid biopsies in clinical practice.
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Affiliation(s)
- Cláudia Freitas
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Catarina Sousa
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Francisco Machado
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Mariana Serino
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Vanessa Santos
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Armando Teixeira
- Institute for Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Faculty of Engineering, University of Porto, Porto, Portugal
| | - António Cunha
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
- Department of Engineering, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
| | - Hélder P. Oliveira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - José Luís Costa
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Venceslau Hespanhol
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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43
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Sabedot T, Malta T, Snyder J, Nelson K, Wells M, deCarvalho A, Mukherjee A, Chitale D, Mosella M, Sokolov A, Asmaro K, Robin A, Rosenblum M, Mikkelsen T, Rock J, Poisson L, Lee I, Walbert T, Kalkanis S, Iavarone A, Castro AV, Noushmehr H. A serum-based DNA methylation assay provides accurate detection of glioma. Neuro Oncol 2021; 23:1494-1508. [PMID: 33560371 DOI: 10.1093/neuonc/noab023] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The detection of somatic mutations in cell-free DNA (cfDNA) from liquid biopsy has emerged as a non-invasive tool to monitor the follow-up of cancer patients. However, the significance of cfDNA clinical utility remains uncertain in patients with brain tumors, primarily because of the limited sensitivity cfDNA has to detect real tumor-specific somatic mutations. This unresolved challenge has prevented accurate follow-up of glioma patients with non-invasive approaches. METHODS Genome-wide DNA methylation profiling of tumor tissue and serum cell-free DNA of glioma patients. RESULTS Here, we developed a non-invasive approach to profile the DNA methylation status in the serum of patients with gliomas and identified a cfDNA-derived methylation signature that is associated with the presence of gliomas and related immune features. By testing the signature in an independent discovery and validation cohorts, we developed and verified a score metric (the "glioma epigenetic liquid biopsy score" or GeLB) that optimally distinguished patients with or without glioma (sensitivity: 100%, specificity: 97.78%). Furthermore, we found that changes in GeLB score reflected clinicopathological changes during surveillance (e.g., progression, pseudoprogression or response to standard or experimental treatment). CONCLUSIONS Our results suggest that the GeLB score can be used as a complementary approach to diagnose and follow up patients with glioma.
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Affiliation(s)
- Thais Sabedot
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
| | - Tathiane Malta
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
| | - James Snyder
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA.,Department of Neuro Oncology, Henry Ford Health System, Detroit, MI, USA
| | - Kevin Nelson
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Michael Wells
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
| | - Ana deCarvalho
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Abir Mukherjee
- Department of Pathology, Henry Ford Health System, Detroit, MI, USA
| | - Dhan Chitale
- Department of Pathology, Henry Ford Health System, Detroit, MI, USA
| | - Maritza Mosella
- Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Karam Asmaro
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
| | - Adam Robin
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Michael Rosenblum
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Tom Mikkelsen
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Jack Rock
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Laila Poisson
- Department of Biostatistics, Henry Ford Health System, Detroit, MI, USA
| | - Ian Lee
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Tobias Walbert
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Department of Neuro Oncology, Henry Ford Health System, Detroit, MI, USA
| | - Steven Kalkanis
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Department of Neurology, Columbia University Medical Center, New York, USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA.,Omics Laboratory, Henry Ford Health System, Detroit, MI, USA
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Abstract
Small-cell lung cancer (SCLC) represents about 15% of all lung cancers and is marked by an exceptionally high proliferative rate, strong predilection for early metastasis and poor prognosis. SCLC is strongly associated with exposure to tobacco carcinogens. Most patients have metastatic disease at diagnosis, with only one-third having earlier-stage disease that is amenable to potentially curative multimodality therapy. Genomic profiling of SCLC reveals extensive chromosomal rearrangements and a high mutation burden, almost always including functional inactivation of the tumour suppressor genes TP53 and RB1. Analyses of both human SCLC and murine models have defined subtypes of disease based on the relative expression of dominant transcriptional regulators and have also revealed substantial intratumoural heterogeneity. Aspects of this heterogeneity have been implicated in tumour evolution, metastasis and acquired therapeutic resistance. Although clinical progress in SCLC treatment has been notoriously slow, a better understanding of the biology of disease has uncovered novel vulnerabilities that might be amenable to targeted therapeutic approaches. The recent introduction of immune checkpoint blockade into the treatment of patients with SCLC is offering new hope, with a small subset of patients deriving prolonged benefit. Strategies to direct targeted therapies to those patients who are most likely to respond and to extend the durable benefit of effective antitumour immunity to a greater fraction of patients are urgently needed and are now being actively explored.
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Affiliation(s)
- Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elisabeth Brambilla
- Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Corinne Faivre-Finn
- Department of Clinical Oncology, The Christie Hospital NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
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45
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Mondelo-Macía P, García-González J, León-Mateos L, Castillo-García A, López-López R, Muinelo-Romay L, Díaz-Peña R. Current Status and Future Perspectives of Liquid Biopsy in Small Cell Lung Cancer. Biomedicines 2021; 9:48. [PMID: 33430290 PMCID: PMC7825645 DOI: 10.3390/biomedicines9010048] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 01/08/2023] Open
Abstract
Approximately 19% of all cancer-related deaths are due to lung cancer, which is the leading cause of mortality worldwide. Small cell lung cancer (SCLC) affects approximately 15% of patients diagnosed with lung cancer. SCLC is characterized by aggressiveness; the majority of SCLC patients present with metastatic disease, and less than 5% of patients are alive at 5 years. The gold standard of SCLC treatment is platinum and etoposide-based chemotherapy; however, its effects are short. In recent years, treatment for SCLC has changed; new drugs have been approved, and new biomarkers are needed for treatment selection. Liquid biopsy is a non-invasive, rapid, repeated and alternative tool to the traditional tumor biopsy that could allow the most personalized medicine into the management of SCLC patients. Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) are the most commonly used liquid biopsy biomarkers. Some studies have reported the prognostic factors of CTCs and cfDNA in SCLC patients, independent of the stage. In this review, we summarize the recent SCLC studies of CTCs, cfDNA and other liquid biopsy biomarkers, and we discuss the future utility of liquid biopsy in the clinical management of SCLC.
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Affiliation(s)
- Patricia Mondelo-Macía
- Liquid Biopsy Analysis Unit, Oncomet, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain; (P.M.-M.); (L.M.-R.)
| | - Jorge García-González
- Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain; (J.G.-G.); (L.L.-M.); (R.L.-L.)
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Luis León-Mateos
- Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain; (J.G.-G.); (L.L.-M.); (R.L.-L.)
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | | | - Rafael López-López
- Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), 15706 Santiago de Compostela, Spain; (J.G.-G.); (L.L.-M.); (R.L.-L.)
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Oncomet, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain; (P.M.-M.); (L.M.-R.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Roberto Díaz-Peña
- Liquid Biopsy Analysis Unit, Oncomet, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain; (P.M.-M.); (L.M.-R.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
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46
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Huang H, Li H. Tumor heterogeneity and the potential role of liquid biopsy in bladder cancer. Cancer Commun (Lond) 2020; 41:91-108. [PMID: 33377623 PMCID: PMC7896752 DOI: 10.1002/cac2.12129] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/28/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is a heterogeneous disease that characterized by genomic instability and a high mutation rate. Heterogeneity in tumor may partially explain the diversity of responses to targeted therapies and the various clinical outcomes. A combination of cytology and cystoscopy is the standard methodology for BC diagnosis, prognosis, and disease surveillance. However, genomics analyses of single tumor‐biopsy specimens may underestimate the mutational burden of heterogeneous tumors. Liquid biopsy, as a promising technology, enables analysis of tumor components in the bodily fluids, such as blood and urine, at multiple time points and provides a minimally invasive approach that can track the evolutionary dynamics and monitor tumor heterogeneity. In this review, we describe the multiple faces of BC heterogeneity at the genomic and transcriptional levels and how they affect clinical care and outcomes. We also summarize the outcomes of liquid biopsy in BC, which plays a potential role in revealing tumor heterogeneity. Finally, we discuss the challenges that must be addressed before liquid biopsy can be widely used in clinical treatment.
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Affiliation(s)
- Hai‐Ming Huang
- Department of Clinical LaboratoryPeking University First HospitalBeijing100034P. R. China
| | - Hai‐Xia Li
- Department of Clinical LaboratoryPeking University First HospitalBeijing100034P. R. China
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Jaworski JJ, Morgan RD, Sivakumar S. Circulating Cell-Free Tumour DNA for Early Detection of Pancreatic Cancer. Cancers (Basel) 2020; 12:E3704. [PMID: 33317202 PMCID: PMC7763954 DOI: 10.3390/cancers12123704] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/04/2020] [Indexed: 01/11/2023] Open
Abstract
Pancreatic cancer is a lethal disease, with mortality rates negatively associated with the stage at which the disease is detected. Early detection is therefore critical to improving survival outcomes. A recent focus of research for early detection is the use of circulating cell-free tumour DNA (ctDNA). The detection of ctDNA offers potential as a relatively non-invasive method of diagnosing pancreatic cancer by using genetic sequencing technology to detect tumour-specific mutational signatures in blood samples before symptoms manifest. These technologies are limited by a number of factors that lower sensitivity and specificity, including low levels of detectable ctDNA in early stage disease and contamination with non-cancer circulating cell-free DNA. However, genetic and epigenetic analysis of ctDNA in combination with other standard diagnostic tests may improve early detection rates. In this review, we evaluate the genetic and epigenetic methods under investigation in diagnosing pancreatic cancer and provide a perspective for future developments.
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Affiliation(s)
- Jedrzej J. Jaworski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK;
| | - Robert D. Morgan
- Department of Medical Oncology, Christie NHS Foundation Trust, Manchester M20 4BX, UK;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Shivan Sivakumar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Department of Medical Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
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48
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Church M, Carter L, Blackhall F. Liquid Biopsy in Small Cell Lung Cancer-A Route to Improved Clinical Care? Cells 2020; 9:E2586. [PMID: 33287165 PMCID: PMC7761700 DOI: 10.3390/cells9122586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 01/22/2023] Open
Abstract
Small cell lung cancer (SCLC) has a particularly poor prognosis despite the high initial response to first-line systemic therapy, and there is a well-recognised lack of meaningful treatments beyond the second line. A number of reasons have been put forward to explain this, including a lack of common, easily-druggable genetic mutations in SCLC and rarity of high-quality tissue samples due to late presentation. Liquid biopsies, including circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA) are increasingly used as surrogates for tumour tissue and have the advantage of being easily obtained serially to inform on the biology of disease progression and acquired chemoresistance, and may provide a pathway to improve care in this notoriously refractory disease. Here we discuss the current evidence behind these liquid biopsy methods in SCLC, and how they could be employed in future clinical care.
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Affiliation(s)
- Matt Church
- Division of Cancer Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (M.C.); (L.C.)
| | - Louise Carter
- Division of Cancer Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (M.C.); (L.C.)
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Fiona Blackhall
- Division of Cancer Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (M.C.); (L.C.)
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
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49
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Yekula A, Muralidharan K, Rosh Z, Youngkin AE, Kang KM, Balaj L, Carter BS. Liquid Biopsy Strategies to Distinguish Progression from Pseudoprogression and Radiation Necrosis in Glioblastomas. ADVANCED BIOSYSTEMS 2020; 4:e2000029. [PMID: 32484293 PMCID: PMC7708392 DOI: 10.1002/adbi.202000029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Liquid biopsy for the detection and monitoring of central nervous system tumors is of significant clinical interest. At initial diagnosis, the majority of patients with central nervous system tumors undergo magnetic resonance imaging (MRI), followed by invasive brain biopsy to determine the molecular diagnosis of the WHO 2016 classification paradigm. Despite the importance of MRI for long-term treatment monitoring, in the majority of patients who receive chemoradiation therapy for glioblastoma, it can be challenging to distinguish between radiation treatment effects including pseudoprogression, radiation necrosis, and recurrent/progressive disease based on imaging alone. Tissue biopsy-based monitoring is high risk and not always feasible. However, distinguishing these entities is of critical importance for the management of patients and can significantly affect survival. Liquid biopsy strategies including circulating tumor cells, circulating free DNA, and extracellular vesicles have the potential to afford significant useful molecular information at both the stage of diagnosis and monitoring for these tumors. Here, current liquid biopsy-based approaches in the context of tumor monitoring to differentiate progressive disease from pseudoprogression and radiation necrosis are reviewed.
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Affiliation(s)
- Anudeep Yekula
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zachary Rosh
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Anna E. Youngkin
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Keiko M. Kang
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
- School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Bob S. Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
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50
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Garrido-Navas MC, García-Díaz A, Molina-Vallejo MP, González-Martínez C, Alcaide Lucena M, Cañas-García I, Bayarri C, Delgado JR, González E, Lorente JA, Serrano MJ. The Polemic Diagnostic Role of TP53 Mutations in Liquid Biopsies from Breast, Colon and Lung Cancers. Cancers (Basel) 2020; 12:E3343. [PMID: 33198130 PMCID: PMC7696715 DOI: 10.3390/cancers12113343] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Being minimally invasive and thus allowing repeated measures over time, liquid biopsies are taking over traditional solid biopsies in certain circumstances such as those for unreachable tumors, very early stages or treatment monitoring. However, regarding TP53 mutation status analysis, liquid biopsies have not yet substituted tissue samples, mainly due to the lack of concordance between the two types of biopsies. This needs to be examined in a study-dependent manner, taking into account the particular type of liquid biopsy analyzed, that is, circulating tumor cells (CTCs) or cell-free DNA (cfDNA), its involvement in the tumor biology and evolution and, finally, the technology used to analyze each biopsy type. Here, we review the main studies analyzing TP53 mutations in either CTCs or cfDNA in the three more prevalent solid tumors: breast, colon and lung cancers. We evaluate the correlation for mutation status between liquid biopsies and tumor tissue, suggesting possible sources of discrepancies, as well as evaluating the clinical utility of using liquid biopsies for the analysis of TP53 mutation status and the future actions that need to be undertaken to make liquid biopsy analysis a reality for the evaluation of TP53 mutations.
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Affiliation(s)
- M. Carmen Garrido-Navas
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Universidad Internacional de la Rioja, Avenida de la Paz, 137, 26006 Logroño, Spain
| | - Abel García-Díaz
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Departamento de Medicina, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain
| | - Maria Pilar Molina-Vallejo
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
| | - Coral González-Martínez
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
| | - Miriam Alcaide Lucena
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Inés Cañas-García
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Clara Bayarri
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Department of Thoracic Surgery, Virgen de las Nieves University Hospital, Av. de las Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Juan Ramón Delgado
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
| | - Encarna González
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
| | - Jose Antonio Lorente
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071 Granada, Spain
| | - M. Jose Serrano
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
- Department of Pathological Anatomy, Faculty of Medicine, Campus de Ciencias de la Salud, University of Granada, 18016 Granada, Spain
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