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Wang W, Huang Y, Kong J, Lu L, Liao Q, Zhu J, Wang T, Yan L, Dai M, Chen Z, You J. Plasma ctDNA enhances the tissue-based detection of oncodriver mutations in colorectal cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03422-7. [PMID: 38777950 DOI: 10.1007/s12094-024-03422-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/24/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE The advent of circulating tumor DNA (ctDNA) technology has provided a convenient and noninvasive means to continuously monitor cancer genomic data, facilitating personalized cancer treatment. This study aimed to evaluate the supplementary benefits of plasma ctDNA alongside traditional tissue-based next-generation sequencing (NGS) in identifying targetable mutations and tumor mutational burden (TMB) in colorectal cancers (CRC). METHODS Our study involved 76 CRC patients, collecting both tissue and plasma samples for NGS. We assessed the concordance of gene mutational status between ctDNA and tissue, focusing on actionable genes such as KRAS, NRAS, PIK3CA, BRAF, and ERBB2. Logistic regression analysis was used to explore variables associated with discordance and positive mutation rates. RESULTS In total, 26 cancer-related genes were identified. The most common variants in tumor tissues and plasma samples were in APC (57.9% vs 19.7%), TP53 (55.3% vs 22.4%) and KRAS (47.4% vs 43.4%). Tissue and ctDNA showed an overall concordance of 73.53% in detecting actionable gene mutations. Notably, plasma ctDNA improved detection for certain genes and gene pools. Variables significantly associated with discordance included gender and peritoneal metastases. TMB analysis revealed a higher detection rate in tissues compared to plasma, but combining both increased detection. CONCLUSIONS Our study highlights the importance of analyzing both tissue and plasma for detecting actionable mutations in CRC, with plasma ctDNA offering added value. Discordance is associated with gender and peritoneal metastases, and TMB analysis can benefit from a combination of tissue and plasma data. This approach provides valuable insights for personalized CRC treatment.
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Affiliation(s)
- Wei Wang
- The First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Yisen Huang
- Department of Gastroenterology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, 362002, Fujian, China
| | - Jianqiao Kong
- Department of General Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, Hubei, China
| | - Lin Lu
- Colorectal Surgery Department, General Hospital of Ningxia Medical University, Yinchuan, 750001, Ningxia, China
| | - Qianxiu Liao
- Department of Laboratory Medicine, Chengdu First People's Hospital, Chengdu, 610041, Sichuan, China
| | - Jingtao Zhu
- The Third Clinical Medical College, Fujian Medical University, Xiamen, 361001, Fujian, China
| | - Tinghao Wang
- The Third Clinical Medical College, Fujian Medical University, Xiamen, 361001, Fujian, China
| | - Linghua Yan
- Shanghai Tongshu Biotechnology Co., Ltd, Shanghai, 201900, China
| | - Min Dai
- Department of Pathology, Wuhu Hospital, East China Normal University (The Second People's Hospital, Wuhu), Wuhu, 241000, Anhui, China.
| | - Zhan Chen
- Department of General Surgery, Chenggong Hospital of Xiamen University School of Medicine, Xiamen, 361001, Fujian, China.
| | - Jun You
- Department of Gastrointestinal Oncology Surgery, Cancer Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361001, Fujian, China.
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Sorbini M, Carradori T, Togliatto GM, Vaisitti T, Deaglio S. Technical Advances in Circulating Cell-Free DNA Detection and Analysis for Personalized Medicine in Patients' Care. Biomolecules 2024; 14:498. [PMID: 38672514 PMCID: PMC11048502 DOI: 10.3390/biom14040498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) refers to small fragments of DNA molecules released after programmed cell death and necrosis in several body fluids such as blood, saliva, urine, and cerebrospinal fluid. The discovery of cfDNA has revolutionized the field of non-invasive diagnostics in the oncologic field, in prenatal testing, and in organ transplantation. Despite the potential of cfDNA and the solid results published in the recent literature, several challenges remain, represented by a low abundance, a need for highly sensitive assays, and analytical issues. In this review, the main technical advances in cfDNA analysis are presented and discussed, with a comprehensive examination of the current available methodologies applied in each field. Considering the potential advantages of cfDNA, this biomarker is increasing its consensus among clinicians, as it allows us to monitor patients' conditions in an easy and non-invasive way, offering a more personalized care. Nevertheless, cfDNA analysis is still considered a diagnostic marker to be further validated, and very few centers are implementing its analysis in routine diagnostics. As technical improvements are enhancing the performances of cfDNA analysis, its application will transversally improve patients' quality of life.
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Affiliation(s)
- Monica Sorbini
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
| | - Tullia Carradori
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
| | - Gabriele Maria Togliatto
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza, 10126 Turin, Italy;
| | - Tiziana Vaisitti
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza, 10126 Turin, Italy;
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (T.C.); (T.V.); (S.D.)
- Immunogenetics and Transplant Biology Service, Città della Salute e della Scienza, 10126 Turin, Italy;
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Teng F, Fu D, Shi CC, Xiong A, Yang MX, Su C, Lei M, Cao YO, Shen XD, Chen Y, Wang PH, Liu SQ. Nano-energy interference: A novel strategy for blunting tumor adaptation and metastasis. Mater Today Bio 2024; 25:100984. [PMID: 38356962 PMCID: PMC10865032 DOI: 10.1016/j.mtbio.2024.100984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Blunting the tumor's stress-sensing ability is an effective strategy for controlling tumor adaptive survival and metastasis. Here, we have designed a cyclically amplified nano-energy interference device based on lipid nanoparticles (LNP), focused on altering cellular energy metabolism. This innovative nano device efficiently targets and monitors the tumor's status while simultaneously inhibiting mitochondrial respiration, biogenesis and ribosome production. To this end, we first identified azelaic acid (AA), a binary acid capable of disrupting the mitochondrial respiratory chain. Upon encapsulation in LNP and linkage to mitochondrial-targeting molecules, this disruptive effect is further augmented. Consequently, tumors exhibit a substantial upregulation of the glycolytic pathway, intensifying their glucose demand and worsening the tumor's energy-deprived microenvironment. Then, the glucose analog, 2-Deoxy-D-glucose (2-DG), linked to the LNP, efficiently targets tumors and competitively inhibits the tumor's normal glucose uptake. The synergetic results of combining AA with 2-DG induce comprehensive energy deficiency within tumors, blocking the generation of energy-sensitive ribosomes. Ultimately, the disruption of both mitochondria and ribosomes depletes energy supply and new protein-generating capacity, weakening tumor's ability to adapt to environmental stress and thereby inhibiting growth and metastasis. Comprehensively, this nano-energy interference device, by controlling the tumor's stress-sensing ability, provides a novel therapeutic strategy for refractory tumors.
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Affiliation(s)
- Fei Teng
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Dong Fu
- Department of Pediatric Orthopedics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, PR China
| | - Chen-Cheng Shi
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - An Xiong
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Meng-Xuan Yang
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Chang Su
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Ming Lei
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Yi-Ou Cao
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Xiao-Dong Shen
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Yi Chen
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Pu-Hua Wang
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
| | - Shao-Qun Liu
- Department of Gastrointestinal Surgery, Minhang Hospital, Fudan University, Shanghai, 201199, PR China
- Key Laboratory of Whole-period Monitoring and Precise Intervention of Digestive Cancer (SMHC), Minhang Hospital & AHS, Fudan University, Shanghai, 201199, PR China
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Aucoin AJ, Chawla H, Holleman GT, Trivedi D, Sahu PD. Primary ductal adenocarcinoma of the lacrimal gland with sarcomatoid differentiation: case report and genomic analysis. Orbit 2023:1-5. [PMID: 37611021 DOI: 10.1080/01676830.2023.2246156] [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: 05/04/2023] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
We describe a case of primary ductal adenocarcinoma of the lacrimal gland with novel histopathological characteristics corresponding to a biphasic growth course and provide a comprehensive genomic profile of this malignancy. A 39-year-old male with a history of slowly progressive unilateral proptosis and hypoglobus presented after 1 month of hyperacute exacerbation. Orbital imaging revealed a superior mass with osseous erosion. The patient underwent orbital exploration and excisional biopsy via lateral orbitotomy. Histopathology demonstrated high-grade adenocarcinoma with a well-differentiated glandular component alongside a poorly differentiated sarcomatoid region. The glandular section was immunopositive for Her-2, CK7, GATA3, and androgen receptor. Tumor recurrence necessitated en-bloc exenteration with dural resection alongside adjuvant radiotherapy and chemotherapy. This represents the first report of sarcomatoid differentiation in primary ductal adenocarcinoma of the lacrimal gland, which may incite hyperacute progression. Conversely, GATA3 immunopositivity may correlate with indolent growth. Genomic variants such as SEMA3C represent potential therapeutic targets for this condition.
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Affiliation(s)
- Alise J Aucoin
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Harshvardhan Chawla
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | | | - Darshan Trivedi
- Department of Pathology & Laboratory Medicine, Ochsner Medical Center, New Orleans, Louisiana, USA
| | - Priya D Sahu
- Division of Oculoplastic Surgery, Department of Ophthalmology, Ochsner Medical Center, New Orleans, Louisiana, USA
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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6
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Bádon ES, Mokánszki A, Mónus A, András C, Méhes G. Clonal diversity in KRAS mutant colorectal adenocarcinoma under treatment: Monitoring of cfDNA using reverse hybridization and DNA sequencing platforms. Mol Cell Probes 2023; 67:101891. [PMID: 36586518 DOI: 10.1016/j.mcp.2022.101891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Biological heterogeneity is a key feature of malignancies that significantly contributes to disease progression and therapy resistance. Residual/relapsed tumor foci may represent genetically divergent subclones, which remain uncovered as repeated and multiple tumor sampling is usually limited. The analysis of circulating free DNA (cfDNA) from the peripheral blood plasma (also called a liquid biopsy, LB) is a new achievement that provides an effective tool for follow-up monitoring of cancer-related genetic status. The present study highlights the phenomenon of mutational variability observed in patients with metastatic KRAS mutant colorectal cancer (mCRC) during treatment with bevacizumab in combination in a longitudinal fashion. The prospective study included 490 mCRC patients evaluated between 2020 and 2022 in our institution. Out of the 211 KRAS mutant cases (43.06%) 12 tumors were identified with multiple KRAS gene variants (5.68%). Detailed follow-up investigations were possible in 3 of these patients including the genotyping of the primary and available metastatic tumors, and the peripheral blood cfDNA. cfDNA was collected from three different time points before and between cycles of combined treatment with bevacizumab chemotherapy. KRAS gene variants were identified using reverse-hybridization strips, and next-generation sequencing (NGS), and confirmed by conventional Sanger sequencing. Interestingly, surgery and multiple treatment cycles reorganized the mutational profiles in the selected cases. The effect of the treatments resulted either in the overrepresentation of one of the pre-existing gene variants or in the appearance of new KRAS variants absent in the primary sample, according to the plasma cfDNA findings. Besides the KRAS variants demonstrated by targeted analysis, NGS mutational profiling identified some additional pathogenic variants from the cfDNA samples (including NRAS and MET alterations). In conclusion, plasma cfDNA sampling enables the monitoring of mutational heterogeneity and subclonal dynamics of the actual metastatic tumor mass in mCRC. The pattern of molecular profile potentially reflects a differential drug response determining further progression.
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Affiliation(s)
- Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Csilla András
- Department of Oncology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary.
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He W, Yang J, Sun X, Jiang S, Jiang J, Liu M, Mu T, Li Y, Zhang X, Duan J, Xu R. Advantages and Limitations of Monitoring Circulating Tumor DNA Levels to Predict the Prognosis of Patients Diagnosed With Gastric Cancer. Biomark Insights 2022; 17:11772719221141525. [PMID: 36533271 PMCID: PMC9751168 DOI: 10.1177/11772719221141525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/17/2022] [Indexed: 08/30/2023] Open
Abstract
Next-generation sequencing-based genomic profiling facilitates biomarker detection by cell-free DNA (cfDNA) liquid biopsy. However, the efficiency of mutation calling and the prognostic value of cfDNA biomarkers are disputed. We investigated 24 patients with gastric cancer in this study, using a 605-gene sequencing panel to sequence their plasma cfDNA and tumor tissue DNA. The mutation concordance between plasma cfDNA and tumor tissue DNA was 70.6% in stage IV gastric cancer and 30.2% in stage III gastric cancer, indicating insufficient mutation detection rates in stage III and early-stage cancer. When compared with total cfDNA load and blood tumor mutation burden (bTMB), the variant allele frequencies (VAF) of commonly mutated genes are highly accurate in representing disease burden. Further, VAF are a better prognostic indicator compared with serum biomarkers including carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), cancer antigen 125 (CA125), and alpha-fetoprotein (AFP). The use of cfDNA in molecular profiling of patients allows prediction of patient survival and clinical response, as well as the development of personalized therapy regimens.
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Affiliation(s)
- Wan He
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
| | - Jingxin Yang
- Center of Medical Genetics, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Xiao Sun
- Department of Gastrointestinal Surgery, Shenzhen People’s Hospital, Shenzhen, China
| | - Shunda Jiang
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
| | - Jinchan Jiang
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
| | - Ming Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen, China
| | - Tianhao Mu
- HaploX Biotechnology, Co., Ltd., Shenzhen, China
| | - Yingmei Li
- HaploX Biotechnology, Co., Ltd., Shenzhen, China
| | - Xiaoni Zhang
- HaploX Biotechnology, Co., Ltd., Shenzhen, China
| | - Jingxian Duan
- HaploX Biotechnology, Co., Ltd., Shenzhen, China
- Department of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ruilian Xu
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
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Nikanjam M, Kato S, Kurzrock R. Liquid biopsy: current technology and clinical applications. J Hematol Oncol 2022; 15:131. [PMID: 36096847 PMCID: PMC9465933 DOI: 10.1186/s13045-022-01351-y] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Liquid biopsies are increasingly used for cancer molecular profiling that enables a precision oncology approach. Circulating extracellular nucleic acids (cell-free DNA; cfDNA), circulating tumor DNA (ctDNA), and circulating tumor cells (CTCs) can be isolated from the blood and other body fluids. This review will focus on current technologies and clinical applications for liquid biopsies. ctDNA/cfDNA has been isolated and analyzed using many techniques, e.g., droplet digital polymerase chain reaction, beads, emulsion, amplification, and magnetics (BEAMing), tagged-amplicon deep sequencing (TAm-Seq), cancer personalized profiling by deep sequencing (CAPP-Seq), whole genome bisulfite sequencing (WGBS-Seq), whole exome sequencing (WES), and whole genome sequencing (WGS). CTCs have been isolated using biomarker-based cell capture, and positive or negative enrichment based on biophysical and other properties. ctDNA/cfDNA and CTCs are being exploited in a variety of clinical applications: differentiating unique immune checkpoint blockade response patterns using serial samples; predicting immune checkpoint blockade response based on baseline liquid biopsy characteristics; predicting response and resistance to targeted therapy and chemotherapy as well as immunotherapy, including CAR-T cells, based on serial sampling; assessing shed DNA from multiple metastatic sites; assessing potentially actionable alterations; analyzing prognosis and tumor burden, including after surgery; interrogating difficult-to biopsy tumors; and detecting cancer at early stages. The latter can be limited by the small amounts of tumor-derived components shed into the circulation; furthermore, cfDNA assessment in all cancers can be confounded by clonal hematopoeisis of indeterminate potential, especially in the elderly. CTCs can be technically more difficult to isolate that cfDNA, but permit functional assays, as well as evaluation of CTC-derived DNA, RNA and proteins, including single-cell analysis. Blood biopsies are less invasive than tissue biopsies and hence amenable to serial collection, which can provide critical molecular information in real time. In conclusion, liquid biopsy is a powerful tool, and remarkable advances in this technology have impacted multiple aspects of precision oncology, from early diagnosis to management of refractory metastatic disease. Future research may focus on fluids beyond blood, such as ascites, effusions, urine, and cerebrospinal fluid, as well as methylation patterns and elements such as exosomes.
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Affiliation(s)
- Mina Nikanjam
- Division of Hematology-Oncology, University of California San Diego, La Jolla, 1200 Garden View Road, Encinitas, CA, 92024, USA.
| | - Shumei Kato
- Division of Hematology-Oncology, University of California San Diego, La Jolla, 1200 Garden View Road, Encinitas, CA, 92024, USA
| | - Razelle Kurzrock
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA.,WIN Consortium, Paris, France
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Kim S, Lim Y, Kang JK, Kim HP, Roh H, Kim SY, Lee D, Bang D, Jeong SY, Park KJ, Han SW, Kim TY. Dynamic changes in longitudinal circulating tumour DNA profile during metastatic colorectal cancer treatment. Br J Cancer 2022; 127:898-907. [DOI: 10.1038/s41416-022-01837-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/09/2022] Open
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Guo S, Ye Y, Liu X, Gong Y, Xu M, Song L, Liu H. Intra-Tumor Heterogeneity of Colorectal Cancer Necessitates the Multi-Regional Sequencing for Comprehensive Mutational Profiling. Cancer Manag Res 2021; 13:9209-9223. [PMID: 34949941 PMCID: PMC8689048 DOI: 10.2147/cmar.s327596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Background The panorama and details of quantitative intratumor heterogeneity have not been fully investigated in colorectal cancer (CRC) patients with solitary lesion without distal metastasis, and its influences on sequencing interpretation and therapeutic strategies have not been explored. Methods Cancer tissues and matched blood from 70 sporadic CRC patients were collected and were divided into two cohorts. Four individual tissue biopsies were obtained from each of the 47 patients (multi-sample cohort). One random cancer tissue biopsy was obtained from each of the rest 23 patients (single-sample cohort). A 10 mL of blood was collected from all patients and the circulating cell-free DNA (cfDNA) was extracted. A 605-gene panel was used for targeted sequencing with tissue and paired blood. Results Mutational landscape revealed significantly higher mutational frequency in APC, CARD11 and CSMD3 in multi-sample cohort than single-sample cohort (P<0.05). The number of mutations and the ratio of trunk, shared and branch mutations showed extensive heterogeneity in multi-sample cohort, and the percentage of trunk mutations in major driver genes, including APC, TP53 and KRAS, was higher than 70%. A total of 929 mutations were detected in tissue/blood in multi-sample group, with 921(99.1%) from tissue and 472(50.8%) from blood (464 common mutations,49.9%). In contrast, 394 mutations were detected in tissue/blood in single-sample group, with 231 (58.6%) from tissue and 219 (55.6%) from blood (56 common mutations, 11.9%). The number of mutations of major driver genes detected in tissue was higher than that in blood in the multi-sample cohort, while it was similar in the single-sample group. Quantification analysis revealed differential correlation between tissue and blood VAF in trunk, shared and branch mutations. Meanwhile, VAF of trunk mutations was significantly higher than shared mutations and branch mutations. VAF exhibited significant differences among distinct stages, locations, differentiation and sex status. Conclusion Characteristic extensive heterogeneity was revealed for solitary CRC without distal metastasis. Multi-regional biopsy was necessary for comprehensive mutation detection in CRC.
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Affiliation(s)
- Shaohua Guo
- Department of General Surgery, The First Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
- Department of General Surgery, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yumeng Ye
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Xinyi Liu
- Department of Medical Division, HaploX Biotechnology, Shenzhen, People’s Republic of China
| | - Yuan Gong
- Department of Gastroenterology, The Second Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Mingyan Xu
- Department of Medical Division, HaploX Biotechnology, Shenzhen, People’s Republic of China
| | - Lele Song
- Department of Medical Division, HaploX Biotechnology, Shenzhen, People’s Republic of China
- Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
- Lele Song Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of ChinaTel +86-13240149188 Email
| | - Hongyi Liu
- Department of General Surgery, The First Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
- Correspondence: Hongyi Liu Department of General Surgery, The First Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of ChinaTel +86-10-66937533 Email
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Clinical Applications of Minimal Residual Disease Assessments by Tumor-Informed and Tumor-Uninformed Circulating Tumor DNA in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13184547. [PMID: 34572774 PMCID: PMC8471730 DOI: 10.3390/cancers13184547] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Circulating tumor DNA, or ctDNA, are fragments of tumor DNA that can be detected in the blood of patients with colorectal cancer. Measuring ctDNA levels in the blood has shown the potential to provide important information that can be helpful in the clinical care of patients with colorectal cancer. For example, in patients with colon cancer that has been removed by surgery, measuring ctDNA in the blood can predict the likelihood of cancer recurrence, while in those with metastatic colorectal cancer, measuring ctDNA can inform the clinician whether chemotherapy is effective at earlier timepoints than currently available tests. In this review, we discuss the results from ongoing studies describing the utility of ctDNA measurements across all stages of colorectal cancer. We also discuss the various clinical scenarios that ctDNA may have the most immediate impact in colorectal cancer management. Abstract Emerging data suggest that circulating tumor DNA (ctDNA) can detect colorectal cancer (CRC)-specific signals across both non-metastatic and metastatic settings. With the development of multiple platforms, including tumor-informed and tumor-agnostic ctDNA assays and demonstration of their provocative analytic performance to detect minimal residual disease, there are now ongoing, phase III randomized clinical trials to evaluate their role in the management paradigm of CRC. In this review, we highlight landmark studies that have formed the basis for ongoing studies on the clinically applicability of plasma ctDNA assays in resected, stage I–III CRC and metastatic CRC. We discuss clinical settings by which ctDNA may have the most immediate impact in routine clinical practice. These include the potential for ctDNA to (1) guide surveillance and intensification or de-intensification strategies of adjuvant therapy in resected, stage I–III CRC, (2) predict treatment response to neoadjuvant therapy in locally advanced rectal cancer inclusive of total neoadjuvant therapy (TNT), and (3) predict response to systemic and surgical therapies in metastatic disease. We end by considering clinical variables that can influence our ability to reliably interpret ctDNA dynamics in the clinic.
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12
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Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as a Liquid Biopsy Marker in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13184500. [PMID: 34572727 PMCID: PMC8469158 DOI: 10.3390/cancers13184500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Colorectal cancer is one of the most frequent malignant tumors worldwide and the spread of tumor cells through the blood circulation followed by the colonization of distant organs (“metastases”) is the main cause of cancer-related death. The blood is, therefore, an important fluid that can be explored for diagnostic purposes. Liquid biopsy is a new diagnostic concept defined as the analysis of circulating tumor cells or cellular products such as cell-free DNA in the blood or other body fluids of cancer patients. In this review, we summarize and discuss the latest findings using circulating tumor cells and cell-free DNA derived from tumor lesions in the blood of patients with colorectal cancer. Clinical applications include early detection of cancer, identification of patients with a high risk for disease progression after curative surgery, monitoring for disease progression in the context of cancer therapies, and discovery of mechanisms of resistance to therapy. Abstract Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. It is a heterogeneous tumor with a wide genomic instability, leading to tumor recurrence, distant metastasis, and therapy resistance. Therefore, adjunct non-invasive tools are urgently needed to help the current classical staging systems for more accurate prognostication and guiding personalized therapy. In recent decades, there has been an increasing interest in the diagnostic, prognostic, and predictive value of circulating cancer-derived material in CRC. Liquid biopsies provide direct non-invasive access to tumor material, which is shed into the circulation; this enables the analysis of circulating tumor cells (CTC) and genomic components such as circulating free DNA (cfDNA), which could provide the key for personalized therapy. Liquid biopsy (LB) allows for the identification of patients with a high risk for disease progression after curative surgery, as well as longitudinal monitoring for disease progression and therapy response. Here, we will review the most recent studies on CRC, demonstrating the clinical potential and utility of CTCs and ctDNA. We will discuss some of the advantages and limitations of LBs and the future perspectives in the field of CRC management.
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13
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Adashek JJ, Janku F, Kurzrock R. Signed in Blood: Circulating Tumor DNA in Cancer Diagnosis, Treatment and Screening. Cancers (Basel) 2021; 13:3600. [PMID: 34298813 PMCID: PMC8306582 DOI: 10.3390/cancers13143600] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/23/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022] Open
Abstract
With the addition of molecular testing to the oncologist's diagnostic toolbox, patients have benefitted from the successes of gene- and immune-directed therapies. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. An important advance in the application of molecular testing is the liquid biopsy, wherein circulating tumor DNA (ctDNA) is analyzed for point mutations, copy number alterations, and amplifications by polymerase chain reaction (PCR) and/or next-generation sequencing (NGS). The advantages of evaluating ctDNA over tissue DNA include (i) ctDNA requires only a tube of blood, rather than an invasive biopsy, (ii) ctDNA can plausibly reflect DNA shedding from multiple metastatic sites while tissue DNA reflects only the piece of tissue biopsied, and (iii) dynamic changes in ctDNA during therapy can be easily followed with repeat blood draws. Tissue biopsies allow comprehensive assessment of DNA, RNA, and protein expression in the tumor and its microenvironment as well as functional assays; however, tumor tissue acquisition is costly with a risk of complications. Herein, we review the ways in which ctDNA assessment can be leveraged to understand the dynamic changes of molecular landscape in cancers.
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Affiliation(s)
- Jacob J. Adashek
- Department of Internal Medicine, University of South Florida, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33606, USA
| | - Filip Janku
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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14
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Yi Z, Ma F, Rong G, Liu B, Guan Y, Li J, Sun X, Wang W, Guan X, Mo H, Wang J, Qian H, Xu B. The molecular tumor burden index as a response evaluation criterion in breast cancer. Signal Transduct Target Ther 2021; 6:251. [PMID: 34230452 PMCID: PMC8260637 DOI: 10.1038/s41392-021-00662-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Circulating tumor DNA (ctDNA) is a potential biomarker of prognosis and therapeutic response. We conducted this study to explore the role of the molecular tumor burden index (mTBI) in ctDNA as a therapeutic response and prognostic biomarker in a larger cohort prospective phase III randomized multicenter study. We collected 291 plasma samples from 125 metastatic breast cancer patients from the CAMELLIA study (NCT01917279). Target-capture deep sequencing of 1021 genes was performed to detect somatic variants in ctDNA from the plasma samples. The pretreatment mTBI value was correlated with tumor burden (P = 0.025). Patients with high-level pretreatment mTBI had shorter overall survival than patients with low-level pretreatment mTBI, and the median overall survival was 40.9 months and 68.4 months, respectively (P = 0.011). Patients with mTBI decrease to less than 0.02% at the first tumor evaluation had longer progression-free survival and overall survival (P < 0.001 and P = 0.007, respectively). The mTBI has good sensitivity to identify complete response/partial response and progressive disease based on computed tomography scans (88.5% and 87.5%, respectively). The patients classified as molecular responders had longer progression-free survival and overall survival than the nonmolecular responders in the overall cohort (P < 0.001 and P = 0.036, respectively), as well as in the cohort in which computed tomography scans were defined as representing stable disease (P = 0.027 and P = 0.015, respectively). The mTBI in ctDNA detected in liquid biopsies is a potential biomarker of therapeutic response and prognosis in patients with metastatic breast cancer.
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Affiliation(s)
- Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Guohua Rong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Jin Li
- Geneplus-Beijing Institute, Beijing, China
| | - Xiaoying Sun
- Department of Medical Oncology, Huanxing Cancer Hospital, Beijing, China
| | - Wenna Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongnan Mo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiani Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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Petrillo A, Salati M, Trapani D, Ghidini M. Circulating Tumor DNA as a Biomarker for Outcomes Prediction in Colorectal Cancer Patients. Curr Drug Targets 2021; 22:1010-1020. [PMID: 33155906 DOI: 10.2174/1389450121999201103194248] [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: 05/23/2020] [Revised: 08/07/2020] [Accepted: 08/23/2020] [Indexed: 12/24/2022]
Abstract
Circulating tumour DNA (ctDNA) is a novel tool that has been investigated in several types of tumours, including colorectal cancer (CRC). In fact, the techniques based on liquid biopsies are proposed as appealing non-invasive alternatives to tissue biopsy, adding more insights into tumour molecular profile, heterogeneity and for cancer detection and monitoring. Additionally, some analysis showed that in CRC patients, ctDNA seems to act as a biomarker able to predict the outcome (prognostic role) and the response to treatments (predictive role). In particular, in the early stage CRC (stage I-III), it could represent a time marker of adjuvant therapy as well as a marker of minimal residual disease and recurrence risk in addition to the already recognized risk factors. In metastatic CRC, the analysis of molecular tumour profile by ctDNA has shown to have high concordance with the tissue biopsy at diagnosis. Additionally, some studies demonstrated that ctDNA level during the treatment was linked with the early response to treatment and prognosis. Finally, the quantitative analysis of ctDNA and copy number alterations may be useful in order to detect resistance to therapy at the time of progression of disease and to help in finding new therapeutic targets.
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Affiliation(s)
| | - Massimiliano Salati
- Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy
| | - Dario Trapani
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - Michele Ghidini
- Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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16
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Ye P, Cai P, Xie J, Wei Y. The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A systematic review and meta-analysis. PLoS One 2021; 16:e0248775. [PMID: 33770081 PMCID: PMC7997033 DOI: 10.1371/journal.pone.0248775] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Introduction Before anti-EGFR therapy is given to patients with colorectal cancer, it is required to determine KRAS mutation status in tumor. When tumor tissue is not available, cell-free DNA (liquid biopsy) is commonly used as an alternative. Due to the low abundance of tumor-derived DNA in cell-free DNA samples, methods with high sensitivity were preferred, including digital polymerase chain reaction, amplification refractory mutation system and next-generation sequencing. The aim of this systemic review and meta-analysis was to investigate the accuracy of those methods in detecting KRAS mutation in cell-free DNA sample from patients with colorectal cancer. Methods Literature search was performed in Pubmed, Embase, and Cochrane Library. After removing duplicates from the 170 publications found by literature search, eligible studies were identified using pre-defined criteria. Quality of the publications and relevant data were assessed and extracted thereafter. Meta-DiSc and STATA softwares were used to pool the accuracy parameters from the extracted data. Results A total of 33 eligible studies were identified for this systemic review and meta-analysis. After pooling, the overall sensitivity, specificity, and diagnostic odds ratio were 0.77 (95%CI: 0.74–0.79), 0.87 (95%CI: 0.85–0.89), and 23.96 (95%CI: 13.72–41.84), respectively. The overall positive and negative likelihood ratios were 5.55 (95%CI: 3.76–8.19) and 0.29 (95%CI: 0.21–0.38), respectively. Area under curve of the summarized ROC curve was 0.8992. Conclusion Digital polymerase chain reaction, amplification refractory mutation system, and next-generation sequencing had overall high accuracy in detecting KRAS mutation in cell-free DNA sample. Large prospective randomized clinical trials are needed to further convince the accuracy and usefulness of KRAS mutation detection using cfDNA/liquid biopsy samples in clinical practice. Trial registration PROSPERO CRD42020176682; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=176682.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People’s Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Yuanyuan Wei
- Department of Physiology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
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17
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Holm M, Andersson E, Osterlund E, Ovissi A, Soveri LM, Anttonen AK, Kytölä S, Aittomäki K, Osterlund P, Ristimäki A. Detection of KRAS mutations in liquid biopsies from metastatic colorectal cancer patients using droplet digital PCR, Idylla, and next generation sequencing. PLoS One 2020; 15:e0239819. [PMID: 33237900 PMCID: PMC7688175 DOI: 10.1371/journal.pone.0239819] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is released from cancer cells and oncogenic mutations in ctDNA can be measured from plasma samples. Droplet digital PCR (ddPCR) is a sensitive and specific method for the detection of mutations in ctDNA. We analyzed serial plasma samples (n = 80) from ten metastatic colorectal cancer (mCRC) patients with a known KRAS mutation in their primary tumor. The patients were undergoing oncological treatment with bevacizumab in combination with alternating capecitabine and oxaliplatin or irinotecan. Baseline ddPCR KRAS mutation allele frequency (MAF) values ranged from 0% to 63%. The first radiologic response evaluation criteria in solid tumors (RECIST) evaluation was performed 45-63 days after the initiation of treatment, and by this time three patients had an undetectable level of KRAS mutation, one had a MAF value of 0.5%, and one had a MAF value of 3% that had been reduced by 95% from the baseline value. In three of these patients the RECIST assessment was stable disease and in two partial response. In seven patients, ddPCR MAF values increased before radiological disease progression or death, while one patient remained disease-free with an undetectable KRAS mutation level. Next, we analyzed all available plasma samples with the Idylla ctKRAS system (n = 60), and found that the overall degree of agreement between ddPCR and Idylla was almost perfect (kappa value = 0.860). We used next-generation sequencing (NGS) to detect treatment-induced mutations in the last serial plasma sample of each patient, but were unable to find any new mutations when compared to the primary tumor. This study shows that ddPCR and Idylla are equally efficient for the detection of KRAS mutations in the liquid biopsies from mCRC patients and that ctDNA may indicate the disappearance of treatment responsive KRAS positive mCRC clones and serve as an early sign of disease progression.
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Affiliation(s)
- Matilda Holm
- Department of Pathology, Medicum, Faculty of Medicine, University of Helsinki and HUSLAB, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Surgery, Medicum, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Cancer Medicine Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emma Andersson
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Emerik Osterlund
- Department of Surgery, Medicum, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ali Ovissi
- Department of Radiology, HUS Diagnostic Center, Helsinki University Hospital, and University of Helsinki, Helsinki, Finland
| | - Leena-Maija Soveri
- Department of Oncology, Clinicum, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Hyvinkää Hospital and Hyvinkää Homecare, Hyvinkää, Finland
| | - Anna-Kaisa Anttonen
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Soili Kytölä
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Pia Osterlund
- Department of Oncology, Clinicum, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Department of Oncology, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Ari Ristimäki
- Department of Pathology, Medicum, Faculty of Medicine, University of Helsinki and HUSLAB, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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18
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Liu Z, Guo H, Zhu Y, Xia Y, Cui J, Shi K, Fan Y, Shi B, Chen S. TP53 alterations of hormone-naïve prostate cancer in the Chinese population. Prostate Cancer Prostatic Dis 2020; 24:482-491. [PMID: 33214693 DOI: 10.1038/s41391-020-00302-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Prostate cancer (PCa) shows racial disparity in clinical and genomic characteristics, and Asian patients with PCa often present with more aggressive phenotypes at diagnosis. The ability of TP53 to serve as a prognostic biomarker of PCa has been well studied in Western populations. However, no studies to date have examined the role of TP53 in the disparities of primary hormone-naïve prostate cancer (HNPC) between Chinese and Western populations. METHODS We collected prostate tumors and matched normal tissues or blood samples to perform targeted next-generation sequencing of 94 Chinese primary localized HNPC samples, and correlated these genomic profiles with clinical outcomes. The OncoKB knowledge database was used to identify and classify actionable alterations. RESULTS The aberrations of PTEN, CDK12, and SPOP in Chinese HNPC samples were similar to those in the Western samples. However, we demonstrated an association of a high frequency of TP53 alterations (21/94) with a relatively higher percentage of alterations in the Wnt signaling pathway (15/94) in Chinese HNPC. Additionally, we highlighted alterations of LRP1B as accounting for a high proportion of PCa and found more frequent alterations in CDH1 in Chinese PCa. Of these, only CDH1 alteration was associated with rapid biochemical recurrence (BCR). However, we verified that TP53 status was at the core of the genomic alteration landscape in Chinese HNPC with putative driver mutations because of the strong connections with other signaling pathways. The mutually exclusive relationship between alterations in TP53 and Wnt/CTNNB1 further molecularly characterizes subsets of prostate cancers. Moreover, the alteration of KMT2C was more likely to co-occur with TP53 alteration, indicating a more aggressive phenotype of PCa, which was associated with sensitivity to treatment with poly ADT-ribose polymerase (PARP) inhibitors. CONCLUSIONS Detection of TP53 alterations has clinical utility for guiding precision cancer therapy for HNPC, especially in the Chinese population.
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Affiliation(s)
- Zhengfang Liu
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China
| | - Hu Guo
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China
| | - Yaofeng Zhu
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China
| | - Yangyang Xia
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China
| | - Jianfeng Cui
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China
| | - Kai Shi
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China.
| | - Benkang Shi
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China. .,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China.
| | - Shouzhen Chen
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, 250012, PR China. .,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Ji'nan, 250012, PR China.
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19
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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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