1
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
2
|
Huang T, Li J, Wang SM. Core promoter mutation contributes to abnormal gene expression in bladder cancer. BMC Cancer 2022; 22:68. [PMID: 35033028 PMCID: PMC8761283 DOI: 10.1186/s12885-022-09178-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Bladder cancer is one of the most mortal cancers. Bladder cancer has distinct gene expression signature, highlighting altered gene expression plays important roles in bladder cancer etiology. However, the mechanism for how the regulatory disorder causes the altered expression in bladder cancer remains elusive. Core promoter controls transcriptional initiation. We hypothesized that mutation in core promoter abnormality could cause abnormal transcriptional initiation thereby the altered gene expression in bladder cancer. METHODS In this study, we performed a genome-wide characterization of core promoter mutation in 77 Spanish bladder cancer cases. RESULTS We identified 69 recurrent somatic mutations in 61 core promoters of 62 genes and 28 recurrent germline mutations in 20 core promoters of 21 genes, including TERT, the only gene known with core promoter mutation in bladder cancer, and many oncogenes and tumor suppressors. From the RNA-seq data from bladder cancer, we observed altered expression of the core promoter-mutated genes. We further validated the effects of core promoter mutation on gene expression by using luciferase reporter gene assay. We also identified potential drugs targeting the core promoter-mutated genes. CONCLUSIONS Data from our study highlights that core promoter mutation contributes to bladder cancer development through altering gene expression.
Collapse
Affiliation(s)
- Teng Huang
- Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau
| | - Jiaheng Li
- Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau
| | - San Ming Wang
- Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau.
| |
Collapse
|
3
|
Meng J, Victor B, He Z, Liu H, Jiang T. DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network. Brief Bioinform 2020; 22:5960414. [PMID: 33164053 DOI: 10.1093/bib/bbaa272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/05/2020] [Accepted: 09/19/2020] [Indexed: 01/16/2023] Open
Abstract
It is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, they take into consideration only limited information about the reference and potential variant allele in both tumor and normal samples at a candidate somatic site. Also, they differ in how biological and technological noises are addressed. Hence, they are expected to produce divergent outputs. To overcome the drawbacks of existing somatic callers, we develop a deep learning-based tool called DeepSSV, which employs a convolutional neural network (CNN) model to learn increasingly abstract feature representations from the raw data in higher feature layers. DeepSSV creates a spatially oriented representation of read alignments around the candidate somatic sites adapted for the convolutional architecture, which enables it to expand to effectively gather scattered evidence. Moreover, DeepSSV incorporates the mapping information of both reference allele-supporting and variant allele-supporting reads in the tumor and normal samples at a genomic site that are readily available in the pileup format file. Together, the CNN model can process the whole alignment information. Such representational richness allows the model to capture the dependencies in the sequence and identify context-based sequencing artifacts. We fitted the model on ground truth somatic mutations and did benchmarking experiments on simulated and real tumors. The benchmarking results demonstrate that DeepSSV outperforms its state-of-the-art competitors in overall F1 score.
Collapse
Affiliation(s)
- Jing Meng
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, Jiangsu, China
| | | | - Zhen He
- La Trobe University, Melbourne, Victoria, Australia
| | | | - Taijiao Jiang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
4
|
Wei T, Zhang Q, Li X, Su W, Li G, Ma T, Gao S, Lou J, Que R, Zheng L, Bai X, Liang T. Monitoring Tumor Burden in Response to FOLFIRINOX Chemotherapy Via Profiling Circulating Cell-Free DNA in Pancreatic Cancer. Mol Cancer Ther 2018; 18:196-203. [PMID: 30301865 DOI: 10.1158/1535-7163.mct-17-1298] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/28/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022]
Abstract
We aimed to explore the application of circulating cell-free DNA (cfDNA) profiling in monitoring tumor burden in patients with pancreatic ductal adenocarcinoma (PDAC). Thirty-eight patients with advanced PDAC receiving first-line FOLFIRINOX chemotherapy were prospectively enrolled. Next-generation sequencing for a panel of 560 genes covering a wide range of cancer-related loci was performed to profile cfDNA. In total, 25 patients (65.8%) had at least one common driver gene alterations (KRAS, TP53, SMAD4, CDKN2A) detected within cfDNA. In contrast, no above tumor-related recurrent mutations were found in plasma from 13 healthy individuals. Concordant alterations in plasma cfDNA and tumor tissue DNA was confirmed in two of three patients with available tissues. Further analysis showed that mutant allele fraction (MAF) for altered loci in cfDNA correlated with tumor stage, metastatic burden, and overall survival. Serial blood samples were collected from 17 patients after chemotherapy. We found that allele fraction for specific altered loci declined in chemotherapy-responding subjects. For cases who were resistant to this therapeutic regimen, increased ctDNA MAF was observed at the time of disease progression. Meanwhile, the dynamics of total cfDNA concentration correlated with tumor burden following chemotherapy. Collectively, we provide evidence that pretreatment ctDNA level correlates with tumor burden in PDAC, and serial cfDNA analysis is a robust tool for monitoring cancer response to chemotherapy.
Collapse
Affiliation(s)
- Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Xiang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Wei Su
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Guogang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Tao Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Shunliang Gao
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Jianying Lou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Risheng Que
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Lei Zheng
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China
| |
Collapse
|
5
|
Lee JH, Jeong H, Choi JW, Oh HE, Kim YS. Liquid biopsy prediction of axillary lymph node metastasis, cancer recurrence, and patient survival in breast cancer: A meta-analysis. Medicine (Baltimore) 2018; 97:e12862. [PMID: 30334995 PMCID: PMC6211877 DOI: 10.1097/md.0000000000012862] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Liquid biopsies using circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) have been developed for early cancer detection and patient monitoring. To investigate the clinical usefulness of ctDNA aberrations and cfDNA levels in patients with breast cancer (BC), we conducted a meta-analysis of 69 published studies on 5736 patients with BC. METHODS The relevant publications were identified by searching PubMed and Embase databases. The effect sizes of outcome parameters were pooled using a random-effects model. RESULTS The ctDNA mutation rates of TP53, PIK3CA, and ESR1 were approximately 38%, 27%, and 32%, respectively. High levels of cfDNA were associated with BCs rather than with healthy controls. However, these detection rates were not satisfactory for BC screening. Although the precise mechanisms have been unknown, high cfDNA levels were significantly associated with axillary lymph node metastasis (odds ratio [OR] = 2.148, P = .030). The ctDNA mutations were significantly associated with cancer recurrence (OR = 3.793, P < .001), short disease-free survival (univariate hazard ratio [HR] = 5.180, P = .026; multivariate HR = 3.605, P = .001), and progression-free survival (HR = 1.311, P = .013) rates, and poor overall survival outcomes (HR = 2.425, P = .007). CONCLUSION This meta-analysis demonstrates that ctDNA mutation status predicts disease recurrence and unfavorable survival outcomes, while cfDNA levels can be predictive of axillary lymph node metastasis in patients with BC.
Collapse
|
6
|
Meng J, Chen YPP. A database of simulated tumor genomes towards accurate detection of somatic small variants in cancer. PLoS One 2018; 13:e0202982. [PMID: 30161165 PMCID: PMC6116990 DOI: 10.1371/journal.pone.0202982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/13/2018] [Indexed: 11/19/2022] Open
Abstract
Somatic mutations promote the transformation of normal cells to cancer. Accurate identification of such mutations facilitates cancer diagnosis and treatment, but biological and technological noises, including intra-tumor heterogeneity, sample contamination, uncertainties in base sequencing and read alignment, pose a big challenge to somatic mutation discovery. A number of callers have been developed to predict them from paired tumor/normal or unpaired tumor sequencing data. However, the small size of currently available experimentally validated somatic sites limits evaluation and then improvement of callers. Fortunately, NIST reference material NA12878 genome has been well-characterized with publicly available high-confidence genotype calls, and biological and technological noises can be computationally generalized to the number of sub-clones, the VAFs, the sequencing and mapping qualities. We used BAMSurgeon to create simulated tumors by introducing somatic small variants (SNVs and small indels) into homozygous reference or wildtype sites of NA12878. We generated 135 simulated tumors from 5 pre-tumors/normals. These simulated tumors vary in sequencing and subsequent mapping error profiles, read length, the number of sub-clones, the VAF, the mutation frequency across the genome and the genomic context. Furthermore, these pure tumor/normal pairs can be mixed at desired ratios within each pair to simulate sample contamination. This database (a total size of 15 terabytes) will be of great use to benchmark somatic small variant callers and guide their improvement.
Collapse
Affiliation(s)
- Jing Meng
- College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria, Australia
| | - Yi-Ping Phoebe Chen
- College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria, Australia
| |
Collapse
|
7
|
Thierry AR, El Messaoudi S, Mollevi C, Raoul JL, Guimbaud R, Pezet D, Artru P, Assenat E, Borg C, Mathonnet M, De La Fouchardière C, Bouché O, Gavoille C, Fiess C, Auzemery B, Meddeb R, Lopez-Crapez E, Sanchez C, Pastor B, Ychou M. Clinical utility of circulating DNA analysis for rapid detection of actionable mutations to select metastatic colorectal patients for anti-EGFR treatment. Ann Oncol 2018; 28:2149-2159. [PMID: 28911069 DOI: 10.1093/annonc/mdx330] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background While tumor-tissue remains the 'gold standard' for genetic analysis in cancer patients, it is challenged with the advent of circulating cell-free tumor DNA (ctDNA) analysis from blood samples. Here, we broaden our previous study on the clinical validation of plasma DNA in metastatic colorectal cancer patients, by evaluating its clinical utility under standard management care. Patients and methods Concordance and data turnaround-time of ctDNA when compared with tumor-tissue analysis were studied in a real-time blinded prospective multicenter clinical study (n = 140 metastatic colorectal patients). Results are presented according to STARD criteria and were discussed in regard with clinical outcomes of patients. Results Much more mutations were found by ctDNA analysis: 59%, 11.8% and 14.4% of the patients were found KRAS, NRAS and BRAF mutant by ctDNA analysis instead of 44%, 8.8% and 7.2% by tumor-tissue analysis. Median tumor-tissue data turnaround-time was 16 days while 2 days for ctDNA analysis. Discordant samples analysis revealed that use of biopsy, long delay between tumor-tissue and blood collection and resection of the tumor at time of blood draw, tumor site, or type of tissue analyzed seem to affect concordance. Altogether, the clinical data with respect to the anti-epidermal growth factor receptor response (RAS status) and the prognosis (BRAF status) of those discordant patients do not appear contradictory to the mutational status as determined by plasma analysis. Lastly, we present the first distribution profile of the RAS and BRAF hotspot mutations as determined by ctDNA analysis (n = 119), revealing a high proportion of patients with multiple mutations (45% of the population and up to 5 mutations) and only 24% of WT scored patients for both genes. Mutation profile as determined from ctDNA analysis with using various detection thresholds highlights the importance of the test sensitivity. Conclusion Our study showed that ctDNA could replace tumor-tissue analysis, and also clinical utility of ctDNA analysis by considerably reducing data turnaround time.
Collapse
Affiliation(s)
- A R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - S El Messaoudi
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - C Mollevi
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier.,Biometry Unit, Regional Institute of Cancer of Montpellier, Montpellier
| | - J L Raoul
- Department of Medical Oncology, Paoli Calmettes Institute, Marseille
| | - R Guimbaud
- Department of Oncology, University Hospital Center of Toulouse - Hospital Rangueil-Purpan, Toulouse
| | - D Pezet
- Digestive Oncology Unit, Department of Digestive Surgery, University Hospital Center of Clermont-Ferrand, UMR Inserm/Auvergne University U1071, Clermont-Ferrand
| | - P Artru
- Jean-Mermoz Private Hospital, Lyon
| | - E Assenat
- CHRU Montpellier, St. Eloi Hospital, Montpellier
| | - C Borg
- CHRU Jean MINJOZ, Besançon
| | - M Mathonnet
- Digestive Surgery Department, Clinical Investigation Centre, University Hospital Center of Limoges, INSERM 0801, Limoges
| | | | | | - C Gavoille
- Alexis Vautrin Oncology Institute of Lorraine, Nancy
| | - C Fiess
- Digestive Oncology Department, Regional Institute of Cancer of Montpellier, Montpellier, France
| | - B Auzemery
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - R Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - E Lopez-Crapez
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - C Sanchez
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - B Pastor
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier
| | - M Ychou
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier.,INSERM, U1194, Montpellier.,Department of Oncology, Montpellier University, Montpellier.,Regional Institute of Cancer of Montpellier, Montpellier.,Digestive Oncology Department, Regional Institute of Cancer of Montpellier, Montpellier, France
| |
Collapse
|
8
|
Condorelli R, Spring L, O’Shaughnessy J, Lacroix L, Bailleux C, Scott V, Dubois J, Nagy R, Lanman R, Iafrate A, Andre F, Bardia A. Polyclonal RB1 mutations and acquired resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer. Ann Oncol 2018; 29:640-645. [DOI: 10.1093/annonc/mdx784] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
9
|
Jia Y, Xu H, Li Y, Wei C, Guo R, Wang F, Wu Y, Liu J, Jia J, Yan J, Qi X, Li Y, Gao X. A Modified Ficoll-Paque Gradient Method for Isolating Mononuclear Cells from the Peripheral and Umbilical Cord Blood of Humans for Biobanks and Clinical Laboratories. Biopreserv Biobank 2017; 16:82-91. [PMID: 29232525 DOI: 10.1089/bio.2017.0082] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although the Ficoll-Paque method is classically used to isolate peripheral blood mononuclear cells (PBMCs), modifications in this method are required for a more rapid and economic output for biobanks and clinical laboratories, particularly in developing countries. In this study, we addressed this issue by modifying the Ficoll-Paque method for the isolation of PBMCs or mononuclear cells from the peripheral and the umbilical cord blood of healthy and diseased (infected, anemic, and chronic obstructive pulmonary disease) adult individuals. In the modified method, we initiated the cell isolation process from the buffy coat layer, which appears in the interface between the plasma and sediments after centrifugation, instead of using the whole blood as described in the classic method. Although the PBMC yield by the modified method was about 12% less than in the classic method, the number of PBMCs isolated by the modified method was more than one million, which is enough for different research/diagnostic purposes, such as multi-omics detection. Assessment of cell viability and purity by hematology analyzer and trypan blue showed no significant difference between the viability and purity of the PBMCs isolated by these two methods in almost all groups, except samples from the infected and cord blood groups, where lower PBMC purity with higher granulocyte contamination were observed. In addition, at delayed processing time points, all parameters for the two methods were decreased in a time-dependent manner, especially at 8, 12, or 24 hours after the sample collection. In summary, the performance of PBMC isolation by the classic and modified methods mainly relies on the PBMC ratio in original samples. The modified method could be preferred for PBMC isolation because of its time and cost savings, especially for the biobanks and clinical laboratories in developing countries.
Collapse
Affiliation(s)
- Yanjuan Jia
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Hui Xu
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Yonghong Li
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Chaojun Wei
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Rui Guo
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Fang Wang
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Yu Wu
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Jing Liu
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Jing Jia
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Junwen Yan
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaoming Qi
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Yuanting Li
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaoling Gao
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| |
Collapse
|
10
|
Mehrotra M, Singh RR, Loghavi S, Duose DY, Barkoh BA, Behrens C, Patel KP, Routbort MJ, Kopetz S, Broaddus RR, Medeiros LJ, Wistuba II, Luthra R. Detection of somatic mutations in cell-free DNA in plasma and correlation with overall survival in patients with solid tumors. Oncotarget 2017. [PMID: 29535804 PMCID: PMC5828199 DOI: 10.18632/oncotarget.21982] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A suitable clinical-grade platform is required for detection of somatic mutations with high sensitivity in cell-free DNA (cfDNA) of patients with solid tumors. In this study, we evaluated in parallel ultra-deep NGS with MassARRAY and allele-specific droplet digital PCR (ddPCR) for cfDNA genotyping and correlated cfDNA yield and mutation status with overall survival (OS) of patients. We assessed plasma samples from 46 patients with various advanced metastatic solid tumors and known mutations by deep sequencing using an Ampliseq cancer hotspot panel V2 on Ion Proton. A subset of these samples with DNA availability was tested by ddPCR and UltraSEEK MassARRAY for mutation detection in 5 genes (IDH1, PIK3CA, KRAS, BRAF, and NRAS). Sixty one of 104 expected tissue mutations and 6 additional mutations not present in the tissue were detected in cfDNA. ddPCR and MassARRAY showed 83% and 77% concordance with NGS for mutation detection with 100% and 79% sensitivity, respectively. The median OS of patients with lower cfDNA yield (74 vs 50 months; P < 0.03) and cfDNA negative for mutations (74.2 vs 53 months; p < 0.04) was significantly longer than in patients with higher cfDNA yield and positive for mutations. A limit-of-detection of 0.1% was demonstrated for ddPCR and MassARRAY platforms using a serially diluted positive cfDNA sample. The MassARRAY and ddPCR systems enable fast and cost-effective genotyping for a targeted set of mutations and can be used for single gene testing to guide response to chemotherapy or for orthogonal validation of NGS results.
Collapse
Affiliation(s)
- Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dzifa Yawa Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bedia A Barkoh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Russell R Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
11
|
Analysis of BRCA1/2 mutation spectrum and prevalence in unselected Chinese breast cancer patients by next-generation sequencing. J Cancer Res Clin Oncol 2017; 143:2011-2024. [DOI: 10.1007/s00432-017-2465-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/22/2017] [Indexed: 01/10/2023]
|
12
|
Janku F, Zhang S, Waters J, Liu L, Huang HJ, Subbiah V, Hong DS, Karp DD, Fu S, Cai X, Ramzanali NM, Madwani K, Cabrilo G, Andrews DL, Zhao Y, Javle M, Kopetz ES, Luthra R, Kim HJ, Gnerre S, Satya RV, Chuang HY, Kruglyak KM, Toung J, Zhao C, Shen R, Heymach JV, Meric-Bernstam F, Mills GB, Fan JB, Salathia NS. Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer. Clin Cancer Res 2017; 23:5648-5656. [PMID: 28536309 DOI: 10.1158/1078-0432.ccr-17-0291] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/22/2017] [Accepted: 05/18/2017] [Indexed: 01/04/2023]
Abstract
Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care.Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03).Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR.
Collapse
Affiliation(s)
- Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | | | - Li Liu
- Illumina, Inc., San Diego, California
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xuyu Cai
- Illumina, Inc., San Diego, California
| | - Nishma M Ramzanali
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kiran Madwani
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Goran Cabrilo
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Debra L Andrews
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yue Zhao
- Illumina, Inc., San Diego, California
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - E Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | | | - Chen Zhao
- Illumina, Inc., San Diego, California
| | | | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | |
Collapse
|
13
|
Tong Y, Li S, Huang C. EGFR induces DNA decomposition via phosphodiester bond cleavage. Sci Rep 2017; 7:43698. [PMID: 28272528 PMCID: PMC5341565 DOI: 10.1038/srep43698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/26/2017] [Indexed: 01/08/2023] Open
Abstract
EGFR may induce DNA degradation. This activity had not been previously described as an EGRF function. To confirm this unexpected activity, testing of EGFR in the presence of ATP and either 5A, 5C, 5G, 5T, or 5U oligonucleotides was performed. HPLC-MS analysis demonstrated that 5A and 5U levels significantly decreased in the presence of EGFR. Furthermore, fragments 4A and 4U were produced in 5A+EGFR+ATP and in 5U+EGFR+ATP reaction mixtures, respectively, but not in EGFR-negative controls. Degradation of Poly(A), Poly(C), Poly(G), Poly(I), Poly(T), and Poly(U) oligomers in the presence of EGFR and ATP correlated with the lower ability of reaction products to pair with complementary oligonucleotides. Gel electrophoresis showed that breakdown products migrated more quickly than controls, especially after addition of paired (complementary) oligomers, Poly(A) and Poly(U). Furthermore, λ DNA reaction products also migrated more quickly after incubation with EGFR. The results suggest that EGFR can induce breakage of certain types of nucleotide phosphodiester bonds, especially within the A residues of DNA or U residues of RNA, to induce DNA or RNA decomposition, respectively. This activity may be important in EGRF signaling, DNA degradation, or repair in normal or cancer cell activities.
Collapse
Affiliation(s)
- Yongpeng Tong
- College of Physics and Energy, Shenzhen University, Shenzhen, 518060, China
| | - Shuiming Li
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chunliu Huang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| |
Collapse
|