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Sadat Kalaki N, Ahmadzadeh M, Najafi M, Mobasheri M, Ajdarkosh H, Karbalaie Niya MH. Systems biology approach to identify biomarkers and therapeutic targets for colorectal cancer. Biochem Biophys Rep 2024; 37:101633. [PMID: 38283191 PMCID: PMC10821538 DOI: 10.1016/j.bbrep.2023.101633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
Background Colorectal cancer (CRC), is the third most prevalent cancer across the globe, and is often detected at advanced stage. Late diagnosis of CRC, leave the chemotherapy and radiotherapy as the main options for the possible treatment of the disease which are associated with severe side effects. In the present study, we seek to explore CRC gene expression data using a systems biology framework to identify potential biomarkers and therapeutic targets for earlier diagnosis and treatment of the disease. Methods The expression data was retrieved from the gene expression omnibus (GEO). Differential gene expression analysis was conducted using R/Bioconductor package. The PPI network was reconstructed by the STRING. Cystoscope and Gephi software packages were used for visualization and centrality analysis of the PPI network. Clustering analysis of the PPI network was carried out using k-mean algorithm. Gene-set enrichment based on Gene Ontology (GO) and KEGG pathway databases was carried out to identify the biological functions and pathways associated with gene groups. Prognostic value of the selected identified hub genes was examined by survival analysis, using GEPIA. Results A total of 848 differentially expressed genes were identified. Centrality analysis of the PPI network resulted in identification of 99 hubs genes. Clustering analysis dissected the PPI network into seven interactive modules. While several DEGs and the central genes in each module have already reported to contribute to CRC progression, survival analysis confirmed high expression of central genes, CCNA2, CD44, and ACAN contribute to poor prognosis of CRC patients. In addition, high expression of TUBA8, AMPD3, TRPC1, ARHGAP6, JPH3, DYRK1A and ACTA1 was found to associate with decreased survival rate. Conclusion Our results identified several genes with high centrality in PPI network that contribute to progression of CRC. The fact that several of the identified genes have already been reported to be relevant to diagnosis and treatment of CRC, other highlighted genes with limited literature information may hold potential to be explored in the context of CRC biomarker and drug target discovery.
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Affiliation(s)
- Niloufar Sadat Kalaki
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
- International Institute of New Sciences (IINS), Tehran, Iran
| | - Mozhgan Ahmadzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Najafi
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Meysam Mobasheri
- Department of Biotechnology, Faculty of Advanced Sciences and Technology, Tehran Islamic Azad University of Medical Sciences, Tehran, Iran
- International Institute of New Sciences (IINS), Tehran, Iran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Karbalaie Niya
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Kwon HJ, Shin SH, Kim HH, Min NY, Lim Y, Joo TW, Lee KJ, Jeong MS, Kim H, Yun SY, Kim Y, Park D, Joo J, Bae JS, Lee S, Jeong BH, Lee K, Lee H, Kim HK, Kim K, Um SW, An C, Lee MS. Advances in methylation analysis of liquid biopsy in early cancer detection of colorectal and lung cancer. Sci Rep 2023; 13:13502. [PMID: 37598236 PMCID: PMC10439900 DOI: 10.1038/s41598-023-40611-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023] Open
Abstract
Methylation patterns in cell-free DNA (cfDNA) have emerged as a promising genomic feature for detecting the presence of cancer and determining its origin. The purpose of this study was to evaluate the diagnostic performance of methylation-sensitive restriction enzyme digestion followed by sequencing (MRE-Seq) using cfDNA, and to investigate the cancer signal origin (CSO) of the cancer using a deep neural network (DNN) analyses for liquid biopsy of colorectal and lung cancer. We developed a selective MRE-Seq method with DNN learning-based prediction model using demethylated-sequence-depth patterns from 63,266 CpG sites using SacII enzyme digestion. A total of 191 patients with stage I-IV cancers (95 lung cancers and 96 colorectal cancers) and 126 noncancer participants were enrolled in this study. Our study showed an area under the receiver operating characteristic curve (AUC) of 0.978 with a sensitivity of 78.1% for colorectal cancer, and an AUC of 0.956 with a sensitivity of 66.3% for lung cancer, both at a specificity of 99.2%. For colorectal cancer, sensitivities for stages I-IV ranged from 76.2 to 83.3% while for lung cancer, sensitivities for stages I-IV ranged from 44.4 to 78.9%, both again at a specificity of 99.2%. The CSO model's true-positive rates were 94.4% and 89.9% for colorectal and lung cancers, respectively. The MRE-Seq was found to be a useful method for detecting global hypomethylation patterns in liquid biopsy samples and accurately diagnosing colorectal and lung cancers, as well as determining CSO of the cancer using DNN analysis.Trial registration: This trial was registered at ClinicalTrials.gov (registration number: NCT04253509) for lung cancer on 5 February 2020, https://clinicaltrials.gov/ct2/show/NCT04253509 . Colorectal cancer samples were retrospectively registered at CRIS (Clinical Research Information Service, registration number: KCT0008037) on 23 December 2022, https://cris.nih.go.kr , https://who.init/ictrp . Healthy control samples were retrospectively registered.
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Affiliation(s)
- Hyuk-Jung Kwon
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Sun Hye Shin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Hyun Ho Kim
- Department of Surgery, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 327 Sosa-Ro, Bucheon, 14647, Republic of Korea
| | - Na Young Min
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - YuGyeong Lim
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Tae-Woon Joo
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Kyoung Joo Lee
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Min-Seon Jeong
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Hyojung Kim
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Seon-Young Yun
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - YoonHee Kim
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Dabin Park
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Joungsu Joo
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Jin-Sik Bae
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Sunghoon Lee
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea
| | - Byeong-Ho Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Kyungjong Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Hayemin Lee
- Department of Surgery, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 327 Sosa-Ro, Bucheon, 14647, Republic of Korea
| | - Hong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Kyongchol Kim
- Gangnam Major Hospital, 452 Dogok-Ro, Gangnam-Gu, Seoul, 06279, Republic of Korea
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea.
| | - Changhyeok An
- Department of Surgery, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 327 Sosa-Ro, Bucheon, 14647, Republic of Korea.
| | - Min Seob Lee
- R&D Department, Eone-Diagnomics Genome Center, Inc., 143 Gaetbeol-Ro, Yeonsu-Gu, Incheon, 21999, Republic of Korea.
- Diagnomics, Inc., 5795 Kearny Villa Rd., San Diego, CA, 92123, USA.
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Li S, Xin K, Pan S, Wang Y, Zheng J, Li Z, Liu X, Liu B, Xu Z, Chen X. Blood-based liquid biopsy: insights into early detection, prediction, and treatment monitoring of bladder cancer. Cell Mol Biol Lett 2023; 28:28. [PMID: 37016296 PMCID: PMC10074703 DOI: 10.1186/s11658-023-00442-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Bladder cancer (BC) is a clinical challenge worldwide with late clinical presentation, poor prognosis, and low survival rates. Traditional cystoscopy and tissue biopsy are routine methods for the diagnosis, prognosis, and monitoring of BC. However, due to the heterogeneity and limitations of tumors, such as aggressiveness, high cost, and limited applicability of longitudinal surveillance, the identification of tumor markers has attracted significant attention in BC. Over the past decade, liquid biopsies (e.g., blood) have proven to be highly efficient methods for the discovery of BC biomarkers. This noninvasive sampling method is used to analyze unique tumor components released into the peripheral circulation and allows serial sampling and longitudinal monitoring of tumor progression. Several liquid biopsy biomarkers are being extensively studied and have shown promising results in clinical applications of BC, including early detection, detection of microscopic residual disease, prediction of recurrence, and response to therapy. Therefore, in this review, we aim to provide an update on various novel blood-based liquid biopsy markers and review the advantages and current limitations of liquid biopsy in BC therapy. The role of blood-based circulating tumor cells, circulating tumor DNA, cell-free RNA, exosomes, metabolomics, and proteomics in diagnosis, prognosis, and treatment monitoring, and their applicability to the personalized management of BC, are highlighted.
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Affiliation(s)
- Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Kerong Xin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Shen Pan
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yang Wang
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, Liaoning, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Xuefeng Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Bitian Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Zhenqun Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
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5
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R HC, Kumar S U, R G, Naayanan PJ, Sathiyarajeswaren P, Devi MSS, K SS, Doss C GP. An integrated investigation of structural and pathway alteration caused by PIK3CA and TP53 mutations identified in cfDNA of metastatic breast cancer. J Cell Biochem 2023; 124:188-204. [PMID: 36563059 DOI: 10.1002/jcb.30354] [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: 09/27/2022] [Revised: 11/12/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
In peripheral blood, cell-free DNA (cfDNA) contains circulating tumor DNA (ctDNA), which indicates molecular abnormalities in metastatic breast tumor tissue. The sequencing of cfDNA of Metastatic Breast Cancer (MBC) patients allows assessment of therapy response and noninvasive treatment. In the proposed study, clinically significant alterations in PIK3CA and TP53 genes associated with MBC resulting in a missense substitution of His1047Arg and Arg282Trp from an next-generation sequencing-based multi-gene panel were reported in a cfDNA of a patient with MBC. To investigate the impact of the reported mutation, we used molecular docking, molecular dynamics simulation, network analysis, and pathway analysis. Molecular Docking analysis determined the distinct binding pattern revealing H1047R-ATP complex has a higher number of Hydrogen bonds (H-bonds) and binding affinity with a slight difference compared to the PIK3CA-ATP complex. Following, molecular dynamics simulation for 200 ns, of which H1047R-ATP complex resulted in the instability of PIK3CA. Similarly, for TP53 mutant R282W, the zinc-free state (apo) and zinc-bounded (holo) complexes were investigated for conformational change between apo and holo complexes, of which the holo complex mutant R282W was unstable. To validate the conformational change of PIK3CA and TP53, 80% mutation of H1047R in the kinase domain of p110α expressed ubiquitously in PIK3CA protein that alters PI3K pathway, while R282W mutation in DNA binding helix (H2) region of P53 protein inhibits the transcription factor in P53 pathway causing MBC. According to our findings, the extrinsic (hypoxia, oxidative stress, and acidosis); intrinsic factors (MYC amplification) in PIK3CA and TP53 mutations will provide potential insights for developing novel therapeutic methods for MBC therapy.
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Affiliation(s)
- Hephzibah Cathryn R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Udhaya Kumar S
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Gnanasambandan R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | | | - M S Shree Devi
- Siddha Central Research Institute (CCRS), Chennai, Tamil Nadu, India
| | - Satish Srinivas K
- Department of Radiation Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Ye J, Wu M, He L, Chen P, Liu H, Yang H. Glutathione-S-Transferase p1 Gene Promoter Methylation in Cell-Free DNA as a Diagnostic and Prognostic Tool for Prostate Cancer: A Systematic Review and Meta-Analysis. Int J Endocrinol 2023; 2023:7279243. [PMID: 36747996 PMCID: PMC9899149 DOI: 10.1155/2023/7279243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Promoter methylation of glutathione-S-transferase p1 (GSTP1) is related to the occurrence of prostate cancer (PCa), but reports are inconsistent about the accuracy of GSTP1 promoter methylation in PCa diagnosis and prognosis. Therefore, we systematically evaluated the diagnostic and prognostic value of GSTP1 promoter methylation in PCa. METHODS The PubMed, EMBASE, Web of Science, and PMC databases were searched for all relevant studies from the date of inception to November 31, 2021. We compared differences in the incidence of GSTP1 promoter methylation in cfDNA between prostate cancer patients and controls. The odds ratio (OR) and hazard ratio (HR) were used as effect sizes, and the result of each effect size is expressed as a 95% confidence interval (95% CI). RESULTS Our meta-analysis showed that the combined sensitivity and specificity of GSTP1 promoter methylation in cfDNA for the diagnosis of prostate cancer were 0.37 (95% CI = 0.23, 0.53) and 0.97 (95% CI = 0.88, 0.99), respectively. The area under the curve (AUC) with 95% CI was 0.78 (95% CI = 0.75, 0.82). For prognostic variables, hypermethylation of GSTP1 was associated with shorter survival in PCa (HR = 2.57, 95% CI = 1.30, 5.10), with statistical significance in between-study heterogeneity (I 2 = 72%, P=0.006). The results of the subgroup analysis indicated that the heterogeneity of studies may be due to differences in the observed indicators. CONCLUSIONS The results of the meta-analysis substantiate the high specificity of promoter methylation of GSTP1 in cfDNA for the diagnosis of prostate cancer, and it may be used to more precisely evaluate the prognosis of patients with prostate cancer. It may be helpful for the early detection of prostate cancer, but it still must be combined with traditional prostate-specific antigen (PSA) or other methylated genes to accomplish this goal.
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Affiliation(s)
- Jinghe Ye
- Department of Graduate School, China Medical University, Shenyang, China
- Department of Organ Transplantation Center, General Hospital of Northern Theatre Command, Shenyang, China
| | - Mao Wu
- Department of Graduate School, China Medical University, Shenyang, China
- Department of Urology, General Hospital of Northern Theatre Command, Shenyang, China
| | - Long He
- Department of Organ Transplantation Center, General Hospital of Northern Theatre Command, Shenyang, China
| | - Peng Chen
- Department of Urology, General Hospital of Northern Theatre Command, Shenyang, China
| | - Hongtao Liu
- Department of Urology, General Hospital of Northern Theatre Command, Shenyang, China
| | - Hongwei Yang
- Department of Organ Transplantation Center, General Hospital of Northern Theatre Command, Shenyang, China
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7
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Lee HW, Kim E, Cho KJ, Park HJ, Seo J, Lee H, Baek E, Choi JR, Han KH, Lee ST, Park JY. Applications of molecular barcode sequencing for the detection of low-frequency variants in circulating tumour DNA from hepatocellular carcinoma. Liver Int 2022; 42:2317-2326. [PMID: 35776657 DOI: 10.1111/liv.15356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/02/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Liquid biopsy has emerged as a promising tool for minimally invasive and accurate detection of various malignancies. We aimed to apply molecular barcode sequencing to circulating tumour DNA (ctDNA) from liquid biopsies of hepatocellular carcinoma (HCC). STUDY DESIGN Patients with HCC or benign liver disease were enrolled between 2017 and 2018. Matched tissue and serum samples were obtained from these patients. Plasma cell-free DNA was extracted and subjected to targeted sequencing with ultra-high coverage and molecular barcoding. RESULTS The study included 143 patients: 102 with HCC, 7 with benign liver tumours and 34 with chronic liver disease. No tier 1/2 or oncogenic mutations were detected in patients with benign liver disease. Among the HCC patients, 49 (48%) had tier 1/2 mutations in at least one gene; detection rates were higher in advanced stages (75%) than in early stages (26%-33%). TERT was the most frequently mutated gene (30%), followed by TP53 (16%), CTNNB1 (14%), ARID2 (5%), ARID1A (4%), NFE2L2 (4%), AXIN1 (3%) and KRAS (1%). Survival among patients with TP53 mutations was significantly worse (p = 0.007) than among patients without these mutations, whereas CTNNB1 and TERT mutations did not affect survival. ctDNA testing combined with α-fetoprotein and prothrombin induced by vitamin K absence-II analyses improved HCC detection, even in early stages. CONCLUSIONS ctDNA detection using molecular barcoding technology offers dynamic and personalized information concerning tumour biology, such information can guide clinical diagnosis and management. This detection also has the potential as a minimally invasive approach for prognostic stratification and post-therapeutic monitoring.
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Affiliation(s)
- Hye Won Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea.,Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Esl Kim
- Department of Medical Science, The Graduate School, Yonsei University, Seoul, South Korea
| | - Kyung Joo Cho
- Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Hye Jung Park
- Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Jieun Seo
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyeonah Lee
- Department of Medical Science, The Graduate School, Yonsei University, Seoul, South Korea
| | - Eunha Baek
- Dxome Co. Ltd., Seongnam-si, Gyeonggi-do, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co. Ltd., Seongnam-si, Gyeonggi-do, South Korea
| | - Kwang-Hyub Han
- Yonsei Liver Center, Severance Hospital, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co. Ltd., Seongnam-si, Gyeonggi-do, South Korea
| | - Jun Yong Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea.,Yonsei Liver Center, Severance Hospital, Seoul, South Korea
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8
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Petrylak DP, Watkins SP, Loehr A. What Plasma Can Tell Us When Tissue Cannot: A Case Report of Genomic Testing in mCRPC and Clinical Response to Treatment With the PARP Inhibitor Rucaparib. Front Oncol 2022; 12:951348. [PMID: 35978838 PMCID: PMC9377337 DOI: 10.3389/fonc.2022.951348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background The poly(ADP-ribose) polymerase (PARP) inhibitor rucaparib was approved in the United States based on the phase 2 TRITON2 study of patients with BRCA1 or BRCA2 (BRCA)-mutated metastatic castration-resistant prostate cancer (mCRPC). Although genomic screening is recommended as part of a comprehensive assessment of prostate cancer prognosis and treatment options, the best way to select patients with mCRPC for treatment with a PARP inhibitor depends on individual clinical circumstances. For example, assessment of tumor tissue may not always be feasible. Genomic testing of DNA from plasma has become more readily available, providing a minimally invasive option to evaluate DNA from primary and metastatic lesions simultaneously. Case Presentation A patient from TRITON2 with BRCA-mutated mCRPC had a response to the PARP inhibitor rucaparib and remained on treatment for 32 weeks, which was >2 times longer than the duration of each of his prior therapies (bicalutamide, docetaxel, abiraterone). The patient enrolled in TRITON2 based on results of local genomic testing of an archival biopsy that indicated the presence of a BRCA1 T1399I (allelic fraction, 19%) mutation. Local testing also identified an ATM G1663C mutation, a TP53 P191del mutation, and a BRAF K601E mutation. Analysis of a plasma sample obtained before the patient started rucaparib detected the same alterations as those in the archival biopsy, but it also revealed the presence of a BRCA2 homozygous loss (whole gene, 26 of 26 exons) and several other alterations of unknown functional impact. We hypothesize the response of the patient's tumor to rucaparib was likely driven by DNA damage repair deficiency caused by homozygous loss of all BRCA2 exons. Following discontinuation from rucaparib due to clinical disease progression, the patient received carboplatin and cabazitaxel for ≈3 weeks. The patient died due to progression of his disease. Conclusions A notable aspect of this case is the differences in alterations detected in the archival tumor sample and a more recent plasma sample. This highlights the advantages of plasma testing compared with tissue testing when selecting targeted therapies for treatment of mCRPC; however, physicians must determine which tool presents the best solution for each individual case.
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Affiliation(s)
- Daniel P. Petrylak
- Smilow Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Simon P. Watkins
- Clinical Science, Clovis Oncology UK, Ltd, Cambridge, United Kingdom
| | - Andrea Loehr
- Translational Medicine, Clovis Oncology, Inc., Boulder, CO, United States
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Sharbatoghli M, Fattahi F, Aboulkheyr Es H, Akbari A, Akhavan S, Ebrahimi M, Asadi-Lari M, Totonchi M, Madjd Z. Copy Number Variation of Circulating Tumor DNA (ctDNA) Detected Using NIPT in Neoadjuvant Chemotherapy-Treated Ovarian Cancer Patients. Front Genet 2022; 13:938985. [PMID: 35938032 PMCID: PMC9355329 DOI: 10.3389/fgene.2022.938985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) can be used to characterize and monitor cancers. Recently, non-invasive prenatal testing (NIPT) as a new next-generation sequencing (NGS)-based approach has been applied for detecting ctDNA. This study aimed to investigate the copy number variations (CNVs) utilizing the non-invasive prenatal testing in plasma ctDNA from ovarian cancer (OC) patients who were treated with neoadjuvant chemotherapy (NAC). The plasma samples of six patients, including stages II–IV, were collected during the pre- and post-NAC treatment that were divided into NAC-sensitive and NAC-resistant groups during the follow-up time. CNV analysis was performed using the NIPT via two methods “an open-source algorithm WISECONDORX and NextGENe software.” Results of these methods were compared in pre- and post-NAC of OC patients. Finally, bioinformatics tools were used for data mining from The Cancer Genome Atlas (TCGA) to investigate CNVs in OC patients. WISECONDORX analysis indicated fewer CNV changes on chromosomes before treatment in the NAC-sensitive rather than NAC-resistant patients. NextGENe data indicated that CNVs are not only observed in the coding genes but also in non-coding genes. CNVs in six genes were identified, including HSF1, TMEM249, MROH1, GSTT2B, ABR, and NOMO2, only in NAC-resistant patients. The comparison of these six genes in NAC-resistant patients with The Cancer Genome Atlas data illustrated that the total alteration frequency is amplification, and the highest incidence of the CNVs (≥35% based on TCGA data) is found in MROH1, TMEM249, and HSF1 genes on the chromosome (Chr) 8. Based on TCGA data, survival analysis showed a significant reduction in the overall survival among chemotherapy-resistant patients as well as a high expression level of these three genes compared to that of sensitive samples (all, p < 0.0001). The continued Chr8 study using WISECONDORX revealed CNV modifications in NAC-resistant patients prior to NAC therapy, but no CNV changes were observed in NAC-sensitive individuals. Our findings showed that low coverage whole-genome sequencing analysis used for NIPT could identify CNVs in ctDNA of OC patients before and after chemotherapy. These CNVs are different in NAC-sensitive and -resistant patients highlighting the potential application of this approach in cancer patient management.
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Affiliation(s)
- Mina Sharbatoghli
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Fahimeh Fattahi
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | | | - Arvand Akbari
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Setareh Akhavan
- Department of Gynecologic Oncology, Vali-Asr Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mohsen Asadi-Lari
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- *Correspondence: Zahra Madjd, ; Mehdi Totonchi,
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- *Correspondence: Zahra Madjd, ; Mehdi Totonchi,
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10
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Identification of Hub Genes for Early Diagnosis and Predicting Prognosis in Colon Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1893351. [PMID: 35774271 PMCID: PMC9239823 DOI: 10.1155/2022/1893351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023]
Abstract
Colon adenocarcinoma (COAD) is among the most common digestive system malignancies worldwide, and its pathogenesis and gene signatures remain unclear. This study explored the genetic characteristics and molecular mechanisms underlying colon cancer development. Three gene expression data sets were obtained from the Gene Expression Omnibus (GEO) database. GEO2R was used to determine differentially expressed genes (DEGs) between COAD and normal tissues. Then, the intersection of the data sets was obtained. Metascape was used to perform the functional enrichment analyses. Next, STRING was used to build protein-protein interaction (PPI) networks. Hub genes were identified and analysed using Cytoscape. Next, survival analysis and expression analysis of the hub genes were performed. ROC curve analysis was performed for further test of the diagnostic efficacy. Finally, alterations in the hub genes were predicted and analysed by cBioPortal. Altogether, 436 DEGs were detected. The DEGs were mainly enriched in cell cycle phase transition, nuclear division, meiotic nuclear division, and cytokinesis. Based on PPI networks, 20 hub genes were selected. Among them, 6 hub genes (CCNB1, CCNA2, AURKA, NCAPG, DLGAP5, and CENPE) showed significant prognostic value in colon cancer (P < 0.05), while 5 hub genes (CDK1, CCNB1, CCNA2, MAD2L1, and DLGAP5) were associated with early colon cancer diagnosis and ROC curve analysis showed good diagnostic accuracy. In conclusion, integrated bioinformatics analysis was used to identify hub genes that reveal the potential mechanism of carcinogenesis and progression of colon cancer. The hub genes might be novel biomarkers for early diagnosis, treatment, and prognosis of colon cancer.
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11
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Liu MC, MacKay M, Kase M, Piwowarczyk A, Lo C, Schaeffer J, Finkle JD, Mason CE, Beaubier N, Blackwell KL, Park BH. Longitudinal Shifts of Solid Tumor and Liquid Biopsy Sequencing Concordance in Metastatic Breast Cancer. JCO Precis Oncol 2022; 6:e2100321. [PMID: 35721584 PMCID: PMC9200387 DOI: 10.1200/po.21.00321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/17/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue-based next-generation sequencing (NGS) in metastatic breast cancer (mBC) is limited by the inability to noninvasively track tumor evolution. Cell-free DNA (cfDNA) NGS has made sequential testing feasible; however, the relationship between cfDNA and tissue-based testing in mBC is not well understood. Here, we evaluate concordance between tissue and cfDNA NGS relative to cfDNA sampling frequency in a large, clinically annotated mBC data set. METHODS Tempus LENS was used to analyze deidentified records of mBC cases with Tempus xT (tissue) and xF (cfDNA) sequencing results. Then, various metrics of concordance were assessed within overlapping probe regions of the tissue and cfDNA assays (104 genes), focusing on pathogenic variants. Variant allele frequencies of discordant and concordant pathogenic variants were also compared. Analyses were stratified by mBC subtype and time between tests. RESULTS Records from 300 paired tissue and liquid biopsies were analyzed. Median time between tissue and blood collection was 78.5 days (standard deviation = 642.99). The median number of pathogenic variants/patient was one for cfDNA and two for tissue. Across the cohort, 77.8% of pathogenic tissue variants were found in cfDNA and 75.7% of pathogenic cfDNA variants were found in tissue when tests were ≤ 7 days apart, which decreased to 50.3% and 51.8%, respectively, for > 365 days. Furthermore, the median patient-level variant concordance was 67% when tests were ≤7 days apart and 30%-37% when > 30 days. The median variant allele frequencies of discordant variants were generally lower than those of concordant variants within the same time frame. CONCLUSION We observed high concordances between tissue and cfDNA results that generally decreased with longer durations between tests. Thus, cfDNA NGS reliably measures tissue genomics and is likely beneficial for longitudinal monitoring of molecular changes in mBC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ben Ho Park
- Vanderbilt University Medical Center, Nashville, TN
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12
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Ionescu F, Zhang J, Wang L. Clinical Applications of Liquid Biopsy in Prostate Cancer: From Screening to Predictive Biomarker. Cancers (Basel) 2022; 14:1728. [PMID: 35406500 PMCID: PMC8996910 DOI: 10.3390/cancers14071728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 01/15/2023] Open
Abstract
Prostate cancer (PC) remains the most common malignancy and the second most common cause of cancer death in men. As a result of highly variable biological behavior and development of resistance to available agents under therapeutic pressure, optimal management is often unclear. Traditional surgical biopsies, even when augmented by genomic studies, may fail to provide adequate guidance for clinical decisions as these can only provide a snapshot of a dynamic process. Additionally, surgical biopsies are cumbersome to perform repeatedly and often involve risk. Liquid biopsies (LB) are defined as the analysis of either corpuscular (circulating tumor cells, extracellular vesicles) or molecular (circulating DNA or RNA) tumor-derived material. LB could more precisely identify clinically relevant alterations that characterize the metastatic potential of tumors, predict response to specific treatments or actively monitor for the emergence of resistance. These tests can potentially be repeated as often as deemed necessary and can detect real-time response to treatment with minimal inconvenience to the patient. In the current review, we consider common clinical scenarios to describe available LB assays in PC as a platform to explore existing evidence for their use in guiding decision making and to discuss current limitations to their adoption in the clinic.
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Affiliation(s)
- Filip Ionescu
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Jingsong Zhang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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13
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Computational challenges in detection of cancer using cell-free DNA methylation. Comput Struct Biotechnol J 2022; 20:26-39. [PMID: 34976309 PMCID: PMC8669313 DOI: 10.1016/j.csbj.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.
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Key Words
- Cancer heterogeneity
- Cell free DNA
- Computation
- DMP, Differentially methylated base position
- DMR, Differentially methylated regions
- Diagnosis
- HELP-seq, HpaII-tiny fragment Enrichment by Ligation-mediated PCR sequencing
- MBD-seq, Methyl-CpG Binding Domain Protein Capture Sequencing
- MCTA-seq, Methylated CpG tandems amplification and sequencing
- MSCC, Methylation Sensitive Cut Counting
- MSRE, methylation sensitive restriction enzymes
- MeDIP-seq, Methylated DNA Immunoprecipitation Sequencing
- RRBS, Reduced-Representation Bisulfite Sequencing
- WGBS, Whole Genome Bisulfite Sequencing
- cfDNA, cell free DNA
- ctDNA, circulating tumor DNA
- dPCR, digital polymerase chain reaction
- ddMCP, droplet digital methylation-specific PCR
- ddPCR, droplet digital polymerase chain reaction
- scCGI, methylated CGIs at single cell level
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14
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Kastrisiou M, Zarkavelis G, Kougioumtzi A, Sakaloglou P, Kostoulas C, Georgiou I, Batistatou A, Pentheroudakis G, Magklara A. Development and Validation of a Targeted ‘Liquid’ NGS Panel for Treatment Customization in Patients with Metastatic Colorectal Cancer. Diagnostics (Basel) 2021; 11:diagnostics11122375. [PMID: 34943612 PMCID: PMC8700616 DOI: 10.3390/diagnostics11122375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023] Open
Abstract
The detection of actionable mutations in tumor tissue is a prerequisite for treatment customization in patients with metastatic colorectal cancer (mCRC). Analysis of circulating tumor DNA (ctDNA) for the identification of such mutations in patients’ plasma is an attractive alternative to invasive tissue biopsies. Despite having the high analytical sensitivity required for ctDNA analysis, digital polymerase chain reaction (dPCR) technologies can only detect a very limited number of hotspot mutations, whilst a broader mutation panel is currently needed for clinical decision making. Recent advances in next-generation sequencing (NGS) have led to high-sensitivity platforms that allow screening of multiple genes at a single assay. Our goal was to develop a small, cost- and time-effective NGS gene panel that could be easily integrated in the day-to-day clinical routine in the management of patients with mCRC. We designed a targeted panel comprising hotspots in six clinically relevant genes (KRAS, NRAS, MET, BRAF, ERBB2 and EGFR) and validated it in a total of 68 samples from 30 patients at diagnosis, first and second disease progression. Results from our NGS panel were compared against plasma testing with BEAMing dPCR regarding the RAS gene status. The overall percent of agreement was 83.6%, with a positive and negative percent agreement of 74.3% and 96.2%, respectively. Further comparison of plasma NGS with standard tissue testing used in the clinic showed an overall percent agreement of 86.7% for RAS status, with a positive and negative percent agreement of 81.2% and 92.8%, respectively. Thus, our study strongly supports the validity and efficiency of an affordable targeted NGS panel for the detection of clinically relevant mutations in patients with mCRC.
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Affiliation(s)
- Myrto Kastrisiou
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (M.K.); (A.K.)
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece;
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece;
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece
| | - Anastasia Kougioumtzi
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (M.K.); (A.K.)
| | - Prodromos Sakaloglou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (P.S.); (C.K.); (I.G.)
| | - Charilaos Kostoulas
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (P.S.); (C.K.); (I.G.)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (P.S.); (C.K.); (I.G.)
| | - Anna Batistatou
- Department of Pathology, Faculty of Medicine, University of Ioannina, 45500 Ioannina, Greece;
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece;
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece
- Correspondence: (G.P.); (A.M.)
| | - Angeliki Magklara
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (M.K.); (A.K.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 45110 Ioannina, Greece
- Institute of Biosciences, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
- Correspondence: (G.P.); (A.M.)
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15
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Gray J, Thompson JC, Carpenter EL, Elkhouly E, Aggarwal C. Plasma Cell-Free DNA Genotyping: From an Emerging Concept to a Standard-of-Care Tool in Metastatic Non-Small Cell Lung Cancer. Oncologist 2021; 26:e1812-e1821. [PMID: 34216176 PMCID: PMC8488793 DOI: 10.1002/onco.13889] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/18/2021] [Indexed: 11/10/2022] Open
Abstract
Plasma cell-free DNA (cfDNA) genotyping is an alternative to tissue genotyping, particularly when tissue specimens are insufficient or unavailable, and provides critical information that can be used to guide treatment decisions in managing patients with non-small cell lung cancer (NSCLC). In this article, we review the evolution of plasma cfDNA genotyping from an emerging concept, through development of analytical methods, to its clinical applications as a standard-of-care tool in NSCLC. The number of driver or resistance mutations recommended for testing in NSCLC continues to increase. Because of the expanding list of therapeutically relevant variants, comprehensive testing to investigate larger regions of multiple genes in a single run is often preferable and saves on time and cost, compared with performing serial single-gene assays. Recent advances in nucleic acid next-generation sequencing have led to a rapid expansion in cfDNA genotyping technologies. Analytic assays that have received regulatory approval are now routinely used as diagnostic companions in the setting of metastatic NSCLC. As the demand for plasma-based technologies increases, more regulatory approvals of cfDNA genotyping assays are expected in the future. Plasma cfDNA genotyping is currently aiding oncologists in the delivery of personalized care by facilitating matching of patients with targeted therapy and monitoring emergence of resistance to therapy in NSCLC. Further advances currently underway to increase assay sensitivity and specificity will potentially expand the use of plasma cfDNA genotyping in early cancer detection, monitoring response to therapy, detection of minimal residual disease, and measurement of tumor mutational burden in NSCLC. IMPLICATIONS FOR PRACTICE: Plasma cell-free DNA (cfDNA) genotyping offers an alternative to tissue genotyping, particularly when tissue specimens are insufficient or unavailable. Advances in cfDNA genotyping technologies have led to analytic assays that are now routinely used to aid oncologists in the delivery of personalized care by facilitating matching of patients with targeted therapy and monitoring emergence of resistance to therapy. Further advances underway to increase assay sensitivity and specificity will potentially expand the use of plasma cfDNA genotyping in early cancer detection, monitoring response to therapy, detection of minimal residual disease, and evaluation of tumor mutational burden in non-small cell lung cancer.
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Affiliation(s)
- Jhanelle Gray
- H. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Jeffrey C. Thompson
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | | | - Charu Aggarwal
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
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16
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Fettke H, Kwan EM, Bukczynska P, Steen JA, Docanto M, Ng N, Parente P, Mant A, Foroughi S, Pezaro C, Hauser C, Nguyen-Dumont T, Southey MC, Azad AA. Independent prognostic impact of plasma NCOA2 alterations in metastatic castration-resistant prostate cancer. Prostate 2021; 81:992-1001. [PMID: 34254334 DOI: 10.1002/pros.24194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The androgen receptor (AR) pathway-associated gene nuclear receptor coactivator 2 (NCOA2) has an established oncogenic role in early prostate cancer and likewise is a driver of metastatic disease and castration-resistant prostate cancer. However, its significance as a biomarker in metastatic castration-resistant prostate cancer (mCRPC), both alone and in conjunction with co-occurring AR alterations using a liquid biopsy approach has not been investigated. METHODS Ninety-one patients were included in this study, (n = 68 receiving an androgen receptor pathway inhibitor and n = 23 receiving taxane chemotherapy). Up to 30 ml of peripheral blood was collected before commencing treatment from each patient. Plasma cell-free DNA, along with a matched germline sample, underwent targeted next-generation sequencing using a validated, highly sensitive in-house prostate cancer panel. Variants in AR and NCOA2 were identified and correlated with clinical outcomes. RESULTS Plasma AR and NCOA2 aberrations were identified in 35% and 13% of the cohort, respectively, whilst 8% had concurrent AR and NCOA2 alterations. NCOA2 copy number gain and any NCOA2 aberration predicted for lower prostate-specific antigen (PSA) response rates. Likewise, median overall survival was shorter for NCOA2 gain (10.1 vs. 18.3 months; p = .004), remaining significant after adjusting for covariates including circulating tumor DNA fraction and tumor suppressor gene alterations. Importantly, dual AR and NCOA2 aberrations were also associated with inferior outcomes, including no PSA responses in patients treated with AR pathway inhibitors (0% vs. 64%; p = .02). CONCLUSIONS These data highlight the importance of identifying multiple markers of AR pathway modulation in mCRPC and represent the first instance of the assessment of plasma NCOA2 status as a prognostic biomarker for standard-of-care therapies. Further assessment is warranted to determine if NCOA2 aberrations are a marker of primary resistance to AR pathway inhibitors.
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Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Department of Medical Oncology, Monash Health, Melbourne, Australia
| | | | - Jason A Steen
- Precision Medicine, School of Clinical Sciences, Monash Health, Melbourne, Australia
| | - Maria Docanto
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | - Nicole Ng
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Phillip Parente
- Medical Oncology Unit, Eastern Health, Melbourne, Australia
- Eastern Health Clinical School, Monash University, Melbourne, Australia
| | - Andrew Mant
- Medical Oncology Unit, Eastern Health, Melbourne, Australia
- Eastern Health Clinical School, Monash University, Melbourne, Australia
| | - Siavash Foroughi
- Personalised Oncology Division, The Water and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Carmel Pezaro
- Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, England
| | - Christine Hauser
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences, Monash Health, Melbourne, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Melissa C Southey
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences, Monash Health, Melbourne, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
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17
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Cai J, Li C, Li H, Wang X, Zhou Y. Establishment of a ferroptosis-related gene signature for prognosis in lung adenocarcinoma patients. PeerJ 2021; 9:e11931. [PMID: 34434660 PMCID: PMC8351575 DOI: 10.7717/peerj.11931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022] Open
Abstract
Objective Lung cancer is the most common malignancy worldwide and exhibits both high morbidity and mortality. In recent years, scientists have made substantial breakthroughs in the early diagnosis and treatment of lung adenocarcinoma (LUAD), however, patient prognosis still shows vast individual differences. In this study, bioinformatics methods were used to identify and analyze ferroptosis-related genes to establish an effective signature for predicting prognosis in LUAD patients. Methods The gene expression profiles of LUAD patients with complete clinical and follow-up information were downloaded from two public databases, univariate Cox regression and multivariate Cox regression analysis were used to obtain ferroptosis-related genes for constructing the prognos tic risk model, AUC and calibration plot were used to evaluate the predictive accuracy of the FRGS and nomogram. Results A total of 74 ferroptosis-related differentially expressed genes (DEGs) were identi fied between LUAD and normal tissues from The Cancer Genome Atlas (TCGA) database. A five-gene panel for prediction of LUAD prognosis was established by multivariate regression and was verified using the GSE68465 cohort from the Gene Expression Omnibus (GEO) database. Patients were divided into two different risk groups according to the median risk score of the five genes. Based on Kaplan-Meier (KM) analysi, the OS rate of the high-risk group was markedly worse than that of the low-risk group. We also found that risk score was an independent prognostic indicator. The receiver operating characteristic ROC curve showed that the proposed model had good prediction ability. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses indicated that risk score was prominently enriched in ferroptosis processes. Moreover, at the score of immune-associated gene sets, significant differences were found between the two risk groups. Conclusions This study demonstrated that ferroptosis-related gene signatures can be used as a potential predictor for the prognosis of LUAD, thus providing a novel strategy for individualized treatment in LUAD patients.
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Affiliation(s)
- Jingjing Cai
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Chunyan Li
- Department of Head and Neck Surgery Section II, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Hongsheng Li
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Xiaoxiong Wang
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Yongchun Zhou
- Molecular Diagnostics Center, The Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital, Kunming, Yunnan, China
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18
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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20
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Zhao J, Sun G, Zhu S, Dai J, Chen J, Zhang M, Ni Y, Zhang H, Shen P, Zhao X, Zhang B, Pan X, Nie L, Yin X, Liang J, Zhang X, Wang Z, Zhu X, Liao B, Liu Z, Armstrong CM, Gao AC, Huang H, Chen N, Zeng H. Circulating tumour DNA reveals genetic traits of patients with intraductal carcinoma of the prostate. BJU Int 2021; 129:345-355. [PMID: 34185954 DOI: 10.1111/bju.15530] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/05/2021] [Accepted: 06/22/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To investigate the genetic alterations of patients with prostate cancer (PCa) with and without intraductal carcinoma of the prostate (IDC-P). PATIENTS AND METHODS We performed targeted sequencing of plasma cell-free DNA on 161 patients with prostate adenocarcinoma (PAC) with IDC-P and 84 without IDC-P. Genomic alterations were compared between these two groups. The association between genetic alterations and patients' survival outcomes was also explored. RESULTS We identified that 29.8% (48/161) and 21.4% (18/84) of patients with and without IDC-P harboured genomic alterations in DNA repair pathways, respectively (P = 0.210). Pathogenic germline DNA repair alterations were frequently detected in IDC-P carriers compared to IDC-P non-carriers (11.8% [19/161] vs 2.4% [two of 84], P = 0.024). Germline BReast CAncer type 2 susceptibility protein (BRCA2) and somatic cyclin-dependent kinase 12 (CDK12) defects were specifically identified in IDC-P carriers relative to PAC (BRCA2: 8.7% [14/161] vs 0% and CDK12: 6.8% [11/161] vs 1.2% [one of 84]). Patients with IDC-P had a distinct androgen receptor (AR) pathway alteration, characterised by an enrichment of nuclear receptor corepressor 2 (NCOR2) mutations compared with patients with pure PAC (21.1% [34/161] vs 6.0% [five of 84], P = 0.004). Increased AR alterations were detected in patients harbouring tumours with an IDC-P proportion of ≥10% vs those with an IDC-P proportion of <10% (6.4% [five of 78] vs 18.1% [15/83], P = 0.045). For IDC-P carriers, tumour protein p53 (TP53) mutation was associated with shorter castration-resistant-free survival (median 10.9 vs 28.9 months, P = 0.026), and BRCA2 alteration was related to rapid prostate-specific antigen progression for those receiving abiraterone treatment (median 9.1 vs 11.9 months, P = 0.036). CONCLUSION Our findings provide genomic evidence explaining the aggressive phenotype of tumours with IDC-P, highlighting the potential therapeutic strategies for this patient population.
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Affiliation(s)
- Jinge Zhao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Guangxi Sun
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Sha Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jindong Dai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Junru Chen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Mengni Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Yuchao Ni
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Haoran Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Pengfei Shen
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaochen Zhao
- Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Bei Zhang
- Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Nie
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoxue Yin
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xingming Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhipeng Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Xudong Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Banghua Liao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhenhua Liu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | | | - Allen C Gao
- Department of Urology, University of California Davis, Davis, CA, USA
| | | | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
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21
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Tian C, Li X, Ge C. High expression of LAMA3/AC245041.2 gene pair associated with KRAS mutation and poor survival in pancreatic adenocarcinoma: a comprehensive TCGA analysis. Mol Med 2021; 27:62. [PMID: 34134622 PMCID: PMC8207728 DOI: 10.1186/s10020-021-00322-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 12/23/2022] Open
Abstract
Background Pancreatic adenocarcinoma (PAAD) is one of the most challenging cancers with high morbidity and mortality. KRAS mutations could occur as an early event in PAAD. The present study aimed to identify the differentially expressed lncRNAs (DE-lncRNAs) and differentially expressed mRNAs (DE-mRNAs) in KRAS-mutant PAAD to explore the pathogenesis and the underlying molecular mechanism of PAAD development. Methods Clinical data of TCGA–PAAD patients were downloaded from the TCGA database and subjected to survival analysis along with the KRAS mutation information data. Weighted gene correlation network analysis (WGCNA) and univariate Cox regression analysis were conducted to construct prognostic risk models to identify the hub DE-mRNAs and DE-lncRNAs associated with PAAD prognosis. GO and KEGG enrichment analyses of the identified hub DE-mRNAs were performed. Multivariate cox regression analysis was performed to analyze the overall prognosis of age, gender, pathologic_T, and KRAS mutations, following which the differences in the clinical characteristics of risk score1 and risk score2 were analyzed. Finally, the mRNAs–lncRNA–TFs regulatory network was constructed. Results Functional enrichment analysis was performed after screening 1671 DE-mRNAs and 324 DE-lncRNAs. It was observed that the associated pathways were enriched mainly in the modulation of chemical synaptic transmission, synaptic membrane, ion-gated channel activity, ligand−receptor interactions that stimulate neural tissue, among others. The univariate Cox regression analysis screened 117 mRNAs and 36 lncRNAs, and the risk ratio models of the mRNAs and lncRNAs were constructed. LAMA3 (mRNA) and AC245041.2 (lncRNA) exhibited a strong expression correlation in the respective two risk models. The genes in the samples with a high expression of these two genes were enriched in several pathways associated with transcription factors (TFs), among which the TFs ATF5, CSHL1, NR1I2, SIPA1, HOXC13, HSF2, and HOXA10 were shared by the two groups. The core enrichment genes in the common TF pathways were collated, and the mRNAs–lncRNAs–TFs regulatory network was constructed. Conclusion In the present study, novel prognostic mRNAs and lncRNAs were identified, and their respective prognostic models and nomograms were constructed to guide clinical practice. An mRNAs–lncRNAs–TFs regulatory network was also constructed, which could assist further research in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-021-00322-2.
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Affiliation(s)
- Chengming Tian
- Department of Hepatopancreatobiliary Surgery, The First Hospital of China Medical University, Shenyang, 110000, Liaoning, People's Republic of China
| | - Xiyao Li
- Department of Hepatopancreatobiliary Surgery, The First Hospital of China Medical University, Shenyang, 110000, Liaoning, People's Republic of China
| | - Chunlin Ge
- Department of Hepatopancreatobiliary Surgery, The First Hospital of China Medical University, Shenyang, 110000, Liaoning, People's Republic of China.
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22
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Sun L, Du M, Kohli M, Huang CC, Chen X, Xu M, Shen H, Wang S, Wang L. An Improved Detection of Circulating Tumor DNA in Extracellular Vesicles-Depleted Plasma. Front Oncol 2021; 11:691798. [PMID: 34178690 PMCID: PMC8226168 DOI: 10.3389/fonc.2021.691798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in plasma has been used as a biomarker for cancer detection and outcome prediction. In this study, we collected the five precipitates (fractions 1–5) and leftover supernatant plasma component (fraction 6) by a sequential centrifugation in plasma samples from nine small cell lung cancer (SCLC) patients. The fractions 3, 5 and 6 were large vesicles, exosomes and extracellular vesicles (EVs)-depleted plasma, respectively. Fragment size analysis using DNAs from these fractions showed dramatical differences from a peak of 7–10 kb in fraction 1 to 140–160 bp in fraction 6. To determine ctDNA content, we performed whole genome sequencing and applied copy number-based algorithm to calculate ctDNA percentage. This analysis showed the highest ctDNA content in EV-depleted plasma (average = 27.22%), followed by exosomes (average = 22.09%) and large vesicles (average = 19.70%). Comparatively, whole plasma, which has been used in most ctDNA studies, showed an average of 23.84% ctDNA content in the same group of patients. To further demonstrate higher ctDNA content in fraction 6, we performed mutational analysis in the plasma samples from 22 non-small cell lung cancer (NSCLC) patients with known EGFR mutations. This analysis confirmed higher mutation detection rates in fraction 6 (14/22) than whole plasma (10/22). This study provides a new insight into potential application of using fractionated plasma for an improved ctDNA detection.
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Affiliation(s)
- Li Sun
- Laboratory Medicine Center, the Second Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meijun Du
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Manish Kohli
- Division of Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States
| | - Chiang-Ching Huang
- Zilber School of Public Health, University of Wisconsin, Milwaukee, WI, United States
| | - Xiaoxiang Chen
- Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Mu Xu
- Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shukui Wang
- Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL, United States
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23
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Gao B, Baudis M. Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes. Front Genet 2021; 12:654887. [PMID: 34054918 PMCID: PMC8155688 DOI: 10.3389/fgene.2021.654887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
Copy number aberrations (CNA) are one of the most important classes of genomic mutations related to oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated by molecular-cytogenetic and genome sequencing based methods. While this data has been instrumental in the identification of cancer-related genes and promoted research into the relation between CNA and histo-pathologically defined cancer types, the heterogeneity of source data and derived CNV profiles pose great challenges for data integration and comparative analysis. Furthermore, a majority of existing studies have been focused on the association of CNA to pre-selected "driver" genes with limited application to rare drivers and other genomic elements. In this study, we developed a bioinformatics pipeline to integrate a collection of 44,988 high-quality CNA profiles of high diversity. Using a hybrid model of neural networks and attention algorithm, we generated the CNA signatures of 31 cancer subtypes, depicting the uniqueness of their respective CNA landscapes. Finally, we constructed a multi-label classifier to identify the cancer type and the organ of origin from copy number profiling data. The investigation of the signatures suggested common patterns, not only of physiologically related cancer types but also of clinico-pathologically distant cancer types such as different cancers originating from the neural crest. Further experiments of classification models confirmed the effectiveness of the signatures in distinguishing different cancer types and demonstrated their potential in tumor classification.
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Affiliation(s)
- Bo Gao
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
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24
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Kinetics of plasma cfDNA predicts clinical response in non-small cell lung cancer patients. Sci Rep 2021; 11:7633. [PMID: 33828112 PMCID: PMC8027214 DOI: 10.1038/s41598-021-85797-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs), VEGF/VEGF receptor inhibitors (VEGFIs) and immune checkpoint inhibitors (ICIs) have revolutionized the treatment of advanced cancers including non-small-cell lung cancer (NSCLC). This study aims to evaluate the utility of plasma cell-free DNA (cfDNA) as a prognostic biomarker and efficacy predictor of chemotherapy (CT) with or without these precision therapies in NSCLC patients. Peripheral cfDNA levels in 154 NSCLC patients were quantified before and after the first target cycle of chemotherapy. The correlations of cfDNA with tumor burden, clinical characteristics, progression-free survival (PFS)/disease-free survival (DFS), objective response ratio (ORR), and therapy regimens were analyzed respectively. Baseline cfDNA, but not post-chemotherapeutic cfDNA, positively correlates with tumor burden. Notably, cfDNA kinetics (cfDNA Ratio, the ratio of post-chemotherapeutic cfDNA to baseline cfDNA) well distinguished responsive individuals (CR/PR) from the non-responsive (PD/SD). Additionally, cfDNA Ratio was found negatively correlated with PFS in lung adenocarcinoma (LUAD), but not lung squamous-cell carcinoma (LUSC) which may be due to a limited number of LUSC patients in this cohort. LUAD patients with low cfDNA Ratio have prolonged PFS and improved ORR, compared to those with high cfDNA Ratio. When stratified by therapy regimen, the predictive value of cfDNA Ratio is significant in patients with chemotherapy plus VEGFIs, while more patients need be included to validate the value of cfDNA Ratio in other regimens. Thus, the kinetics of plasma cfDNA during chemotherapy may function as a prognostic biomarker and efficacy predictor for NSCLC patients.
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Kwan EM, Dai C, Fettke H, Hauser C, Docanto MM, Bukczynska P, Ng N, Foroughi S, Graham LJK, Mahon K, Tan W, Wang X, Zhao Z, Zheng T, Zhou K, Yu J, Du P, Horvath LG, Jia S, Kohli M, Azad AA. Plasma Cell-Free DNA Profiling of PTEN-PI3K-AKT Pathway Aberrations in Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol 2021; 5:PO.20.00424. [PMID: 34250422 PMCID: PMC8232889 DOI: 10.1200/po.20.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor tissue from metastatic castration-resistant prostate cancer (mCRPC) harbors frequent copy number variations (CNVs) in the PTEN-PI3K-AKT pathway. However, identifying CNVs in plasma cell-free DNA (cfDNA) has proven to be challenging. With emerging data supporting Akt inhibition in PTEN-deficient mCRPC, we profiled PTEN-PI3K-AKT pathway aberrations in patients with mCRPC using a novel cfDNA assay optimized for CNV detection. METHODS A next-generation sequencing-based cfDNA assay was used to profile 231 patients with mCRPC from two independent cohorts (Australian, n = 78; United States, n = 153). PTEN-PI3K-AKT pathway genomic aberrations were correlated with clinical outcomes, including progression-free survival and overall survival (OS). RESULTS PTEN loss and PIK3CA gain were detected in 37% (85 of 231) and 17% (39 of 231) of patients, respectively. Poorer outcomes were observed in patients with PTEN-PI3K-AKT pathway aberrations, including those with dual PTEN loss and PIK3CA gain (hazard ratio 2.3, 95% CI 1.2 to 4.4). Cumulative CNV burden in the PTEN-PI3K-AKT and androgen receptor (AR) pathways was associated with significantly worse clinical outcomes (0 v 1 v ≥ 2 CNVs in Australian cohort: median OS 33.5 v 17.2 v 9.7 months, P < .001; 0 v 1 v ≥ 2 CNVs in US cohort: median OS 35.5 v 14.3 v 9.2 months, P < .001). Notably, 21% (31 of 146) of PTEN-neutral patients harbored alternative PTEN-PI3K-AKT pathway aberrations. CONCLUSION PTEN-PI3K-AKT pathway CNVs were readily detected using our cfDNA assay, with the prevalence of PTEN loss comparable with tissue-based studies. Additional PTEN-PI3K-AKT pathway aberrations were found in one fifth of PTEN-neutral cases. Concurrent CNVs in the PTEN-PI3K-AKT and AR pathways portended poor survival, and identifying this high-risk patient subset for dual AR/Akt inhibition may optimize precision treatment with Akt inhibitors in mCRPC.
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Affiliation(s)
- Edmond M. Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Department of Medical Oncology, Monash Health, Melbourne, Australia
| | | | - Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | | | - Maria M. Docanto
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | | | - Nicole Ng
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Siavash Foroughi
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | | | - Kate Mahon
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, Australia
- University of Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Winston Tan
- Division of Medical Oncology, Department of Medicine, Mayo Clinic, Jacksonville, FL
| | | | | | | | | | | | - Pan Du
- Predicine Inc, Hayward, CA
| | - Lisa G. Horvath
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, Australia
- University of Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Manish Kohli
- Division of Medical Oncology, Department of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Arun A. Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
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Herranz R, Oto J, Plana E, Fernández-Pardo Á, Cana F, Martínez-Sarmiento M, Vera-Donoso CD, España F, Medina P. Circulating Cell-Free DNA in Liquid Biopsies as Potential Biomarker for Bladder Cancer: A Systematic Review. Cancers (Basel) 2021; 13:1448. [PMID: 33810039 PMCID: PMC8005001 DOI: 10.3390/cancers13061448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/03/2021] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is among the most frequent cancer types in the world and is the most lethal urological malignancy. Presently, diagnostic and follow-up methods for BC are expensive and invasive. Thus, the identification of novel predictive biomarkers for diagnosis, progression, and prognosis of BC is of paramount importance. To date, several studies have evidenced that cell-free DNA (cfDNA) found in liquid biopsies such as blood and urine may play a role in the particular scenario of urologic tumors, and its analysis may improve BC diagnosis report about cancer progression or even evaluate the effectiveness of a specific treatment or anticipate whether a treatment would be useful for a specific patient depending on the tumor characteristics. In the present review, we have summarized the up-to-date studies evaluating the value of cfDNA as potential diagnostic, prognostic, or monitoring biomarker for BC in several biofluids.
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Affiliation(s)
- Raquel Herranz
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
| | - Julia Oto
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
| | - Emma Plana
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
- Angiology and Vascular Surgery Service, La Fe University and Polytechnic Hospital, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Álvaro Fernández-Pardo
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
| | - Fernando Cana
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
| | - Manuel Martínez-Sarmiento
- Department of Urology, La Fe University and Polytechnic Hospital, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (M.M.-S.); (C.D.V.-D.)
| | - César D. Vera-Donoso
- Department of Urology, La Fe University and Polytechnic Hospital, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (M.M.-S.); (C.D.V.-D.)
| | - Francisco España
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
| | - Pilar Medina
- Haemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe, Avenida Fernando Abril Martorell 106, 46026 Valencia, Spain; (R.H.); (J.O.); (E.P.); (Á.F.-P.); (F.C.); (F.E.)
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27
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Andersson D, Kristiansson H, Kubista M, Ståhlberg A. Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations. Expert Rev Mol Diagn 2021; 21:299-310. [PMID: 33683971 DOI: 10.1080/14737159.2021.1889371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation.Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications.Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Helena Kristiansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Kubista
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic.,TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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Merseburger AS, Waldron N, Ribal MJ, Heidenreich A, Perner S, Fizazi K, Sternberg CN, Mateo J, Wirth MP, Castro E, Olmos D, Petrylak DP, Chowdhury S. Genomic Testing in Patients with Metastatic Castration-resistant Prostate Cancer: A Pragmatic Guide for Clinicians. Eur Urol 2021; 79:519-529. [PMID: 33494937 DOI: 10.1016/j.eururo.2020.12.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/26/2020] [Indexed: 12/19/2022]
Abstract
CONTEXT Genomic testing is becoming increasingly important in patients with advanced prostate cancer (PC) and is being incorporated in clinical practice to guide treatment. OBJECTIVE To review the current understanding of genomic alterations and the status of genomic testing in patients with metastatic castration-resistant PC (mCRPC), and the potential use of genomic tests in clinical practice. EVIDENCE ACQUISITION We reviewed recent publications (past 15 yr) from PubMed, proceedings of scientific conferences, and published guidelines. Reports on mCRPC in the following areas were selected: development, testing, and validation of techniques for identifying genomic alterations; molecular characterization; and trials of genetically targeted therapies. EVIDENCE SYNTHESIS mCRPC tumors harbor molecular alterations that are possible targets for treatment, and a number of therapies are in development to exploit these alterations (eg, PD-1 inhibitors, PARP inhibitors, tyrosine kinase inhibitors). Next-generation sequencing of DNA from tumor tissue can identify somatic alterations that would not be identified by germline testing. Work is ongoing to evaluate the use of less invasive somatic testing methods (eg, sequencing of cell-free circulating tumor DNA). Current international guidelines recommend germline and/or somatic testing for men with advanced and/or high-risk PC regardless of family history to identify those with homologous recombination repair gene mutations or mismatch repair defects/microsatellite instability who may be eligible for treatment with a PARP inhibitor or pembrolizumab, respectively. CONCLUSIONS Genomic testing for mCRPC may provide information on prognostic, predictive, and resistance biomarkers. Although the incorporation of testing into clinical practice remains challenging, routine genomic testing of men with advanced PC is recommended to guide management and treatment decisions. PATIENT SUMMARY Similar to many cancers, prostate cancer is caused by defects in the cancer's DNA, which are called genetic or genomic defects. New treatments targeting these defects are approved for metastatic castration-resistant prostate cancer. Specific new tests are under development to detect these potentially treatable genetic defects.
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Affiliation(s)
| | | | - Maria J Ribal
- Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Sven Perner
- Institute of Pathology, University Hospital Schleswig Holstein, Campus Lübeck, Lübeck, Germany; Pathology Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Karim Fizazi
- University of Paris Institut Gustave Roussy, Villejuif Cedex, France
| | - Cora N Sternberg
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York-Presbyterian, New York, NY, USA
| | - Joaquin Mateo
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Elena Castro
- Spanish National Cancer Research Centre, Madrid, Spain; University Hospitals Regional and Virgen de la Victoria, Málaga, Spain
| | - David Olmos
- Spanish National Cancer Research Centre, Madrid, Spain; University Hospitals Regional and Virgen de la Victoria, Málaga, Spain
| | | | - Simon Chowdhury
- Guy's Hospital, London, UK; Sarah Cannon Research Institute, London, UK
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29
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Barefoot ME, Lindberg MR, Wellstein A. Decoding the Tissue of Origin of Cellular Damage from Cell-Free DNA in Liquid Biopsies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11669-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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30
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Tang Z, Huang J, He H, Ma C, Wang K. Contributing to liquid biopsy: Optical and electrochemical methods in cancer biomarker analysis. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213317] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Zhao C, Pan Y, Wang Y, Li Y, Han W, Lu L, Tang W, Li P, Ou Z, Zhang M, Xiong Z, Xu R, Lu Q, Xu Z, Qi L, Wang L, Xu G. A novel cell-free single-molecule unique primer extension resequencing (cf-SUPER) technology for bladder cancer non-invasive detection in urine. Transl Androl Urol 2020; 9:1222-1231. [PMID: 32676405 PMCID: PMC7354286 DOI: 10.21037/tau-19-774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The clinical diagnostic method for bladder cancer is cystoscopy, an invasive, expensive and inconvenient clinical test. Using urinary cell-free DNA (cfDNA) to develop non-invasive test for bladder cancer was a promising liquid biopsy. Methods To improve the using rate of cfDNA template and decrease the PCR bias for liquid biopsy using urinary cfDNA, we developed a cell-free single-molecule unique primer extension resequencing (cf-SUPER) technology which was done for 29 matched urinary cfDNA and tumor DNA samples of bladder cancer patients to evaluate consistency of mutation profiles. Then, a 22 high mutational frequence genes was selected to form an uriprier panel, which was analyzed in 100 patients (47 bladder cancer cases and 53 controls) using cf-SUPER technology. This performance of the technology was evaluated using bioinformatic tools and clinical samples. Results The study showed that cf-SUPER technology can accurately detect mutations with allele fractions even low as 0.01% and the DNA input as low as 1 ng. The consistency of mutation profiles and clinical pathological diagnose between 29 matched urinary cfDNA and tumor DNA samples was respectively 82.76% and 89.66% by using cf-SUPER technology. Using cf-SUPER technology, the sensitivity and specificity were 98%, 94% respectively for uriprier panel in non-invasive test. Conclusions The preliminary work shows that cf-SUPER technology will be a promising method for liquid biopsy. Focusing urinary cfDNA, the non-invasive diagnose and monitoring of bladder cancer can come true by using cf-SUPER technology.
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Affiliation(s)
- Cheng Zhao
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha 410013, China.,Department of Urology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Pan
- Yearth Biotechnology Co. Ltd., Changsha 410008, China
| | - Yinhuai Wang
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Yuanwei Li
- Department of Urology, Hunan Provincial People's Hospital, First Affiliated Hospital of Hunan Normal University, Changsha 410000, China
| | - Weiqing Han
- Department of Urology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medical, Central South University, Changsha 410013, China
| | - Li Lu
- Yearth Biotechnology Co. Ltd., Changsha 410008, China
| | - Wei Tang
- Yearth Biotechnology Co. Ltd., Changsha 410008, China
| | - Pei Li
- Yearth Biotechnology Co. Ltd., Changsha 410008, China
| | - Zhenyu Ou
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha 410013, China.,Department of Urology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Mengda Zhang
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Zhuang Xiong
- Yearth Biotechnology Co. Ltd., Changsha 410008, China
| | - Ran Xu
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Qiang Lu
- Department of Urology, Hunan Provincial People's Hospital, First Affiliated Hospital of Hunan Normal University, Changsha 410000, China
| | - Zhenzhou Xu
- Department of Urology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medical, Central South University, Changsha 410013, China
| | - Lin Qi
- Department of Urology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Long Wang
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha 410013, China.,Department of Urology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Genming Xu
- Yearth Biotechnology Co. Ltd., Changsha 410008, China
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The Detection of 8-Oxo-7,8-Dihydro-2′-Deoxyguanosine in Circulating Cell-Free DNA: A Step Towards Longitudinal Monitoring of Health. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:125-138. [DOI: 10.1007/978-3-030-41283-8_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA. Sci Rep 2020; 10:6190. [PMID: 32277101 PMCID: PMC7148341 DOI: 10.1038/s41598-020-63102-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients.
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Bacolod MD, Huang J, Giardina SF, Feinberg PB, Mirza AH, Swistel A, Soper SA, Barany F. Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection. BMC Cancer 2020; 20:85. [PMID: 32005108 PMCID: PMC6995062 DOI: 10.1186/s12885-020-6574-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/23/2020] [Indexed: 12/24/2022] Open
Abstract
Background Interrogation of site-specific CpG methylation in circulating tumor DNAs (ctDNAs) has been employed in a number of studies for early detection of breast cancer (BrCa). In many of these studies, the markers were identified based on known biology of BrCa progression, and interrogated using methyl-specific PCR (MSP), a technique involving bisulfite conversion, PCR, and qPCR. Methods In this report, we are demonstrating the development of a novel assay (Multiplex Bisulfite PCR-LDR-qPCR) which can potentially offer improvements to MSP, by integrating additional steps such as ligase detection reaction (LDR), methylated CpG target enrichment, carryover protection (use of uracil DNA glycosylase), and minimization of primer-dimer formation (use of ribose primers and RNAseH2). The assay is designed to for breast cancer-specific CpG markers identified through integrated analyses of publicly available genome-wide methylation datasets for 31 types of primary tumors (including BrCa), as well as matching normal tissues, and peripheral blood. Results Our results indicate that the PCR-LDR-qPCR assay is capable of detecting ~ 30 methylated copies of each of 3 BrCa-specific CpG markers, when mixed with excess amount unmethylated CpG markers (~ 3000 copies each), which is a reasonable approximation of BrCa ctDNA overwhelmed with peripheral blood cell-free DNA (cfDNA) when isolated from patient plasma. The bioinformatically-identified CpG markers are located in promoter regions of NR5A2 and PRKCB, and a non-coding region of chromosome 1 (upstream of EFNA3). Additional bioinformatic analyses would reveal that these methylation markers are independent of patient race and age, and positively associated with signaling pathways associated with BrCa progression (such as those related to retinoid nuclear receptor, PTEN, p53, pRB, and p27). Conclusion This report demonstrates the potential utilization of bisulfite PCR-LDR-qPCR assay, along with bioinformatically-driven biomarker discovery, in blood-based BrCa detection.
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Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Aashiq H Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Alexander Swistel
- Department of Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Steven A Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS, 66047, USA
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA.
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35
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Zhang C, Zhang B, Meng D, Ge C. Comprehensive analysis of DNA methylation and gene expression profiles in cholangiocarcinoma. Cancer Cell Int 2019; 19:352. [PMID: 31889904 PMCID: PMC6933876 DOI: 10.1186/s12935-019-1080-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/17/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The incidence of cholangiocarcinoma (CCA) has risen in recent years, and it has become a significant health burden worldwide. However, the mechanisms underlying tumorigenesis and progression of this disease remain largely unknown. An increasing number of studies have demonstrated crucial biological functions of epigenetic modifications, especially DNA methylation, in CCA. The present study aimed to identify and analyze methylation-regulated differentially expressed genes (MeDEGs) involved in CCA tumorigenesis and progression by bioinformatics analysis. METHODS The gene expression profiling dataset (GSE119336) and gene methylation profiling dataset (GSE38860) were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified using the limma packages of R and GEO2R, respectively. The MeDEGs were obtained by overlapping the DEGs and DMGs. Functional enrichment analyses of these genes were then carried out. Protein-protein interaction (PPI) networks were constructed using STRING and visualized in Cytoscape to determine hub genes. Finally, the results were verified based on The Cancer Genome Atlas (TCGA) database. RESULTS We identified 98 hypermethylated, downregulated genes and 93 hypomethylated, upregulated genes after overlapping the DEGs and DMGs. These genes were mainly enriched in the biological processes of the cell cycle, nuclear division, xenobiotic metabolism, drug catabolism, and negative regulation of proteolysis. The top nine hub genes of the PPI network were F2, AHSG, RRM2, AURKB, CCNA2, TOP2A, BIRC5, PLK1, and ASPM. Moreover, the expression and methylation status of the hub genes were significantly altered in TCGA. CONCLUSIONS Our study identified novel methylation-regulated differentially expressed genes (MeDEGs) and explored their related pathways and functions in CCA, which may provide novel insights into a further understanding of methylation-mediated regulatory mechanisms in CCA.
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Affiliation(s)
- Cheng Zhang
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Bingye Zhang
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Di Meng
- Department of Gerontology, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
| | - Chunlin Ge
- Department of Pancreatic and Biliary Surgery, The First Hospital of China Medical University, Shenyang, 110001 Liaoning China
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Applications of Bioinformatics in Cancer. Cancers (Basel) 2019; 11:cancers11111630. [PMID: 31652939 PMCID: PMC6893424 DOI: 10.3390/cancers11111630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/02/2023] Open
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37
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Boerrigter E, Groen LN, Van Erp NP, Verhaegh GW, Schalken JA. Clinical utility of emerging biomarkers in prostate cancer liquid biopsies. Expert Rev Mol Diagn 2019; 20:219-230. [DOI: 10.1080/14737159.2019.1675515] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Emmy Boerrigter
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Levi N. Groen
- Department of Experimental Urology, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Nielka P. Van Erp
- Department of Pharmacy, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Gerald W. Verhaegh
- Department of Experimental Urology, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Jack A. Schalken
- Department of Experimental Urology, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
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