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Kim J, Hong SP, Lee S, Lee W, Lee D, Kim R, Park YJ, Moon S, Park K, Cha B, Kim JI. Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids. Hum Genomics 2023; 17:96. [PMID: 37898819 PMCID: PMC10613368 DOI: 10.1186/s40246-023-00533-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/11/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Fragmentomics, the investigation of fragmentation patterns of cell-free DNA (cfDNA), has emerged as a promising strategy for the early detection of multiple cancers in the field of liquid biopsy. However, the clinical application of this approach has been hindered by a limited understanding of cfDNA biology. Furthermore, the prevalence of hematopoietic cell-derived cfDNA in plasma complicates the in vivo investigation of tissue-specific cfDNA other than that of hematopoietic origin. While conventional two-dimensional cell lines have contributed to research on cfDNA biology, their limited representation of in vivo tissue contexts underscores the need for more robust models. In this study, we propose three-dimensional organoids as a novel in vitro model for studying cfDNA biology, focusing on multifaceted fragmentomic analyses. RESULTS We established nine patient-derived organoid lines from normal lung airway, normal gastric, and gastric cancer tissues. We then extracted cfDNA from the culture medium of these organoids in both proliferative and apoptotic states. Using whole-genome sequencing data from cfDNA, we analyzed various fragmentomic features, including fragment size, footprints, end motifs, and repeat types at the end. The distribution of cfDNA fragment sizes in organoids, especially in apoptosis samples, was similar to that found in plasma, implying occupancy by mononucleosomes. The footprints determined by sequencing depth exhibited distinct patterns depending on fragment sizes, reflecting occupancy by a variety of DNA-binding proteins. Notably, we discovered that short fragments (< 118 bp) were exclusively enriched in the proliferative state and exhibited distinct fragmentomic profiles, characterized by 3 bp palindromic end motifs and specific repeats. CONCLUSIONS In conclusion, our results highlight the utility of in vitro organoid models as a valuable tool for studying cfDNA biology and its associated fragmentation patterns. This, in turn, will pave the way for further enhancements in noninvasive cancer detection methodologies based on fragmentomics.
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Affiliation(s)
- Jaeryuk Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Pyo Hong
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seyoon Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Woochan Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dakyung Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rokhyun Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Jun Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungji Moon
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea.
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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Wang L, Zhuang Y, Yu Y, Guo Z, Guo Q, Qiao L, Wang X, Liang X, Zhang P, Li Q, Huang C, Cong R, Li Y, Che B, Xiong H, Lin G, Rao M, Hu R, Wang W, Yang G, Lou J. An ultrasensitive method for detecting mutations from short and rare cell-free DNA. Biosens Bioelectron 2023; 238:115548. [PMID: 37542979 DOI: 10.1016/j.bios.2023.115548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Circulating tumor DNA (ctDNA) was short and rare, making the detection performance of the current targeted sequencing methods unsatisfying. We developed the One-PrimER Amplification (OPERA) system and examined its performance in detecting mutations of low variant allelic frequency (VAF) in various samples with short-sized DNA fragments. In cell line-derived samples containing sonication-sheared DNA fragments with 50-150 bp, OPERA was capable of detecting mutations as low as 0.0025% VAF, while CAPP-Seq only detected mutations of >0.03% VAF. Both single nucleotide variant and insertion/deletion can be detected by OPERA. In synthetic fragments as short as 80 bp with low VAF (0.03%-0.1%), the detection sensitivity of OPERA was significantly higher compared to that of droplet digital polymerase chain reaction. The error rate was 5.9×10-5 errors per base after de-duplication in plasma samples collected from healthy volunteers. By suppressing "single-strand errors", the error rate can be further lowered by >5 folds in EGFR T790M hotspot. In plasma samples collected from lung cancer patients, OPERA detected mutations in 57.1% stage I patients with 100% specificity and achieved a sensitivity of 30.0% in patients with tumor volume of less than 1 cm3. OPERA can effectively detect mutations in rare and highly-fragmented DNA.
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Affiliation(s)
- Lin Wang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Zhuang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Thoracic Surgery, Nanjing Chest Hospital, Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiwei Guo
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Qiaomei Guo
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lihua Qiao
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueqing Wang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Liang
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qifan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenjun Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Cong
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Yinghui Li
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Bin Che
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Huihui Xiong
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Guomin Lin
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Mingming Rao
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Rongjun Hu
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Guohua Yang
- Department of Research & Development, Apogenomics Co. Ltd., Shanghai, China.
| | - Jiatao Lou
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Wei F, Yu P, Cheng J, Li F, Chia D, Wong DTW. Single-Droplet Microsensor for Ultra-Short Circulating EFGR Mutation Detection in Lung Cancer Based on Multiplex EFIRM Liquid Biopsy. Int J Mol Sci 2023; 24:10387. [PMID: 37373532 DOI: 10.3390/ijms241210387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Liquid biopsy is a rapidly emerging field that involves the minimal/non-invasive assessment of signature somatic mutations through the analysis of circulating tumor DNA (ctDNA) shed by tumor cells in bodily fluids. Broadly speaking, the unmet need in liquid biopsy lung cancer detection is the lack of a multiplex platform that can detect a mutation panel of lung cancer genes using a minimum amount of sample, especially for ultra-short ctDNA (usctDNA). Here, we developed a non-PCR and non-NGS-based single-droplet-based multiplexing microsensor technology, "Electric-Field-Induced Released and Measurement (EFIRM) Liquid Biopsy" (m-eLB), for lung cancer-associated usctDNA. The m-eLB provides a multiplexable assessment of usctDNA within a single droplet of biofluid in only one well of micro-electrodes, as each electrode is coated with different probes for the ctDNA. This m-eLB prototype demonstrates accuracy for three tyrosine-kinase-inhibitor-related EGFR target sequences in synthetic nucleotides. The accuracy of the multiplexing assay has an area under the curve (AUC) of 0.98 for L858R, 0.94 for Ex19 deletion, and 0.93 for T790M. In combination, the 3 EGFR assay has an AUC of 0.97 for the multiplexing assay.
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Affiliation(s)
- Fang Wei
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Peter Yu
- Department of Physics, University of California, Los Angeles, CA 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
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Barthelemy D, Lescuyer G, Geiguer F, Grolleau E, Gauthier A, Balandier J, Raffin M, Bardel C, Bouyssounouse B, Rodriguez-Lafrasse C, Couraud S, Wozny AS, Payen L. Paired Comparison of Routine Molecular Screening of Patient Samples with Advanced Non-Small Cell Lung Cancer in Circulating Cell-Free DNA Using Three Targeted Assays. Cancers (Basel) 2023; 15. [PMID: 36900363 DOI: 10.3390/cancers15051574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
INTRODUCTION Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancers. Approximately 10-50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors. PATIENTS AND METHODS Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay. RESULTS In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay. CONCLUSIONS The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.
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Tanaka J, Nakagawa T, Harada K, Morizane C, Tanaka H, Shiba S, Ohba A, Hijioka S, Takai E, Yachida S, Kamura Y, Ishida T, Yokoi T, Uematsu C. Efficient and accurate KRAS genotyping using digital PCR combined with melting curve analysis for ctDNA from pancreatic cancer patients. Sci Rep 2023; 13:3039. [PMID: 36810451 PMCID: PMC9944920 DOI: 10.1038/s41598-023-30131-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
A highly sensitive and highly multiplexed quantification technique for nucleic acids is necessary to predict and evaluate cancer treatment by liquid biopsy. Digital PCR (dPCR) is a highly sensitive quantification technique, but conventional dPCR discriminates multiple targets by the color of the fluorescent dye of the probe, which limits multiplexing beyond the number of colors of fluorescent dyes. We previously developed a highly multiplexed dPCR technique combined with melting curve analysis. Herein, we improved the detection efficiency and accuracy of multiplexed dPCR with melting curve analysis to detect KRAS mutations in circulating tumor DNA (ctDNA) prepared from clinical samples. The mutation detection efficiency was increased from 25.9% of the input DNA to 45.2% by shortening the amplicon size. The limit of detection of mutation was improved from 0.41 to 0.06% by changing the mutation type determination algorithm for G12A, resulting in a limit of detection of less than 0.2% for all the target mutations. Then, ctDNA in plasma from pancreatic cancer patients was measured and genotyped. The measured mutation frequencies correlated well with those measured by conventional dPCR, which can measure only the total frequency of KRAS mutants. KRAS mutations were detected in 82.3% of patients with liver or lung metastasis, which was consistent with other reports. Accordingly, this study demonstrated the clinical utility of multiplex dPCR with melting curve analysis to detect and genotype ctDNA from plasma with sufficient sensitivity.
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Affiliation(s)
- Junko Tanaka
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Tatsuo Nakagawa
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Kunio Harada
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hidenori Tanaka
- Department of Cancer Genome Informatics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Shiba
- Division of Genomic Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akihiro Ohba
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Susumu Hijioka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Erina Takai
- Department of Cancer Genome Informatics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Genomic Medicine, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yoshio Kamura
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Takeshi Ishida
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Takahide Yokoi
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Chihiro Uematsu
- Center for Digital Services - Healthcare, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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Li Y, Wu J, Li E, Xiao Z, Lei J, Zhou F, Yin X, Hu D, Mao Y, Wu L, Wenjun L. TP53 mutation detected in circulating exosomal DNA is associated with prognosis of patients with hepatocellular carcinoma. Cancer Biol Ther 2022; 23:439-445. [PMID: 35921289 PMCID: PMC9354767 DOI: 10.1080/15384047.2022.2094666] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Exosome DNA (exoDNA) can be used for liquid biopsy. This study was the first to use droplet digital PCR (ddPCR) to detect tumor-specific mutations in exoDNA and to evaluate the prognosis of hepatocellular carcinoma (HCC) patients. 60 HCC patients were enrolled in the study. We used ddPCR to detect c.747 G > T mutation in TP53 gene. We analyzed the correlation between detectable mutation in exoDNA and clinicopathologic characteristics using Multivariate logistics regression analysis. We performed Cox regression to assess the correlation between mutation frequency (mutant droplets/total droplets, MD/TD) and prognostic. We found that 48 of 60 patients had c.747 G > T mutation in TP53 gene in exoDNA (80.0%). We found that detectable mutation in exoDNA and age were associated with microvascular invasion (MVI) (P < .01). The ROC curve analysis revealed that the best cutoff value of mutation frequency to predict MVI was 67% (sensitivity 48.15%, specificity 93.94%,), the corresponding AUC was 0.761 (95%CI, 0.640–0.866; P < .01). Furthermore, we found that patients suffered high-frequency mutation (>67%) had shorted median recurrence-free survival (RFS) with 63 days (range, 53–202 days), compared with 368 days (range, 51–576 days) for patients with low-frequency mutation (<67%) (HR:4.61; 95% CI, 1.70–12.48; P = 0 .003). We also found that high-frequency mutation was associated with poor prognosis though patients had better pathological characteristics, such as AFP (<400 ng/mL), Liver cirrhosis (Negative), Tumor thrombus (Negative), Tumor numbers (Single) and Post-operation TACE (Executed). We provided evidence that the mutations in exoDNA might be used to predict patients with poor RFS. Abbreviations: TP53: Tumor protein p53; ExoDNA: Exosomal DNA; HCC: Hepatocellular carcinoma; ddPCR: Droplet digital Polymerase Chain Reaction (PCR); MD/TD: The ratio of mutant droplets/total droplets; AFP: Alpha-fetoprotein; MVI: Microvascular invasion; RFS: Recurrence-free survival.
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Affiliation(s)
- Yong Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Junjun Wu
- Department of Hepatobiliary and Pancreatic Surgery, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Enliang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhouqing Xiao
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Lei
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fan Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiangbao Yin
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dandan Hu
- Department of Hepatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yilei Mao
- Department of Hepatobiliary Surgery, Peking Union Medical College, Beijing, China
| | - Linquan Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Liao Wenjun
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Huang CJ, Huang WY, Chen CY, Chao YJ, Chiang NJ, Shan YS. Cancer-cell-derived cell-free DNA can predict distant metastasis earlier in pancreatic cancer: a prospective cohort study. Ther Adv Med Oncol 2022; 14:17588359221106558. [PMID: 35747164 PMCID: PMC9210094 DOI: 10.1177/17588359221106558] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Carbohydrate antigen 19-9 (CA19-9) is the only biomarker for monitoring responses during treatments of pancreatic cancer, but its accuracy for disease outcome is controversial. Fluid biopsy is a new method for diagnosis and monitoring treatment response. In this study, we investigate the usefulness of cell-free DNA (cfDNA) in predicting disease progression during the treatment of pancreatic cancer. Methods: Biopsy-proved advanced pancreatic cancer patients who received systemic chemotherapy were enrolled after signed informed consent. CA19-9 and cfDNA in blood were measured before and after every two cycles of treatments, and the disease progression was monitored by computed tomography (CT) with 3-month interval. Results: In total, 74 patients and 148 blood samples were enrolled in this study. Patients whose average blood cfDNA concentration of >9.71 ng/mL before and after first two courses of chemotherapy would subsequently show new distant metastasis (NDM) on CT scans 3 months later. The accuracy was 94.37% (AUC 0.9705, p < 0.0001) and the progression-free survival (PFS) and overall survival (OS) of patients with cfDNA concentration of >9.71 ng/mL were worse than those patients with cfDNA concentration of <9.71 ng/mL (median PFS: 95 days versus 322 days, p < 0.0001; median OS: 150 days versus 431 days, p < 0.0001). The cfDNA concentration of >9.71 ng/mL is a predictor for PFS, OS, and distant metastasis-free survival by multivariate analysis. Comparison of KRAS G12 variants detected by next-generation sequencing from tumor tissue issue and remnant DNA of cfDNA showed that increased cfDNA was primarily derived from cancer cells. Conclusion: The cancer-cell-derived cfDNA levels could be served as a powerful biomarker for prediction of NDM in patients with advanced/metastatic pancreatic cancer.
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Affiliation(s)
- Chien-Jui Huang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan
| | - Wen-Yen Huang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Yu Chen
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Jui Chao
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nai-Jung Chiang
- Department of Oncology, Taipei Veterans General Hospital, Taipei
| | - Yan-Shen Shan
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, Tainan
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Vonka V, Hirsch I. Prophylactic vaccines against cancers of non-infectious origin: a dream or a real possibility? Cent Eur J Public Health 2022; 29:247-258. [PMID: 35026062 DOI: 10.21101/cejph.a7219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/23/2021] [Indexed: 11/15/2022]
Abstract
The dramatic progress in tumour biology and immunology in the past several years has opened new avenues for the treatment and prevention of cancer. One of the great contributions of the immunotherapeutic approaches is an increasing understanding of the immunology of cancer, which is, gradually creating conditions for the development of prophylactic anti-cancer vaccines. Efficient vaccines have been developed and employed for the prophylaxis of two frequent cancers of viral origin, namely cervical cancer and liver cancer. The new knowledge on the interactions between the immune system and the malignant tumors seems to provide means for the development of prophylactic vaccines against cancers developing due to the mutations in the proto-oncogenes converting their products into oncoproteins. According to the present estimates, these cancers form a great majority of human malignancies. Recent evidence has indicated that the immune system recognizes such mutated proteins, and that the development of cancer is due to the failure of the immune system to eliminate neoplastic cells. Followingly, it can be expected that inducing immunity against the mutated epitopes will increase the capacity of the body to deal with the initiated precancerous cells. In the present paper this hypothesis is primarily discussed in the relationship with colorectal cancer (CRC), which seems to be a well-fitting candidate for prophylactic vaccination. CRC is the third most frequent malignancy and the fourth most common cause of cancer mortality. Mutations of two proto-oncogenes, namely RAS and RAF, are involved in the majority of CRC cases and, in addition, they are shared with other human malignancies. Therefore, the strategy to be used for prophylaxis of CRC is discussed together with several other frequent human cancers, namely lung cancer, pancreatic duct cancer and melanoma. The prophylactic vaccines proposed are aimed at the reduction of the incidence of these and, to a lesser extent, some other cancers.
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Affiliation(s)
- Vladimír Vonka
- Institute of Haematology and Blood Transfusion, Emeritus, Prague, Czech Republic
| | - Ivan Hirsch
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Chang A, Mzava O, Lenz JS, Cheng AP, Burnham P, Motley ST, Bennett C, Connelly JT, Dadhania DM, Suthanthiran M, Lee JR, Steadman A, De Vlaminck I. Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays. Clin Chem 2021; 68:163-171. [PMID: 34718476 PMCID: PMC8718127 DOI: 10.1093/clinchem/hvab142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/24/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Metagenomic sequencing of microbial cell-free DNA (cfDNA) in blood and urine is increasingly used as a tool for unbiased infection screening. The sensitivity of metagenomic cfDNA sequencing assays is determined by the efficiency by which the assay recovers microbial cfDNA vs host-specific cfDNA. We hypothesized that the choice of methods used for DNA isolation, DNA sequencing library preparation, and sequencing would affect the sensitivity of metagenomic cfDNA sequencing. METHODS We characterized the fragment length biases inherent to select DNA isolation and library preparation procedures and developed a model to correct for these biases. We analyzed 305 cfDNA sequencing data sets, including publicly available data sets and 124 newly generated data sets, to evaluate the dependence of the sensitivity of metagenomic cfDNA sequencing on pre-analytical variables. RESULTS Length bias correction of fragment length distributions measured from different experimental procedures revealed the ultrashort (<100 bp) nature of microbial-, mitochondrial-, and host-specific urinary cfDNA. The sensitivity of metagenomic sequencing assays to detect the clinically reported microorganism differed by more than 5-fold depending on the combination of DNA isolation and library preparation used. CONCLUSIONS Substantial gains in the sensitivity of microbial and other short fragment recovery can be achieved by easy-to-implement changes in the sample preparation protocol, which highlights the need for standardization in the liquid biopsy field.
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Affiliation(s)
- Adrienne Chang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Omary Mzava
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joan S Lenz
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Alexandre P Cheng
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Philip Burnham
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Crissa Bennett
- Global Good Fund, Intellectual Ventures Lab, Bellevue, WA, USA
| | | | - Darshana M Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital, Weill Cornell Medical Center, New York, NY, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital, Weill Cornell Medical Center, New York, NY, USA
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital, Weill Cornell Medical Center, New York, NY, USA
| | | | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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10
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Yuwono NL, Henry CE, Ford CE, Warton K. Total and endothelial cell-derived cell-free DNA in blood plasma does not change during menstruation. PLoS One 2021; 16:e0250561. [PMID: 33901234 PMCID: PMC8075187 DOI: 10.1371/journal.pone.0250561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Assays measuring cell-free DNA (cfDNA) in blood have widespread potential in modern medicine. However, a comprehensive understanding of cfDNA dynamics in healthy individuals is required to assist in the design of assays that maximise the signal driven by pathological changes, while excluding fluctuations that are part of healthy physiological processes. The menstrual cycle involves major remodelling of endometrial tissue and associated apoptosis, yet there has been little investigation of the impact of the menstrual cycle on cfDNA levels. Paired plasma samples were collected from 40 healthy women on menstruating (M) and non-menstruating (NM) days of their cycle. We measured total cfDNA by targeting ALU repetitive sequences and measured endothelial-derived cfDNA by methylation-specific qPCR targeting an endothelium-unique unmethylated CDH5 DNA region. CfDNA integrity and endothelial cfDNA concentration, but not total cfDNA, are consistent across time between NM and M. No significant changes in total (ALU-115 p = 0.273; ALU-247 p = 0.385) or endothelial cell specific (p = 0.301) cfDNA were observed, leading to the conclusion that menstrual status at the time of diagnostic blood collection should not have a significant impact on the quantitation of total cfDNA and methylation-based cancer assays.
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Affiliation(s)
- Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Claire Elizabeth Henry
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, Lowy Cancer Research Centre, Department of Obstetrics & Gynaecology, School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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11
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Toledano-Fonseca M, Cano MT, Inga E, Rodríguez-Alonso R, Gómez-España MA, Guil-Luna S, Mena-Osuna R, de la Haba-Rodríguez JR, Rodríguez-Ariza A, Aranda E. Circulating Cell-Free DNA-Based Liquid Biopsy Markers for the Non-Invasive Prognosis and Monitoring of Metastatic Pancreatic Cancer. Cancers (Basel) 2020; 12:cancers12071754. [PMID: 32630266 PMCID: PMC7409337 DOI: 10.3390/cancers12071754] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Liquid biopsy may assist in the management of cancer patients, which can be particularly applicable in pancreatic ductal adenocarcinoma (PDAC). In this study, we investigated the utility of circulating cell-free DNA (cfDNA)-based markers as prognostic tools in metastatic PDAC. Plasma was obtained from 61 metastatic PDAC patients, and cfDNA levels and fragmentation were determined. BEAMing technique was used for quantitative determination of RAS mutation allele fraction (MAF) in cfDNA. We found that the prognosis was more accurately predicted by RAS mutation detection in plasma than in tissue. RAS mutation status in plasma was a strong independent prognostic factor for both overall survival (OS) and progression-free survival (PFS). Moreover, RAS MAF in cfDNA was also an independent risk factor for poor OS, and was strongly associated with primary tumours in the body/tail of the pancreas and liver metastases. Higher cfDNA levels and fragmentation were also associated with poorer OS and shorter PFS, body/tail tumors, and hepatic metastases, whereas cfDNA fragmentation positively correlated with RAS MAF. Remarkably, the combination of CA19-9 with MAF, cfDNA levels and fragmentation improved the prognostic stratification of patients. Furthermore, dynamics of RAS MAF better correlated with patients’ outcome than standard CA19-9 marker. In conclusion, our study supports the use of cfDNA-based liquid biopsy markers as clinical tools for the non-invasive prognosis and monitoring of metastatic PDAC patients.
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Affiliation(s)
- Marta Toledano-Fonseca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), E14004 Córdoba, Spain; (M.T.-F.); (S.G.-L.); (R.M.-O.); (J.R.d.l.H.-R.); (E.A.)
- Cancer Network Biomedical Research Center (CIBERONC), E28029 Madrid, Spain;
| | - M. Teresa Cano
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
| | - Elizabeth Inga
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
| | - Rosa Rodríguez-Alonso
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
| | - M. Auxiliadora Gómez-España
- Cancer Network Biomedical Research Center (CIBERONC), E28029 Madrid, Spain;
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
| | - Silvia Guil-Luna
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), E14004 Córdoba, Spain; (M.T.-F.); (S.G.-L.); (R.M.-O.); (J.R.d.l.H.-R.); (E.A.)
- Cancer Network Biomedical Research Center (CIBERONC), E28029 Madrid, Spain;
| | - Rafael Mena-Osuna
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), E14004 Córdoba, Spain; (M.T.-F.); (S.G.-L.); (R.M.-O.); (J.R.d.l.H.-R.); (E.A.)
| | - Juan R. de la Haba-Rodríguez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), E14004 Córdoba, Spain; (M.T.-F.); (S.G.-L.); (R.M.-O.); (J.R.d.l.H.-R.); (E.A.)
- Cancer Network Biomedical Research Center (CIBERONC), E28029 Madrid, Spain;
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
| | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), E14004 Córdoba, Spain; (M.T.-F.); (S.G.-L.); (R.M.-O.); (J.R.d.l.H.-R.); (E.A.)
- Cancer Network Biomedical Research Center (CIBERONC), E28029 Madrid, Spain;
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
- Correspondence:
| | - Enrique Aranda
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), E14004 Córdoba, Spain; (M.T.-F.); (S.G.-L.); (R.M.-O.); (J.R.d.l.H.-R.); (E.A.)
- Cancer Network Biomedical Research Center (CIBERONC), E28029 Madrid, Spain;
- Medical Oncology Department, Reina Sofía University Hospital, E14004 Córdoba, Spain; (M.T.C.); (E.I.); (R.R.-A.)
- Department of Medicine, Faculty of Medicine, University of Córdoba, E14004 Córdoba, Spain
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