1
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Kim AL, Shin HJ, Lee JY, Bae YK. Development of a media cell-free DNA direct digital PCR method for cell viability estimation. Anal Chim Acta 2024; 1323:343064. [PMID: 39182967 DOI: 10.1016/j.aca.2024.343064] [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: 03/19/2024] [Revised: 06/28/2024] [Accepted: 08/05/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Accurate estimation of cell viability is crucial in various applications such as cytotoxicity testing and routine cell culture on both industrial and laboratory scales. For this, the real-time monitoring of cell status would be beneficial. Conventional cell-based assays for cell viability have limitations in sensitivity and time-effectiveness. Analysis of cell-free DNA (cfDNA) in (culture) media is a good alternative as cfDNA release are a well-known phenomenon during cell death. RESULTS We demonstrate a direct digital PCR (dPCR) method to estimate cell viability by analyzing cfDNA in media during induced cell death. After validating the duplex dPCR method for short and long amplicons of the SMAD4 and RPP30 loci, we determined that a media volume of 2 μL is feasible to measure the target DNA copy number with minimal negative effects on amplification. dPCR inhibition was evident with a higher media volume per reaction targeting long amplicons. Next, we applied our dPCR method using media cfDNA and other conventional methods to the monitoring of camptothecin (CPT)-induced cell death. Copy numbers increased significantly after 4 h of CPT treatment, showing a fold change of approximately 4-6 compared to the controls. Cell-based assays such as the 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay and annexin V/7-AAD assay also indicated increased cell death at 4 h, but the trypan blue exclusion assay did not. SIGNIFICANCE The developed media cfDNA direct dPCR method allows for efficient measurements of the degree of cell viability. Unlike other conventional cell-based assays, our method has advantages of no loss of cultured cells and the ability to implement online analysis. Accurate and sensitive media cfDNA analysis using dPCR can be adopted in various applications such as determining cytotoxicity levels in large-scale bioreactors or screening for effective anticancer drugs.
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Affiliation(s)
- Ah Leum Kim
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea; Department of Analytical Science and Technology, Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea; Present address: Department of Forensics, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hye Ji Shin
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea; Department of Analytical Science and Technology, Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ji Youn Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea; Department of Analytical Science and Technology, Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Young-Kyung Bae
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea; Department of Analytical Science and Technology, Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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2
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Li Y, Li Z, Lu J, Qu G, Qin Q, Zhang C, Bai Y, Wang D, Luo S, Li B, Han Y, Chen W, Zhen Q, Sun L. Correlation between double-stranded DNA and acute urticaria. Int J Dermatol 2024; 63:e140-e147. [PMID: 38385899 DOI: 10.1111/ijd.17086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Acute urticaria is a prevalent inflammatory dermatosis characterized by fulminant wheals, often accompanied by severe pruritis. It may also cause nausea, vomiting, and abdominal pain. Numerous studies have substantiated the pivotal involvement of double-stranded DNA (dsDNA) in autoimmunity. However, the role of dsDNA in the pathogenesis of acute urticaria is unclear. METHODS We measured serum dsDNA levels in patients and controls. The relationship between dsDNA levels and environmental exposures (temperature, ultraviolet [UV] index, and season) was investigated by correlating disease onset dates with archived meteorological data. Finally, we used quantitative PCR to determine the expressions of genes encoding dsDNA receptors, single-stranded RNA (ssRNA) receptors, exosome formation, and type I interferon in the peripheral blood of patients and controls. RESULTS Serum dsDNA levels were significantly higher in patients with acute urticaria compared with controls (mean values 1.38 and 0.94 ng/ml, respectively, P < 0.001). dsDNA levels were higher in patients exposed to higher environmental temperatures and UV indices and were higher during the summer months. We also found that the expressions of genes encoding dsDNA receptors, ssRNA receptors, absent in melanoma factor 2 (AIM2)-related inflammatory factors, and interferon alpha were up-regulated in patients. CONCLUSIONS We demonstrated that serum dsDNA levels are elevated in acute urticaria and are influenced by climatic factors such as temperature, ultraviolet index, and season. We also found that elevated dsDNA promotes the expression of AIM2-related factors and type I interferons. This study generates new hypotheses regarding the pathogenesis of acute urticaria and suggests novel therapeutic targets.
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Affiliation(s)
- Yuanyuan Li
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Zhuo Li
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Jiayi Lu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Guangbo Qu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Qin Qin
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Chang Zhang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Yuanming Bai
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Daiyue Wang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Sihan Luo
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Bao Li
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Comprehensive Lab, College of Basic Medicine, Anhui Medical University, Hefei, China
| | - Yang Han
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
- Health Science Center, North China University of Science and Technology, Tangshan, China
- Inflammation and Immune Diseases Laboratory of North China University of Science and Technology, Tangshan, China
| | - Weiwei Chen
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Qi Zhen
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
- Health Science Center, North China University of Science and Technology, Tangshan, China
- Inflammation and Immune Diseases Laboratory of North China University of Science and Technology, Tangshan, China
| | - Liangdan Sun
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
- Health Science Center, North China University of Science and Technology, Tangshan, China
- Inflammation and Immune Diseases Laboratory of North China University of Science and Technology, Tangshan, China
- School of Public Health, North China University of Science and Technology, Tangshan, China
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3
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Davidson BA, Miranda AX, Reed SC, Bergman RE, Kemp JDJ, Reddy AP, Pantone MV, Fox EK, Dorand RD, Hurley PJ, Croessmann S, Park BH. An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release. Commun Biol 2024; 7:441. [PMID: 38600351 PMCID: PMC11006667 DOI: 10.1038/s42003-024-06129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
ABTRACT Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.
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Affiliation(s)
- Brad A Davidson
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Adam X Miranda
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah C Reed
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Riley E Bergman
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Justin D J Kemp
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Anvith P Reddy
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Morgan V Pantone
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ethan K Fox
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - R Dixon Dorand
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Paula J Hurley
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Sarah Croessmann
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ben Ho Park
- Division of Hematology, Oncology, Department of Medicine, Vanderbilt University Medical Center and the Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
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4
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Das D, Avssn R, Chittela RK. A phenol-chloroform free method for cfDNA isolation from cell conditioned media: development, optimization and comparative analysis. Anal Biochem 2024; 687:115454. [PMID: 38158107 DOI: 10.1016/j.ab.2023.115454] [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: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The non-invasive invasive nature of cell-free DNA (cfDNA) as diagnostic, prognostic, and theragnostic biomarkers has gained immense popularity in recent years. The clinical utility of cfDNA biomarkers may depend on understanding their origin and biological significance. Apoptosis, necrosis, and/or active release are possible mechanisms of cellular DNA release into the cell-free milieu. In-vitro cell culture models can provide useful insights into cfDNA biology. The yields and quality of cfDNA in the cell conditioned media (CCM) are largely dependent on the extraction method used. Here, we developed a phenol-chloroform-free cfDNA extraction method from CCM and compared it with three others published cfDNA extraction methods and four commercially available kits. Real-Time PCR (qPCR) targeting two different loci and a fluorescence-based Qubit assay were performed to quantify the extracted cfDNA. The absolute concentration of the extracted cfDNA varies with the target used for the qPCR assay; however, the relative trend remains similar for both qPCR assays. The cfDNA yield from CCM provided by the developed method was found to be either higher or comparable to the other methods used. In conclusion, we developed a safe, rapid and cost-effective cfDNA extraction protocol with minimal hands-on time; with no compromise in cfDNA yields.
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Affiliation(s)
- Dhruv Das
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India
| | - Rao Avssn
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Rajani Kant Chittela
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India.
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5
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Pomerantz T, Brooks R. Circulating Tumor DNA (ctDNA) and Its Role in Gynecologic Malignancies. Curr Treat Options Oncol 2024; 25:510-522. [PMID: 38472567 DOI: 10.1007/s11864-024-01180-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] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
OPINION STATEMENT Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation. These results have the potential for use in cancer diagnosis, determining prognosis, targeting gene-specific therapies, and monitoring for/predicting disease recurrence and response to treatment. ctDNA offers an alternative to tissue biopsy; it is less invasive and can be monitored serially over time without multiple procedures. Moreover it may have the ability to detect disease recurrence or predict behavior in a way that solid tissue biopsies, tumor marker surveillance, and imaging cannot. Recent explosion in interest in ctDNA shows promising developments for widespread adoption of these techniques in cancer care. However, the use of ctDNA in diagnosis and treatment of gynecologic malignancies is currently limited, compared to adoption in other solid-organ tumors such as breast and colorectal cancers. Compared to other cancer types, there appear to be fewer comprehensive studies and clinical validations specifically focusing on the use of ctDNA in gynecologic cancers. More research is needed in this area to advance the potential for use of ctDNA in ovarian, endometrial, and cervical cancers before this can be routinely adopted to improve care for patients with gynecologic malignancies.
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Affiliation(s)
- Tali Pomerantz
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA.
| | - Rebecca Brooks
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA
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6
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Di Bona M, Bakhoum SF. Micronuclei and Cancer. Cancer Discov 2024; 14:214-226. [PMID: 38197599 PMCID: PMC11265298 DOI: 10.1158/2159-8290.cd-23-1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
Chromosome-containing micronuclei are a feature of human cancer. Micronuclei arise from chromosome mis-segregation and characterize tumors with elevated rates of chromosomal instability. Although their association with cancer has been long recognized, only recently have we broadened our understanding of the mechanisms that govern micronuclei formation and their role in tumor progression. In this review, we provide a brief historical account of micronuclei, depict the mechanisms underpinning their creation, and illuminate their capacity to propel tumor evolution through genetic, epigenetic, and transcriptional transformations. We also posit the prospect of leveraging micronuclei as biomarkers and therapeutic targets in chromosomally unstable cancers. SIGNIFICANCE Micronuclei in chromosomally unstable cancer cells serve as pivotal catalysts for cancer progression, instigating transformative genomic, epigenetic, and transcriptional alterations. This comprehensive review not only synthesizes our present comprehension but also outlines a framework for translating this knowledge into pioneering biomarkers and therapeutics, thereby illuminating novel paths for personalized cancer management.
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Affiliation(s)
- Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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7
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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8
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Chauhan US, Kohale MG, Jaiswal N, Wankhade R. Emerging Applications of Liquid Biopsies in Ovarian Cancer. Cureus 2023; 15:e49880. [PMID: 38174205 PMCID: PMC10762500 DOI: 10.7759/cureus.49880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Liquid biopsy is a new diagnostic tool in precision oncology that can be used as a complementary or alternative method to surgical biopsies. It is a cutting-edge sampling technique that examines distinct cancer components, such as exosomes and circulating tumor cells discharged into the peripheral circulation, to identify tumor biomarkers through various methods, including polymerase chain reaction (PCR). Liquid biopsy has several benefits, including its non-invasiveness and practicality, which permit serial sampling and long-term monitoring of dynamic tumor changes. Ovarian cancer (OC), the most lethal gynecologic malignancy in the world, is typically diagnosed at stages II and III, which makes recovery and treatment extremely difficult. Relapsed OC and chemotherapy resistance of ovarian tumor cells are other clinical challenges. Although liquid biopsy is not a routinely used diagnostic test, it should be utilized in the diagnosis and prognosis of OC for early detection and treatment. It is less intrusive than conventional tissue biopsies, allowing for the continuous collection of serial blood samples to track cancer development in real time. Before therapeutic application, more investigation is required to pinpoint the particular release processes, the source tissue, and the biological significance of the bulk of liquid biopsy contents.
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Affiliation(s)
- Urvi S Chauhan
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Mangesh G Kohale
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Neha Jaiswal
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Rashmi Wankhade
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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9
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Batool SM, Yekula A, Khanna P, Hsia T, Gamblin AS, Ekanayake E, Escobedo AK, You DG, Castro CM, Im H, Kilic T, Garlin MA, Skog J, Dinulescu DM, Dudley J, Agrawal N, Cheng J, Abtin F, Aberle DR, Chia D, Elashoff D, Grognan T, Krysan K, Oh SS, Strom C, Tu M, Wei F, Xian RR, Skates SJ, Zhang DY, Trinh T, Watson M, Aft R, Rawal S, Agarwal A, Kesmodel SB, Yang C, Shen C, Hochberg FH, Wong DTW, Patel AA, Papadopoulos N, Bettegowda C, Cote RJ, Srivastava S, Lee H, Carter BS, Balaj L. The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring. Cell Rep Med 2023; 4:101198. [PMID: 37716353 PMCID: PMC10591039 DOI: 10.1016/j.xcrm.2023.101198] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/01/2022] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The emerging field of liquid biopsy stands at the forefront of novel diagnostic strategies for cancer and other diseases. Liquid biopsy allows minimally invasive molecular characterization of cancers for diagnosis, patient stratification to therapy, and longitudinal monitoring. Liquid biopsy strategies include detection and monitoring of circulating tumor cells, cell-free DNA, and extracellular vesicles. In this review, we address the current understanding and the role of existing liquid-biopsy-based modalities in cancer diagnostics and monitoring. We specifically focus on the technical and clinical challenges associated with liquid biopsy and biomarker development being addressed by the Liquid Biopsy Consortium, established through the National Cancer Institute. The Liquid Biopsy Consortium has developed new methods/assays and validated existing methods/technologies to capture and characterize tumor-derived circulating cargo, as well as addressed existing challenges and provided recommendations for advancing biomarker assays.
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Affiliation(s)
| | - Anudeep Yekula
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Prerna Khanna
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dong Gil You
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cesar M Castro
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hyungsoon Im
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tugba Kilic
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Johan Skog
- Exosome Diagnostics Inc., Waltham, MA, USA
| | | | - Jonathan Dudley
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jordan Cheng
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - David Chia
- University of California Los Angeles, Los Angeles, CA, USA
| | - David Elashoff
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Scott S Oh
- University of California Los Angeles, Los Angeles, CA, USA
| | - Charles Strom
- University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Tu
- Liquid Diagnostics LLC., Los Angeles, CA, USA
| | - Fang Wei
- University of California Los Angeles, Los Angeles, CA, USA
| | - Rena R Xian
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven J Skates
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thi Trinh
- Yale University School of Medicine, New Haven, CT, USA
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Aft
- Washington University School of Medicine, St. Louis, MO, USA
| | - Siddarth Rawal
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | | | | | | | - Cheng Shen
- California Institute of Technology, Pasadena, CA, USA
| | | | - David T W Wong
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Richard J Cote
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Hakho Lee
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Ning W, Zhang C, Tian Z, Wu M, Luo Z, Hu S, Pan H, Li Y. Ω-shaped fiber optic LSPR biosensor based on mismatched hybridization chain reaction and gold nanoparticles for detection of circulating cell-free DNA. Biosens Bioelectron 2023; 228:115175. [PMID: 36871422 DOI: 10.1016/j.bios.2023.115175] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Circulating cell-free DNA (cfDNA) is a promising biomarker of liquid biopsy, but it still faces some difficulties in achieving sensitive and convenient detection. Herein, an Ω-shaped fiber optic localized surface plasmon resonance (FO-LSPR) biosensor based on hybridization chain reaction (HCR) coupled with gold nanoparticles (AuNPs) was developed, and applied in simple and sensitive detection of cfDNA. Specifically, one-base mismatch was designed in HCR hairpins (H1 and H2) to obtain high reaction efficiency, and AuNPs was introduced onto H1 through poly-adenine to construct HCR coupled with AuNPs strategy. Meanwhile, target cfDNA was designed into two domains: one could trigger HCR to generate dsDNA concatemer carrying numerous AuNPs, and the other could hybridize with capture DNA on the surface of Ω-shaped fiber optic (FO) probes. Thus, the presence of target cfDNA would initiate HCR, and bring the formed dsDNA concatemer and AuNPs to approach the probe surface, resulting in dramatically amplified LSPR signal. Besides, HCR required simple isothermal and enzyme-free condition, and Ω-shaped FO probe with high refractive index sensitivity just needed to be immersed into HCR solution directly for signal monitoring. Benefiting from the synergetic amplification of mismatched HCR and AuNPs, the proposed biosensor exhibited high sensitivity with a limit of detection of 14.0 pM, and therefore could provide a potential strategy for biomedical analysis and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuyan Zhang
- Medical Equipment Innovation Research Center, Precision Medicine Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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11
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Trinidad EM, Juan-Ribelles A, Pisano G, Castel V, Cañete A, Gut M, Heath S, Font de Mora J. Evaluation of circulating tumor DNA by electropherogram analysis and methylome profiling in high-risk neuroblastomas. Front Oncol 2023; 13:1037342. [PMID: 37251933 PMCID: PMC10213460 DOI: 10.3389/fonc.2023.1037342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background Liquid biopsy has emerged as a promising, non-invasive diagnostic approach in oncology because the analysis of circulating tumor DNA (ctDNA) reflects the precise status of the disease at diagnosis, progression, and response to treatment. DNA methylation profiling is also a potential solution for sensitive and specific detection of many cancers. The combination of both approaches, DNA methylation analysis from ctDNA, provides an extremely useful and minimally invasive tool with high relevance in patients with childhood cancer. Neuroblastoma is an extracranial solid tumor most common in children and responsible for up to 15% of cancer-related deaths. This high death rate has prompted the scientific community to search for new therapeutic targets. DNA methylation also offers a new source for identifying these molecules. However, the limited blood sample size which can be obtained from children with cancer and the fact that ctDNA content may occasionally be diluted by non-tumor cell-free DNA (cfDNA) complicate optimal quantities of material for high-throughput sequencing studies. Methods In this article, we present an improved method for ctDNA methylome studies of blood-derived plasma from high-risk neuroblastoma patients. We assessed the electropherogram profiles of ctDNA-containing samples suitable for methylome studies, using 10 ng of plasma-derived ctDNA from 126 samples of 86 high-risk neuroblastoma patients, and evaluated several bioinformatic approaches to analyze DNA methylation sequencing data. Results We demonstrated that enzymatic methyl-sequencing (EM-seq) outperformed bisulfite conversion-based method, based on the lower proportion of PCR duplicates and the higher percentage of unique mapping reads, mean coverage, and genome coverage. The analysis of the electropherogram profiles revealed the presence of nucleosomal multimers, and occasionally high molecular weight DNA. We established that 10% content of the mono-nucleosomal peak is sufficient ctDNA for successful detection of copy number variations and methylation profiles. Quantification of mono-nucleosomal peak also showed that samples at diagnosis contained a higher amount of ctDNA than relapse samples. Conclusions Our results refine the use of electropherogram profiles to optimize sample selection for subsequent high-throughput analysis and support the use of liquid biopsy followed by enzymatic conversion of unmethylated cysteines to assess the methylomes of neuroblastoma patients.
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Affiliation(s)
- Eva María Trinidad
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Antonio Juan-Ribelles
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Giulia Pisano
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Victoria Castel
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
- Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
- School of Medicine, University of Valencia, Valencia, Spain
| | - Marta Gut
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- National Center for Genomic Analysis – Centre for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
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12
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Cell-Free DNA in Plasma and Serum Indicates Disease Severity and Prognosis in Blunt Trauma Patients. Diagnostics (Basel) 2023; 13:diagnostics13061150. [PMID: 36980458 PMCID: PMC10047705 DOI: 10.3390/diagnostics13061150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
Background: Trauma is still a major cause of mortality in people < 50 years of age. Biomarkers are needed to estimate the severity of the condition and the patient outcome. Methods: Cell-free DNA (cfDNA) and further laboratory markers were determined in plasma and serum of 164 patients at time of admission to the emergency room. Among them were 64 patients with severe trauma (Injury Severity Score (ISS) ≥ 16), 51 patients with moderate trauma (ISS < 16) and 49 patients with single fractures (24 femur neck and 25 ankle fractures). Disease severity was objectified by ISS and Glasgow Coma Scale (GCS). Results: cfDNA levels in plasma and serum were significantly higher in patients with severe multiple trauma (SMT) than in those with moderate trauma (p = 0.002, p = 0.003, respectively) or with single fractures (each p < 0.001). CfDNA in plasma and serum correlated very strongly with each other (R = 0.91; p < 0.001). The AUC in ROC curves for identification of SMT patients was 0.76 and 0.74 for cfDNA in plasma and serum, respectively—this was further increased to 0.84 by the combination of cfDNA and hemoglobin. Within the group of multiple trauma patients, cfDNA levels were significantly higher in more severely injured patients and patients with severe traumatic brain injury (GCS ≤ 8 versus GCS > 8). Thirteen (20.3%) of the multiple trauma patients died during the first week after trauma. Levels of cfDNA were significantly higher in non-surviving patients than in survivors (p < 0.001), reaching an AUC of 0.81 for cfDNA in both, plasma and serum, which was further increased by the combination with hemoglobin and leukocytes. Conclusions: cfDNA is valuable for estimation of trauma severity and prognosis of trauma patients.
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13
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Lou E. Immunotherapy Success for Microsatellite Stable Colorectal Cancers-Searching for the Horizon. JAMA Oncol 2023; 9:615-617. [PMID: 36892823 DOI: 10.1001/jamaoncol.2022.7786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Affiliation(s)
- Emil Lou
- Division of Hematology, Oncology and Transplantation, University of Minnesota Twin Cities, Minneapolis
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14
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Horndalsveen H, Alver TN, Dalsgaard AM, Rogg LV, Helbekkmo N, Grønberg BH, Halvorsen TO, Ramberg C, Haakensen VD, Öjlert ÅK, Bjaanaes MM, Helland Å. Atezolizumab and stereotactic body radiotherapy in patients with advanced non-small cell lung cancer: safety, clinical activity and ctDNA responses-the ComIT-1 trial. Mol Oncol 2023; 17:487-498. [PMID: 36330681 PMCID: PMC9980306 DOI: 10.1002/1878-0261.13330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/02/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The introduction of immune checkpoint inhibitors has transformed the treatment landscape of metastatic non-small cell lung cancer. However, challenges remain to increase the fraction of patients achieving durable clinical responses to these drugs and to help monitor the treatment effect. In this phase II trial, we investigated the toxicity, systemic responses and circulating tumour DNA responses in patients (n = 21) with advanced non-small-cell lung cancer treated with atezolizumab and stereotactic body radiotherapy in the second or later line. We found the combined treatment to be safe with grade 3 toxicity reported in three patients. As the best overall response, four patients had a partial response, eight had stable disease and five had progressive disease. Median overall survival time was still not reached after a median follow-up of 26.5 months and 10/15 patients with programmed death-ligand 1 negative tumours were alive >18 months after the start of the study treatment. ctDNA was detectable at baseline in 11 patients. A rapid decline in ctDNA to <30% of baseline levels was seen in three patients, two of which were radiographic responders and one was considered clinically benefiting from therapy for almost 1 year.
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Affiliation(s)
- Henrik Horndalsveen
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Tine Norman Alver
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway.,Department of Clinical Medicine, University of Oslo, Norway
| | - Astrid Marie Dalsgaard
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | | | - Nina Helbekkmo
- Department of Pulmonology, University Hospital of North Norway, Tromsø, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Norway
| | | | - Vilde Drageset Haakensen
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | - Åsa Kristina Öjlert
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway
| | | | - Åslaug Helland
- Department of Oncology, Oslo University Hospital, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway.,Department of Clinical Medicine, University of Oslo, Norway
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15
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Therapeutic strategies for non-small cell lung cancer: Experimental models and emerging biomarkers to monitor drug efficacies. Pharmacol Ther 2023; 242:108347. [PMID: 36642389 DOI: 10.1016/j.pharmthera.2023.108347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
While new targeted therapies have considerably changed the treatment and prognosis of non-small cell lung cancer (NSCLC), they are frequently unsuccessful due to primary or acquired resistances. Chemoresistance is a complex process that combines cancer cell intrinsic mechanisms including molecular and genetic abnormalities, aberrant interactions within the tumor microenvironment, and the pharmacokinetic characteristics of each molecule. From a pharmacological point of view, two levers could improve the response to treatment: (i) developing tools to predict the response to chemo- and targeted therapies and (ii) gaining a better understanding of the influence of the tumor microenvironment. Both personalized medicine approaches require the identification of relevant experimental models and biomarkers to understand and fight against chemoresistance mechanisms. After describing the main therapies in NSCLC, the scope of this review will be to identify and to discuss relevant in vitro and ex vivo experimental models that are able to mimic tumors. In addition, the interests of these models in the predictive responses to proposed therapies will be discussed. Finally, this review will evaluate the involvement of novel secreted biomarkers such as tumor DNA or micro RNA in predicting responses to anti-tumor therapies.
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16
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Madueke I, Lee RJ, Miyamoto DT. Circulating Tumor Cells and Circulating Tumor DNA in Urologic Cancers. Urol Clin North Am 2023; 50:109-114. [DOI: 10.1016/j.ucl.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Promises and Challenges of Predictive Blood Biomarkers for Locally Advanced Rectal Cancer Treated with Neoadjuvant Chemoradiotherapy. Cells 2023; 12:cells12030413. [PMID: 36766755 PMCID: PMC9913546 DOI: 10.3390/cells12030413] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
The treatment of locally advanced rectal cancer (LARC) requires a multimodal approach combining neoadjuvant radiotherapy or chemoradiotherapy (CRT) and surgery. Predicting tumor response to CRT can guide clinical decision making and improve patient care while avoiding unnecessary toxicity and morbidity. Circulating biomarkers offer both the advantage to be easily accessed and followed over time. In recent years, biomarkers such as proteins, blood cells, or nucleic acids have been investigated for their predictive value in oncology. We conducted a comprehensive literature review with the aim to summarize the status of circulating biomarkers predicting response to CRT in LARC. Forty-nine publications, of which forty-seven full-text articles, one review and one systematic review, were retrieved. These studies evaluated circulating markers (CEA and CA 19-9), inflammatory biomarkers (CRP, albumin, and lymphocytes), hematologic markers (hemoglobin and thrombocytes), lipids and circulating nucleic acids (cell-free DNA [cfDNA], circulating tumor DNA [ctDNA], and microRNA [miRNA]). Post-CRT CEA levels had the most consistent association with tumor response, while cfDNA integrity index, MGMT promoter methylation, ERCC-1, miRNAs, and miRNA-related SNPs were identified as potential predictive markers. Although circulating biomarkers hold great promise, inconsistent results, low statistical power, and low specificity and sensibility prevent them from reliably predicting tumor response following CRT. Validation and standardization of methods and technologies are further required to confirm results.
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18
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Stejskal P, Goodarzi H, Srovnal J, Hajdúch M, van ’t Veer LJ, Magbanua MJM. Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance. Mol Cancer 2023; 22:15. [PMID: 36681803 PMCID: PMC9862574 DOI: 10.1186/s12943-022-01710-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/29/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Despite advances in early detection and therapies, cancer is still one of the most common causes of death worldwide. Since each tumor is unique, there is a need to implement personalized care and develop robust tools for monitoring treatment response to assess drug efficacy and prevent disease relapse. MAIN BODY Recent developments in liquid biopsies have enabled real-time noninvasive monitoring of tumor burden through the detection of molecules shed by tumors in the blood. These molecules include circulating tumor nucleic acids (ctNAs), comprising cell-free DNA or RNA molecules passively and/or actively released from tumor cells. Often highlighted for their diagnostic, predictive, and prognostic potential, these biomarkers possess valuable information about tumor characteristics and evolution. While circulating tumor DNA (ctDNA) has been in the spotlight for the last decade, less is known about circulating tumor RNA (ctRNA). There are unanswered questions about why some tumors shed high amounts of ctNAs while others have undetectable levels. Also, there are gaps in our understanding of associations between tumor evolution and ctNA characteristics and shedding kinetics. In this review, we summarize current knowledge about ctNA biology and release mechanisms and put this information into the context of tumor evolution and clinical utility. CONCLUSIONS A deeper understanding of the biology of ctDNA and ctRNA may inform the use of liquid biopsies in personalized medicine to improve cancer patient outcomes.
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Affiliation(s)
- Pavel Stejskal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Josef Srovnal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
| | - Laura J. van ’t Veer
- Department of Laboratory Medicine, University of California San Francisco, 2340 Sutter Street, San Francisco, CA USA
| | - Mark Jesus M. Magbanua
- Department of Laboratory Medicine, University of California San Francisco, 2340 Sutter Street, San Francisco, CA USA
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19
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Kohabir KAV, Nooi LO, Brink A, Brakenhoff RH, Sistermans EA, Wolthuis RMF. In Vitro CRISPR-Cas12a-Based Detection of Cancer-Associated TP53 Hotspot Mutations Beyond the crRNA Seed Region. CRISPR J 2023; 6:127-139. [PMID: 36637878 PMCID: PMC10123810 DOI: 10.1089/crispr.2022.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cost-effective and time-efficient detection of oncogenic mutations supports improved presymptomatic cancer diagnostics and post-treatment disease monitoring. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a is an RNA-guided endonuclease that, upon protospacer adjacent motif (PAM)-dependent recognition of target DNA in cis, exhibits indiscriminate ssDNase activity in trans, which can be harnessed for diagnostics. TP53, one of the most frequently mutated tumor suppressor genes in cancer, displays recurring point mutations at so-called "hotspots." In this study, we optimized Cas12a-based assay conditions for in vitro detection of six TP53 hotspot mutations at the codon for p.R273, located outside the Cas12a seed region, and evaluated the specificities of four commercial Cas12a variants. We found that nonengineered LbCas12a significantly outperformed the other tested nucleases specifically in distinguishing mutant p.R273 codons in synthetic DNA, mock cell-free DNA, and tissue biopsies, despite the suboptimal PAM-distal positioning of the corresponding mutations. Future clinical Cas12a-based applications may include point-of-care tumor analysis, cost-effective mutation screening, and improved monitoring of individual cancer patients.
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Affiliation(s)
- Kavish A V Kohabir
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Embryonic & Fetal Development, Amsterdam Reproduction & Development, Amsterdam, The Netherlands.,Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Lars O Nooi
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjen Brink
- Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Otolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ruud H Brakenhoff
- Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Otolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Embryonic & Fetal Development, Amsterdam Reproduction & Development, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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20
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ÖZGÜR E, YILDIZ A, BADEMLER S, GEZER U. Kan Plazmasında Satellit-2 Tekrar Elementi DNA Dizilerinin Karakterizasyonu. İSTANBUL GELIŞIM ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.38079/igusabder.1105142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Amaç: Son yıllarda tıp biliminin farklı disiplinlerinde sıkça karşılaşılan kavramlardan biri olan “sıvı biyopsi”, hastaların tanı, prognoz analizi ve tedaviye cevabını değerlendirme gibi konularda girişimsel doku biyopsisi yerine, kan ve çeşitli vücut sıvılarındaki moleküler ve epigenetik biyobelirteçlerin kullanılmasını içerir. Dolaşımda serbest halde dolaşan DNA’da (‘cell-free DNA’, cfDNA) kanser hücrelerine özgü gen mutasyonlarının saptanması, kanser hücrelerinin içeriğinin vücut sıvılarına geçtiğinin kesin kanıtı olarak kabul edilmektedir. cfDNA’nın bileşiminin belirlenmesine yönelik dizileme çalışmaları, perisentrik satellit DNA dizilerinin, cfDNA’da genom oranlarına kıyasla daha fazla oranda temsil edildiğini bildirmiştir. Bu çalışmada, kanser açısından spesifik dizilerin saptanması amacıyla, Sat-2 dizilerinin polimeraz zincir reaksiyonunda (PCR) çoğaltılmaları sonrasında daha detaylı karakterizasyonu amaçlanmıştır.Yöntem: Çalışmada, sağlıklı ve metastatik meme kanserli hastaların plazmalarından 1. ve 10. kromozoma spesifik Sat-2 dizileri PCR ile çoğaltıldıktan sonra, otomatik elektroforez sisteminde ayrıştırıldılar.Bulgular: Yapılan büyüklük analizinde, iki bölgeden çok sayıda amplikon oluştuğu, bunların yaklaşık %50’ni sırasıyla 143 ve 115 bç uzunluğunda ürünlerin oluşturduğu belirlenmiştir. Bu iki PCR amplikonunun miktarı meme kanserli hastalarda daha yüksek olarak hesaplandı. Onuncu kromozoma özgü 115 bç’lik fargman dışındaki Sat-2 dizileri açısından kontroller ile hastalar arasında önemli farklar olduğu belirlenmiştir.Sonuç: Çalışma kapsamında elde edilen bulgular, Sat-2 tekrar elementine ait DNA dizilerinin sekanslanması sonrası kansere spesifik hedef bölgelerin saptanabileceğini ortaya koymaktadır.
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Affiliation(s)
- Emre ÖZGÜR
- İSTANBUL ÜNİVERSİTESİ, ONKOLOJİ ENSTİTÜSÜ, TEMEL ONKOLOJİ ANABİLİM DALI
| | - Anıl YILDIZ
- İSTANBUL ÜNİVERSİTESİ, ONKOLOJİ ENSTİTÜSÜ, KLİNİK ONKOLOJİ ANABİLİM DALI
| | - Süleyman BADEMLER
- İSTANBUL OKAN ÜNİVERSİTESİ, TIP FAKÜLTESİ, CERRAHİ TIP BİLİMLERİ BÖLÜMÜ, GENEL CERRAHİ ANABİLİM DALI
| | - Uğur GEZER
- İSTANBUL ÜNİVERSİTESİ, ONKOLOJİ ENSTİTÜSÜ, TEMEL ONKOLOJİ ANABİLİM DALI
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21
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Optimization Protocol of the PEG-Based Method for OSCC-Derived Exosome Isolation and Downstream Applications. SEPARATIONS 2022. [DOI: 10.3390/separations9120435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The exosome precipitation method affects the purity of the exosome and the quality of the downstream application. Polymer-based precipitation is a cost-effective method widely used in different research fields. The percentage of the polymer should be modified in different cell types or liquid biopsy before precipitation. This study aimed to optimize the protocol of the poly(ethylene glycol) (PEG)-based approach for extracting oral squamous cell carcinoma (OSCC)-derived exosomes, and its downstream applications. We used 8%, 10%, and 12% PEG to isolate the exosomes from the culture medium and compared the purity with that of the ultracentrifugation method. In addition, we extracted exosomal protein, DNA, and RNA, and tested the cell transfection efficiency for downstream application. The results reveal that 8% PEG and the medium mixture incubated at 4 °C overnight effectively precipitated exosomes of higher purity and more proper size and particle numbers compared with the ultracentrifuge method. PEG-precipitated exosomes cocultured with fibroblasts showed better transfection efficiency compared to exosomes alone. Therefore, 8% PEG is ideal for OSCC-derived exosome isolation and downstream applications. We recommend that the cost-effective PEG precipitation method be used for precipitating exosomes from OSCC cell experiments.
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22
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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The Continuing Question of Adjuvant Therapy in Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14246018. [PMID: 36551504 PMCID: PMC9776072 DOI: 10.3390/cancers14246018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Treatment advances in kidney cancer continually evolve. The focus of treatment options continues with oral vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitors (TKIs) or intravenous immune checkpoint inhibitors (ICIs). Multiple trials exploring the role of adjuvant treatment after cytoreductive nephrectomy in high-risk clear cell renal cell carcinoma are currently ongoing. The discovery of biomarkers may help determine which patients benefit from these treatments, but these are not yet available outside clinical studies. Trials with combination therapies are also ongoing, especially using novel therapies with new mechanisms of action, and will hopefully provide more clues on proper patient and therapy selection in the adjuvant setting.
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24
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Műzes G, Bohusné Barta B, Szabó O, Horgas V, Sipos F. Cell-Free DNA in the Pathogenesis and Therapy of Non-Infectious Inflammations and Tumors. Biomedicines 2022; 10:biomedicines10112853. [PMID: 36359370 PMCID: PMC9687442 DOI: 10.3390/biomedicines10112853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
The basic function of the immune system is the protection of the host against infections, along with the preservation of the individual antigenic identity. The process of self-tolerance covers the discrimination between self and foreign antigens, including proteins, nucleic acids, and larger molecules. Consequently, a broken immunological self-tolerance results in the development of autoimmune or autoinflammatory disorders. Immunocompetent cells express pattern-recognition receptors on their cell membrane and cytoplasm. The majority of endogenous DNA is located intracellularly within nuclei and mitochondria. However, extracellular, cell-free DNA (cfDNA) can also be detected in a variety of diseases, such as autoimmune disorders and malignancies, which has sparked interest in using cfDNA as a possible biomarker. In recent years, the widespread use of liquid biopsies and the increasing demand for screening, as well as monitoring disease activity and therapy response, have enabled the revival of cfDNA research. The majority of studies have mainly focused on the function of cfDNA as a biomarker. However, research regarding the immunological consequences of cfDNA, such as its potential immunomodulatory or therapeutic benefits, is still in its infancy. This article discusses the involvement of various DNA-sensing receptors (e.g., absent in melanoma-2; Toll-like receptor 9; cyclic GMP-AMP synthase/activator of interferon genes) in identifying host cfDNA as a potent danger-associated molecular pattern. Furthermore, we aim to summarize the results of the experimental studies that we recently performed and highlight the immunomodulatory capacity of cfDNA, and thus, the potential for possible therapeutic consideration.
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Affiliation(s)
| | | | | | | | - Ferenc Sipos
- Correspondence: ; Tel.: +36-20-478-0752; Fax: +36-1-266-0816
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25
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Endogenous cell-free DNA in fetal bovine serum introduces artifacts to in vitro cell-free DNA models. Biotechniques 2022; 73:219-226. [DOI: 10.2144/btn-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cell-free DNA (cfDNA) is of growing clinical and research significance. In vitro cfDNA models are a useful tool in cfDNA research; however, artifacts in these models may have implications for the interpretation of new and published data. This report aimed to establish how endogenous cfDNA in fetal bovine serum (FBS) may influence in vitro cfDNA measurements. Three commercial cell culture media, supplemented with 10% FBS, were analyzed for the presence of cfDNA, with and without culture with ovarian cancer cell lines. cfDNA from FBS was identified with all three commercial media and contributed a major portion of 167-bp cfDNA. Future studies should account for bovine cfDNA in FBS-supplemented media when conducting in vitro cfDNA research.
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26
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Tsering T, Li M, Chen Y, Nadeau A, Laskaris A, Abdouh M, Bustamante P, Burnier JV. EV-ADD, a database for EV-associated DNA in human liquid biopsy samples. J Extracell Vesicles 2022; 11:e12270. [PMID: 36271888 PMCID: PMC9587709 DOI: 10.1002/jev2.12270] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022] Open
Abstract
Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at www.evdnadatabase.com.
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Affiliation(s)
- Thupten Tsering
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mingyang Li
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Yunxi Chen
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Amélie Nadeau
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Alexander Laskaris
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mohamed Abdouh
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Prisca Bustamante
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Julia V. Burnier
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Experimental Pathology UnitDepartment of PathologyMcGill UniversityMontrealQuebecCanada
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27
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Bronkhorst AJ, Ungerer V, Oberhofer A, Gabriel S, Polatoglou E, Randeu H, Uhlig C, Pfister H, Mayer Z, Holdenrieder S. New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:2147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Affiliation(s)
- Abel J. Bronkhorst
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
| | | | | | | | | | | | | | | | | | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
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28
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Österlund T, Filges S, Johansson G, Ståhlberg A. UMIErrorCorrect and UMIAnalyzer: Software for Consensus Read Generation, Error Correction, and Visualization Using Unique Molecular Identifiers. Clin Chem 2022; 68:1425-1435. [PMID: 36031761 DOI: 10.1093/clinchem/hvac136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/08/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Targeted sequencing using unique molecular identifiers (UMIs) enables detection of rare variant alleles in challenging applications, such as cell-free DNA analysis from liquid biopsies. Standard bioinformatics pipelines for data processing and variant calling are not adapted for deep-sequencing data containing UMIs, are inflexible, and require multistep workflows or dedicated computing resources. METHODS We developed a bioinformatics pipeline using Python and an R package for data analysis and visualization. To validate our pipeline, we analyzed cell-free DNA reference material with known mutant allele frequencies (0%, 0.125%, 0.25%, and 1%) and public data sets. RESULTS We developed UMIErrorCorrect, a bioinformatics pipeline for analyzing sequencing data containing UMIs. UMIErrorCorrect only requires fastq files as inputs and performs alignment, UMI clustering, error correction, and variant calling. We also provide UMIAnalyzer, a graphical user interface, for data mining, visualization, variant interpretation, and report generation. UMIAnalyzer allows the user to adjust analysis parameters and study their effect on variant calling. We demonstrated the flexibility of UMIErrorCorrect by analyzing data from 4 different targeted sequencing protocols. We also show its ability to detect different mutant allele frequencies in standardized cell-free DNA reference material. UMIErrorCorrect outperformed existing pipelines for targeted UMI sequencing data in terms of variant detection sensitivity. CONCLUSIONS UMIErrorCorrect and UMIAnalyzer are comprehensive and customizable bioinformatics tools that can be applied to any type of library preparation protocol and enrichment chemistry using UMIs. Access to simple, generic, and open-source bioinformatics tools will facilitate the implementation of UMI-based sequencing approaches in basic research and clinical applications.
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Affiliation(s)
- Tobias Österlund
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Filges
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Gustav Johansson
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,SiMSen Diagnostics AB, Gothenburg, Sweden
| | - Anders Ståhlberg
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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29
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Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line. Diagnostics (Basel) 2022; 12:diagnostics12081896. [PMID: 36010246 PMCID: PMC9406536 DOI: 10.3390/diagnostics12081896] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 12/20/2022] Open
Abstract
Unique bits of genetic, biological and pathological information occur in differently sized cell-free DNA (cfDNA) populations. This is a significant discovery, but much of the phenomenon remains to be explored. We investigated cfDNA fragmentation patterns in cultured human bone cancer (143B) cells using increasingly sensitive electrophoresis assays, including four automated microfluidic capillary electrophoresis assays from Agilent, i.e., DNA 1000, High Sensitivity DNA, dsDNA 915 and dsDNA 930, and an optimized manual agarose gel electrophoresis protocol. This comparison showed that (i) as the sensitivity and resolution of the sizing methods increase incrementally, additional nucleosomal multiples are revealed (hepta-nucleosomes were detectable with manual agarose gel electrophoresis), while the estimated size range of high molecular weight (HMW) cfDNA fragments narrow correspondingly; (ii) the cfDNA laddering pattern extends well beyond the 1–3 nucleosomal multiples detected by commonly used methods; and (iii) the modal size of HMW cfDNA populations is exaggerated due to the limited resolving power of electrophoresis, and instead consists of several poly-nucleosomal subpopulations that continue the series of DNA laddering. Furthermore, the most sensitive automated assay used in this study (Agilent dsDNA 930) revealed an exponential decay in the relative contribution of increasingly longer cfDNA populations. This power-law distribution suggests the involvement of a stochastic inter-nucleosomal DNA cleavage process, wherein shorter populations accumulate rapidly as they are fed by the degradation of all larger populations. This may explain why similar size profiles have historically been reported for cfDNA populations originating from different processes, such as apoptosis, necrosis, accidental cell lysis and purported active release. These results not only demonstrate the diversity of size profiles generated by different methods, but also highlight the importance of caution when drawing conclusions on the mechanisms that generate different cfDNA size populations, especially when only a single method is used for sizing.
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30
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Dawson RE, Deswaerte V, West AC, Tang K, West AJ, Balic JJ, Gearing LJ, Saad MI, Yu L, Wu Y, Bhathal PS, Kumar B, Chakrabarti JT, Zavros Y, Oshima H, Klinman DM, Oshima M, Tan P, Jenkins BJ. STAT3-mediated upregulation of the AIM2 DNA sensor links innate immunity with cell migration to promote epithelial tumourigenesis. Gut 2022; 71:1515-1531. [PMID: 34489308 DOI: 10.1136/gutjnl-2020-323916] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/27/2021] [Indexed: 01/26/2023]
Abstract
OBJECTIVE The absent in melanoma 2 (AIM2) cytosolic pattern recognition receptor and DNA sensor promotes the pathogenesis of autoimmune and chronic inflammatory diseases via caspase-1-containing inflammasome complexes. However, the role of AIM2 in cancer is ill-defined. DESIGN The expression of AIM2 and its clinical significance was assessed in human gastric cancer (GC) patient cohorts. Genetic or therapeutic manipulation of AIM2 expression and activity was performed in the genetically engineered gp130 F/F spontaneous GC mouse model, as well as human GC cell line xenografts. The biological role and mechanism of action of AIM2 in gastric tumourigenesis, including its involvement in inflammasome activity and functional interaction with microtubule-associated end-binding protein 1 (EB1), was determined in vitro and in vivo. RESULTS AIM2 expression is upregulated by interleukin-11 cytokine-mediated activation of the oncogenic latent transcription factor STAT3 in the tumour epithelium of GC mouse models and patients with GC. Genetic and therapeutic targeting of AIM2 in gp130 F/F mice suppressed tumourigenesis. Conversely, AIM2 overexpression augmented the tumour load of human GC cell line xenografts. The protumourigenic function of AIM2 was independent of inflammasome activity and inflammation. Rather, in vivo and in vitro AIM2 physically interacted with EB1 to promote epithelial cell migration and tumourigenesis. Furthermore, upregulated expression of AIM2 and EB1 in the tumour epithelium of patients with GC was independently associated with poor patient survival. CONCLUSION AIM2 can play a driver role in epithelial carcinogenesis by linking cytokine-STAT3 signalling, innate immunity and epithelial cell migration, independent of inflammasome activation.
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Affiliation(s)
- Ruby E Dawson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Virginie Deswaerte
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Alison C West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Ke Tang
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Alice J West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Jesse J Balic
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Mohamed I Saad
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Liang Yu
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Yonghui Wu
- Cellular and Molecular Research, National Cancer Centre of Singapore, Singapore
| | - Prithi S Bhathal
- Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Beena Kumar
- Department of Anatomical Pathology, Monash Health, Clayton, Victoria, Australia
| | - Jayati T Chakrabarti
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Yana Zavros
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Hiroko Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Dennis M Klinman
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Patrick Tan
- Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore.,Genome Institute of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Brendan J Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia .,Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
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31
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Oberhofer A, Bronkhorst AJ, Uhlig C, Ungerer V, Holdenrieder S. Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures. Diagnostics (Basel) 2022; 12:diagnostics12081834. [PMID: 36010184 PMCID: PMC9406971 DOI: 10.3390/diagnostics12081834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g., methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.
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32
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Abstract
Cancer cells shed naked DNA molecules into the circulation. This circulating tumor DNA (ctDNA) has become the predominant analyte for liquid biopsies to understand the mutational landscape of cancer. Coupled with next-generation sequencing, ctDNA can serve as an alternative substrate to tumor tissues for mutation detection and companion diagnostic purposes. In fact, recent advances in precision medicine have rapidly enabled the use of ctDNA to guide treatment decisions for predicting response and resistance to targeted therapies and immunotherapies. An advantage of using ctDNA over conventional tissue biopsies is the relatively noninvasive approach of obtaining peripheral blood, allowing for simple repeated and serial assessments. Most current clinical practice using ctDNA has endeavored to identify druggable and resistance mutations for guiding systemic therapy decisions, albeit mostly in metastatic disease. However, newer research is evaluating potential for ctDNA as a marker of minimal residual disease in the curative setting and as a useful screening tool to detect cancer in the general population. Here we review the history of ctDNA and liquid biopsies, technologies to detect ctDNA, and some of the current challenges and limitations in using ctDNA as a marker of minimal residual disease and as a general blood-based cancer screening tool. We also discuss the need to develop rigorous clinical studies to prove the clinical utility of ctDNA for future applications in oncology.
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33
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The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies. Diagnostics (Basel) 2022; 12:diagnostics12061363. [PMID: 35741173 PMCID: PMC9221655 DOI: 10.3390/diagnostics12061363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.
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34
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Zhu JW, Charkhchi P, Akbari MR. Potential clinical utility of liquid biopsies in ovarian cancer. Mol Cancer 2022; 21:114. [PMID: 35545786 PMCID: PMC9092780 DOI: 10.1186/s12943-022-01588-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. One of the main challenges in the management of OC is the late clinical presentation of disease that results in poor survival. Conventional tissue biopsy methods and serological biomarkers such as CA-125 have limited clinical applications. Liquid biopsy is a novel sampling method that analyzes distinctive tumour components released into the peripheral circulation, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs) and exosomes. Increasing evidence suggests that liquid biopsy could enhance the clinical management of OC by improving early diagnosis, predicting prognosis, detecting recurrence, and monitoring response to treatment. Capturing the unique tumour genetic landscape can also guide treatment decisions and the selection of appropriate targeted therapies. Key advantages of liquid biopsy include its non-invasive nature and feasibility, which allow for serial sampling and longitudinal monitoring of dynamic tumour changes over time. In this review, we outline the evidence for the clinical utility of each liquid biopsy component and review the advantages and current limitations of applying liquid biopsy in managing ovarian cancer. We also highlight future directions considering the current challenges and explore areas where more studies are warranted to elucidate its emerging clinical potential.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada.
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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Transcending Blood—Opportunities for Alternate Liquid Biopsies in Oncology. Cancers (Basel) 2022; 14:cancers14051309. [PMID: 35267615 PMCID: PMC8909855 DOI: 10.3390/cancers14051309] [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: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Cell-free DNA—DNA that has been expelled from cells and can be isolated from blood plasma and other body fluids—is a useful tool in medicine, with applications as a biomarker in diagnosis, prognosis, disease profiling, and treatment selection. In oncology, the ease of access to the tumour genome is a major advantage of cell-free DNA, but while this has led to significant research in blood, other body fluids have not received equal attention. This review article summarises the current research into cell-free DNA in non-blood body fluids, highlighting its values and limitations, and suggesting the direction of future studies. We conclude that cell-free DNA from non-blood body fluids may provide additional information to supplement traditional biopsies, allowing informative and improved patient care across many cancer types. Abstract Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, faeces, pleural effusions, and ascites has unique advantages over blood, and has potential as an alternative ‘liquid biopsy’ template. This review summarises the state of current knowledge and identifies the gaps in our understanding of non-blood liquid biopsies; where their advantages lie, where caution is needed, where they might fit clinically, and where research should focus in order to accelerate clinical implementation. An emphasis is placed on ascites and pleural effusions, being pathological fluids directly associated with cancer. We conclude that non-blood fluids are viable sources of cfDNA in situations where solid tissue biopsies are inaccessible, or only accessible from dated archived specimens. In addition, we show that due to the abundance of cfDNA in non-blood fluids, they can outperform blood in many circumstances. We demonstrate multiple instances in which DNA from various sources can provide additional information, and thus we advocate for analysing non-blood sources as a complement to blood and/or tissue. Further research into these fluids will highlight opportunities to improve patient outcomes across cancer types.
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Boniface CT, Spellman PT. Blood, Toil, and Taxoteres: Biological Determinates of Treatment-Induce ctDNA Dynamics for Interpreting Tumor Response. Pathol Oncol Res 2022; 28:1610103. [PMID: 35665409 PMCID: PMC9160182 DOI: 10.3389/pore.2022.1610103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022]
Abstract
Collection and analysis of circulating tumor DNA (ctDNA) is one of the few methods of liquid biopsy that measures generalizable and tumor specific molecules, and is one of the most promising approaches in assessing the effectiveness of cancer care. Clinical assays that utilize ctDNA are commercially available for the identification of actionable mutations prior to treatment and to assess minimal residual disease after treatment. There is currently no clinical ctDNA assay specifically intended to monitor disease response during treatment, partially due to the complex challenge of understanding the biological sources of ctDNA and the underlying principles that govern its release. Although studies have shown pre- and post-treatment ctDNA levels can be prognostic, there is evidence that early, on-treatment changes in ctDNA levels are more accurate in predicting response. Yet, these results also vary widely among cohorts, cancer type, and treatment, likely due to the driving biology of tumor cell proliferation, cell death, and ctDNA clearance kinetics. To realize the full potential of ctDNA monitoring in cancer care, we may need to reorient our thinking toward the fundamental biological underpinnings of ctDNA release and dissemination from merely seeking convenient clinical correlates.
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Affiliation(s)
- Christopher T. Boniface
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
| | - Paul T. Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
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Malignant pleural effusions for cancer genotyping: A matter of trans-pleural traffic of cell-free tumor DNA. Mol Cell Probes 2022; 61:101793. [DOI: 10.1016/j.mcp.2022.101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022]
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Sipos F, Bohusné Barta B, Simon Á, Nagy L, Dankó T, Raffay RE, Petővári G, Zsiros V, Wichmann B, Sebestyén A, Műzes G. Survival of HT29 Cancer Cells Is Affected by IGF1R Inhibition via Modulation of Self-DNA-Triggered TLR9 Signaling and the Autophagy Response. Pathol Oncol Res 2022; 28:1610322. [PMID: 35651701 PMCID: PMC9148969 DOI: 10.3389/pore.2022.1610322] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023]
Abstract
Purpose: In HT29 colon cancer cells, a close interplay between self-DNA-induced TLR9 signaling and autophagy response was found, with remarkable effects on cell survival and differentiation. IGF1R activation drives the development and malignant progression of colorectal cancer. IGF1R inhibition displays a controversial effect on autophagy. The interrelated roles of IGF1R inhibition and TLR9/autophagy signaling in HT29 cancer cells have not yet been clarified. In our study, we aimed to investigate the complex interplay of IGF1R inhibition and TLR9/autophagy signaling in HT29 cells. Methods: HT29 cells were incubated with tumor-originated self-DNA with or without inhibitors of IGF1R (picropodophyllin), autophagy (chloroquine), and TLR9 (ODN2088), respectively. Cell proliferation and metabolic activity measurements, direct cell counting, NanoString and Taqman gene expression analyses, immunocytochemistry, WES Simple Western blot, and transmission electron microscopy investigations were performed. Results: The concomitant use of tumor-derived self-DNA and IGF1R inhibitors displays anti-proliferative potential, which can be reversed by parallel TLR9 signaling inhibition. The distinct effects of picropodophyllin, ODN2088, and chloroquine per se or in combination on HT29 cell proliferation and autophagy suggest that either the IGF1R-associated or non-associated autophagy machinery is "Janus-faced" regarding its actions on cell proliferation. Autophagy, induced by different combinations of self-DNA and inhibitors is not sufficient to rescue HT29 cells from death but results in the survival of some CD133-positive stem-like HT29 cells. Conclusion: The creation of new types of combined IGF1R, autophagy, and/or TLR9 signaling inhibitors would play a significant role in the development of more personalized anti-tumor therapies for colorectal cancer.
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Affiliation(s)
- Ferenc Sipos
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
- *Correspondence: Ferenc Sipos,
| | - Bettina Bohusné Barta
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Ágnes Simon
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Lőrinc Nagy
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Titanilla Dankó
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Regina Eszter Raffay
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Petővári
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória Zsiros
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | | | - Anna Sebestyén
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Györgyi Műzes
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
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Palande V, Siegal T, Detroja R, Gorohovski A, Glass R, Flueh C, Kanner AA, Laviv Y, Har-Nof S, Levy-Barda A, Viviana Karpuj M, Kurtz M, Perez S, Raviv Shay D, Frenkel-Morgenstern M. Detection of gene mutations and gene-gene fusions in circulating cell-free DNA of glioblastoma patients: an avenue for clinically relevant diagnostic analysis. Mol Oncol 2021; 16:2098-2114. [PMID: 34875133 PMCID: PMC9120899 DOI: 10.1002/1878-0261.13157] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 09/04/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Glioblastoma (GBM) is the most common type of glioma and is uniformly fatal. Currently, tumour heterogeneity and mutation acquisition are major impedances for tailoring personalized therapy. We collected blood and tumour tissue samples from 25 GBM patients and 25 blood samples from healthy controls. Cell‐free DNA (cfDNA) was extracted from the plasma of GBM patients and from healthy controls. Tumour DNA was extracted from fresh tumour samples. Extracted DNA was sequenced using a whole‐genome sequencing procedure. We also collected 180 tumour DNA datasets from GBM patients publicly available at the TCGA/PANCANCER project. These data were analysed for mutations and gene–gene fusions that could be potential druggable targets. We found that plasma cfDNA concentrations in GBM patients were significantly elevated (22.6 ± 5 ng·mL−1), as compared to healthy controls (1.4 ± 0.4 ng·mL−1) of the same average age. We identified unique mutations in the cfDNA and tumour DNA of each GBM patient, including some of the most frequently mutated genes in GBM according to the COSMIC database (TP53, 18.75%; EGFR, 37.5%; NF1, 12.5%; LRP1B, 25%; IRS4, 25%). Using our gene–gene fusion database, ChiTaRS 5.0, we identified gene–gene fusions in cfDNA and tumour DNA, such as KDR–PDGFRA and NCDN–PDGFRA, which correspond to previously reported alterations of PDGFRA in GBM (44% of all samples). Interestingly, the PDGFRA protein fusions can be targeted by tyrosine kinase inhibitors such as imatinib, sunitinib, and sorafenib. Moreover, we identified BCR–ABL1 (in 8% of patients), COL1A1–PDGFB (8%), NIN–PDGFRB (8%), and FGFR1–BCR (4%) in cfDNA of patients, which can be targeted by analogues of imatinib. ROS1 fusions (CEP85L–ROS1 and GOPC–ROS1), identified in 8% of patient cfDNA, might be targeted by crizotinib, entrectinib, or larotrectinib. Thus, our study suggests that integrated analysis of cfDNA plasma concentration, gene mutations, and gene–gene fusions can serve as a diagnostic modality for distinguishing GBM patients who may benefit from targeted therapy. These results open new avenues for precision medicine in GBM, using noninvasive liquid biopsy diagnostics to assess personalized patient profiles. Moreover, repeated detection of druggable targets over the course of the disease may provide real‐time information on the evolving molecular landscape of the tumour.
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Affiliation(s)
- Vikrant Palande
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Tali Siegal
- Neuro-Oncology Center, Rabin Medical Center, Petach Tikva, Israel and Hebrew University, 4941492, Jerusalem, Israel
| | - Rajesh Detroja
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | | | - Rainer Glass
- Department of Neurosurgery, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Charlotte Flueh
- Department of Neurosurgery, University Hospital of Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Andrew A Kanner
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoseph Laviv
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sagi Har-Nof
- Department of Neurosurgery, Rabin Medical Center, Petach Tikva, 4941492, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adva Levy-Barda
- Department of Pathology, Rabin Medical Center, Petach Tikva, 4941492, Israel
| | | | - Marina Kurtz
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Shira Perez
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Dorith Raviv Shay
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel.,The Dangoor Centre For Personalized Medicine, Bar-Ilan University, Ramat Gan, 5290002, Israel
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Anticancer effects of mifepristone on human uveal melanoma cells. Cancer Cell Int 2021; 21:607. [PMID: 34789240 PMCID: PMC8597220 DOI: 10.1186/s12935-021-02306-y] [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: 08/10/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022] Open
Abstract
Background Uveal melanoma (UM), the most prevalent intraocular tumor in adults, is a highly metastatic and drug resistant lesion. Recent studies have demonstrated cytotoxic and anti-metastatic effects of the antiprogestin and antiglucocorticoid mifepristone (MF) in vitro and in clinical trials involving meningioma, colon, breast, and ovarian cancers. Drug repurposing is a cost-effective approach to bring approved drugs with good safety profiles to the clinic. This current study assessed the cytotoxic effects of MF in human UM cell lines of different genetic backgrounds. Methods The effects of incremental concentrations of MF (0, 5, 10, 20, or 40 μM) on a panel of human UM primary (MEL270, 92.1, MP41, and MP46) and metastatic (OMM2.5) cells were evaluated. Cells were incubated with MF for up to 72 h before subsequent assays were conducted. Cellular functionality and viability were assessed by Cell Counting Kit-8, trypan blue exclusion assay, and quantitative label-free IncuCyte live-cell analysis. Cell death was analyzed by binding of Annexin V-FITC and/or PI, caspase-3/7 activity, and DNA fragmentation. Additionally, the release of cell-free DNA was assessed by droplet digital PCR, while the expression of progesterone and glucocorticoid receptors was determined by quantitative real-time reverse transcriptase PCR. Results MF treatment reduced cellular proliferation and viability of all UM cell lines studied in a concentration-dependent manner. A reduction in cell growth was observed at lower concentrations of MF, with evidence of cell death at higher concentrations. A significant increase in Annexin V-FITC and PI double positive cells, caspase-3/7 activity, DNA fragmentation, and cell-free DNA release suggests potent cytotoxicity of MF. None of the tested human UM cells expressed the classical progesterone receptor in the absence or presence of MF treatment, suggesting a mechanism independent of the modulation of the cognate nuclear progesterone receptor. In turn, all cells expressed non-classical progesterone receptors and the glucocorticoid receptor. Conclusion This study demonstrates that MF impedes the proliferation of UM cells in a concentration-dependent manner. We report that MF treatment at lower concentrations results in cell growth arrest, while increasing the concentration leads to lethality. MF, which has a good safety profile, could be a reliable adjuvant of a repurposing therapy against UM. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02306-y.
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Yuan Z, Wang X, Geng X, Li Y, Tan F, Xue Q, Gao S, He J. Multi-region sequencing reveals genetic correlation between esophageal squamous cell carcinoma and matched cell-free DNA. Cancer Genet 2021; 258-259:93-100. [PMID: 34688997 DOI: 10.1016/j.cancergen.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/23/2021] [Accepted: 08/28/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE This study aimed to determine if both ubiquitous and heterogeneous somatic mutations could be detected in circulating cell-free DNA (cfDNA) in patients with esophageal squamous cell carcinoma (ESCC). METHODS Paired multi-regional tumor tissues, cfDNA, and white blood cells (WBCs) were collected from five ESCC patients before treatment, as part of an ongoing prospective study (NCT02395705). Samples from Cohort 1 were sequenced by whole-exome sequencing and samples from Cohort 2 were sequenced by targeted capture sequencing. Somatic single-nucleotide variations (SNVs) were detected by comparing solid tumor or cfDNA with matched WBCs, with a minimum variant allele frequency (VAF) of 0.1% and P value <0.05. RESULTS Genomic DNA (gDNA) and plasma-derived cfDNA from 26 samples were sequenced successfully. In Cohort 1, a significant linear relationship between the tumor and cfDNA VAFs (R2= 0.78, P < 0.0001) was found. In Cohort 2, cfDNA could recover an average of 60.7% (31/51; range, 35.7-76.2%) of somatic mutations present in matched solid tumors. There was a significant positive correlation in VAFs between cfDNA and matched solid tumor tissues (R2= 0.92, P < 0.0001). CONCLUSIONS Both sequencing approaches revealed high intratumoral heterogeneity in ESCC, and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiao Geng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Yin Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China.
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Gong Y, Huang Q, Deng Y, Zhou L, Yi X, Zhu J, Wu W. Analysis of cf-mtDNA and cf-nDNA fragment size distribution using different isolation methods in BV-2 cell supernatant of starvation-induced autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119147. [PMID: 34600918 DOI: 10.1016/j.bbamcr.2021.119147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 12/14/2022]
Abstract
Fragment size distribution, the important biological properties of cell-free DNA (cfDNA), provides useful information required for diagnostic assay development. However, besides methodological discrepancies, it varies due to the complicated origins and occurrences of in vivo cfDNA. In addition, limited data are available concerning the cfDNA associated with autophagy and distributional difference between cf-mitochondrial DNA (cf-mtDNA) and cf-nuclear DNA (cf-nDNA) fragments. Here we developed an in vitro model of mouse microglial cell (BV-2) with starvation-induced autophagy, in which cfDNA was isolated from the cell supernatant by ultrafiltration (UF) and column-based commercial kit (CC), respectively. Using Agilent 2100 Bioanalyzer, a DNA ladder pattern as the presence of peaks corresponding to mono-, di- and tri-nucleosomes was clearly visualized both in isolation products of UF and CC. However, we also detected shorter fragments than mono-nucleosome by UF. In comparing the UF and CC, we found that the former produced the higher recovery efficiency for spiked-in DNA of shorter fragments than mono-nucleosome in both water and medium, but the latter was superior for spiked-in DNA fragments which were longer than or equal to mono-nucleosome in medium. Combined with these two isolation methods, we have observed that autophagy-associated cf-mtDNA and cf-nDNA were both highly enriched in <mono-nucleosomes fragments more than 71%, and showed no significant differences in the relative percentages for these four fragment sizes. These results have improved our understanding of the fragment size distribution of autophagy-derived cf-mtDNA and cf-nDNA in vitro, and might further develop application of cfDNA as a diagnostic tool.
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Affiliation(s)
- Yuxiang Gong
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qin Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yuping Deng
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Liyan Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xiaoqing Yi
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jiajin Zhu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wenhe Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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Bredno J, Lipson J, Venn O, Aravanis AM, Jamshidi A. Clinical correlates of circulating cell-free DNA tumor fraction. PLoS One 2021; 16:e0256436. [PMID: 34432811 PMCID: PMC8386888 DOI: 10.1371/journal.pone.0256436] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/08/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Oncology applications of cell-free DNA analysis are often limited by the amount of circulating tumor DNA and the fraction of cell-free DNA derived from tumor cells in a blood sample. This circulating tumor fraction varies widely between individuals and cancer types. Clinical factors that influence tumor fraction have not been completely elucidated. METHODS AND FINDINGS Circulating tumor fraction was determined for breast, lung, and colorectal cancer participant samples in the first substudy of the Circulating Cell-free Genome Atlas study (CCGA; NCT02889978; multi-cancer early detection test development) and was related to tumor and patient characteristics. Linear models were created to determine the influence of tumor size combined with mitotic or metabolic activity (as tumor mitotic volume or excessive lesion glycolysis, respectively), histologic type, histologic grade, and lymph node status on tumor fraction. For breast and lung cancer, tumor mitotic volume and excessive lesion glycolysis (primary lesion volume scaled by percentage positive for Ki-67 or PET standardized uptake value minus 1.0, respectively) were the only statistically significant covariates. For colorectal cancer, the surface area of tumors invading beyond the subserosa was the only significant covariate. The models were validated with cases from the second CCGA substudy and show that these clinical correlates of circulating tumor fraction can predict and explain the performance of a multi-cancer early detection test. CONCLUSIONS Prognostic clinical variables, including mitotic or metabolic activity and depth of invasion, were identified as correlates of circulating tumor DNA by linear models that relate clinical covariates to tumor fraction. The identified correlates indicate that faster growing tumors have higher tumor fractions. Early cancer detection from assays that analyze cell-free DNA is determined by circulating tumor fraction. Results support that early detection is particularly sensitive for faster growing, aggressive tumors with high mortality, many of which have no available screening today.
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Affiliation(s)
- Joerg Bredno
- GRAIL, Inc., Menlo Park, California, United States of America
| | - Jafi Lipson
- GRAIL, Inc., Menlo Park, California, United States of America
| | - Oliver Venn
- GRAIL, Inc., Menlo Park, California, United States of America
| | | | - Arash Jamshidi
- GRAIL, Inc., Menlo Park, California, United States of America
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de Miranda FS, Barauna VG, dos Santos L, Costa G, Vassallo PF, Campos LCG. Properties and Application of Cell-Free DNA as a Clinical Biomarker. Int J Mol Sci 2021; 22:9110. [PMID: 34502023 PMCID: PMC8431421 DOI: 10.3390/ijms22179110] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022] Open
Abstract
Biomarkers are valuable tools in clinical practice. In 2001, the National Institutes of Health (NIH) standardized the definition of a biomarker as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. A biomarker has clinical relevance when it presents precision, standardization and reproducibility, suitability to the patient, straightforward interpretation by clinicians, and high sensitivity and/or specificity by the parameter it proposes to identify. Thus, serum biomarkers should have advantages related to the simplicity of the procedures and to the fact that venous blood collection is commonplace in clinical practice. We described the potentiality of cfDNA as a general clinical biomarker and focused on endothelial dysfunction. Circulating cell-free DNA (cfDNA) refers to extracellular DNA present in body fluid that may be derived from both normal and diseased cells. An increasing number of studies demonstrate the potential use of cfDNA as a noninvasive biomarker to determine physiologic and pathologic conditions. However, although still scarce, increasing evidence has been reported regarding using cfDNA in cardiovascular diseases. Here, we have reviewed the history of cfDNA, its source, molecular features, and release mechanism. We also show recent studies that have investigated cfDNA as a possible marker of endothelial damage in clinical settings. In the cardiovascular system, the studies are quite new, and although interesting, stronger evidence is still needed. However, some drawbacks in cfDNA methodologies should be overcome before its recommendation as a biomarker in the clinical setting.
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Affiliation(s)
- Felipe Silva de Miranda
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Valério Garrone Barauna
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Molecular Physiology Laboratory of Exercise Science, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Leandro dos Santos
- Academic Unit of Serra Talhada, Rural Federal University of Pernambuco, Serra Talhada 56909-535, Pernambuco, Brazil;
| | - Gustavo Costa
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
| | - Paula Frizera Vassallo
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil; (G.C.); (P.F.V.)
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Luciene Cristina Gastalho Campos
- Post Graduation Program in Biology and Biotechnology of Microorganisms, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
- Department of Biological Science, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Post Graduation Program in Health Sciences, State University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil;
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45
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Haupts A, Vogel A, Foersch S, Hartmann M, Maderer A, Wachter N, Huber T, Kneist W, Roth W, Lang H, Moehler M, Hartmann N. Comparative analysis of nuclear and mitochondrial DNA from tissue and liquid biopsies of colorectal cancer patients. Sci Rep 2021; 11:16745. [PMID: 34408162 PMCID: PMC8373949 DOI: 10.1038/s41598-021-95006-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/20/2021] [Indexed: 01/05/2023] Open
Abstract
The current standard for molecular profiling of colorectal cancer (CRC) is using resected or biopsied tissue specimens. However, they are limited regarding sampling frequency, representation of tumor heterogeneity, and sampling can expose patients to adverse side effects. The analysis of cell-free DNA (cfDNA) from blood plasma, which is part of a liquid biopsy, is minimally invasive and in principle enables detection of all tumor-specific mutations. Here, we analyzed cfDNA originating from nucleus and mitochondria and investigated their characteristics and mutation status in a cohort of 18 CRC patients and 10 healthy controls using targeted next-generation sequencing (NGS) and digital PCR. Longitudinal analyses of nuclear cfDNA level and size during chemotherapy revealed a decreasing cfDNA content and a shift from short to long fragments, indicating an appropriate therapy response, while shortened cfDNAs and increased cfDNA content corresponded with tumor recurrence. Comparative NGS analysis of nuclear tissue and plasma DNA demonstrated a good patient-level concordance and cfDNA revealed additional variants in three of the cases. Analysis of mitochondrial cfDNA surprisingly revealed a higher plasma copy number in healthy subjects than in CRC patients. These results highlight the potential clinical utility of liquid biopsies in routine diagnostics and surveillance of CRC patients as complementation to tissue biopsies or as an attractive alternative in cases where tissue biopsies are risky or the quantity/quality does not allow testing.
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Affiliation(s)
- Anna Haupts
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
| | - Anne Vogel
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Sebastian Foersch
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Monika Hartmann
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Annett Maderer
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Nicolas Wachter
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Tobias Huber
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Werner Kneist
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.,Department of General and Visceral Surgery, St. Georg Hospital Eisenach gGmbH, Mühlhäuser Straße 94, 99817, Eisenach, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Markus Moehler
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
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46
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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47
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Li M, Xie S, Lu C, Zhu L, Zhu L. Application of Data Science in Circulating Tumor DNA Detection: A Promising Avenue Towards Liquid Biopsy. Front Oncol 2021; 11:692322. [PMID: 34367974 PMCID: PMC8337081 DOI: 10.3389/fonc.2021.692322] [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: 04/08/2021] [Accepted: 07/05/2021] [Indexed: 01/10/2023] Open
Abstract
The circulating tumor DNA (ctDNA), as a promising biomarker of liquid biopsy, has potential clinical relevance on the molecular diagnosis and monitoring of cancer. However, the trace concentration level of ctDNA in the peripheral blood restricts its extensive clinical application. Recently, high-throughput-based methodologies have been leveraged to improve the sensitivity and specificity of ctDNA detection, showing a promising avenue towards liquid biopsy. This review briefly summarizes the high-throughput data features concerned by current ctDNA detection strategies and the technical obstacles, potential solutions, and clinical relevance of current ctDNA profiling technologies. We also highlight future directions improving the limit of detection of ctDNA for better clinical application. This review may serve as a reference for the crosslinks between data science and ctDNA-based liquid biopsy, benefiting clinical translation in advanced cancer diagnosis.
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Affiliation(s)
| | | | | | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
| | - Lvyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
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48
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Al Sulaiman D, Gatehouse A, Ivanov AP, Edel JB, Ladame S. Length-Dependent, Single-Molecule Analysis of Short Double-Stranded DNA Fragments through Hydrogel-Filled Nanopores: A Potential Tool for Size Profiling Cell-Free DNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26673-26681. [PMID: 34085806 DOI: 10.1021/acsami.1c01145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fast sampling followed by sequence-independent sensing and length-dependent detection of short double-stranded DNA fragments, the size of those found in blood and other bodily fluids, is achieved using engineered molecular sensors, dubbed hydrogel-filled nanopores (HFNs). Fragments as short as 100 base pairs were blindly sampled and concentrated at the tip of an HFN before reversing the applied potential to detect and distinguish individual molecules based on fragment length as they translocate out of the nanopore. A remarkable 16-fold increase in the signal-to-noise ratio was observed in the eject configuration compared to the load configuration, enabling the resolution of fragments with a size difference of 50 nucleotides in length. This fast and versatile technology offers great tunability for both sampling and detection. While increasing sampling time leads to an increase in the local DNA concentration at the tip prior to detection, a linear correlation between the peak current and DNA fragment size enables good resolution of fragments up to 250 bp long.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alfie Gatehouse
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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49
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Wang X, Yamamoto Y, Imanishi M, Zhang X, Sato M, Sugaya A, Hirose M, Endo S, Natori Y, Moriwaki T, Yamato K, Hyodo I. Enhanced G1 arrest and apoptosis via MDM4/MDM2 double knockdown and MEK inhibition in wild-type TP53 colon and gastric cancer cells with aberrant KRAS signaling. Oncol Lett 2021; 22:558. [PMID: 34084225 PMCID: PMC8161467 DOI: 10.3892/ol.2021.12819] [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: 12/20/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
Murine double minute homolog 2 (MDM2) is an oncoprotein that induces p53 degradation via ubiquitin-ligase activity. MDM4 cooperates with MDM2-mediated p53 degradation, directly inhibiting p53 transcription by binding to its transactivation domain. Our previous study reported that the simultaneous inhibition of MDM2 and MDM4 using nutlin-3 (an inhibitor of the MDM2-p53 interaction) and chimeric small interfering RNA with DNA-substituted seed arms (named chiMDM2 and chiMDM4) more potently activated p53 than the MDM2 or MDM4 inhibitor alone and synergistically augmented antitumor effects in various types of cancer cells with the wild-type (wt) TP53. Recently, the synergism of MDM2 and mitogen-activated protein kinase kinase (MEK) inhibitors has been demonstrated in wt TP53 colorectal and non-small cell lung cancer cells harboring mutant-type (mt) KRAS. The current study examined whether chiMDM4 augmented the synergistic antitumor effects of MDM2 and MEK inhibition using chiMDM2 or nutlin-3 and trametinib, respectively. ChiMDM2 and trametinib used in combination demonstrated a synergistic antitumor activity in HCT116 and LoVo colon cancer cells, and SNU-1 gastric cancer cells harboring wt TP53 and mt KRAS. Furthermore, chiMDM4 synergistically enhanced this combinational effect. Similar results were observed when nutlin-3 was used instead of chiMDM2. MDM4/MDM2 double knockdown combined with trametinib treatment enhanced G1 arrest and apoptosis induction. This was associated with the accumulation of p53, suppression of phosphorylated-extracellular signal-regulated kinase 2, inhibition of retinoblastoma phosphorylation, suppression of E2F1-activated proteins, and potent activation of pro-apoptotic proteins, such as Fas and p53 upregulated modulator of apoptosis. The results inidcated that the triple inhibition of MDM4, MDM2 and MEK exerted a potent antitumor effect in wt TP53 colon and gastric cancer cells with mt KRAS. Simultaneous activation of p53 and inhibition of aberrant KRAS signaling may be a rational treatment strategy for gastrointestinal tumors.
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Affiliation(s)
- Xiaoxuan Wang
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshiyuki Yamamoto
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Mamiko Imanishi
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Xiaochen Zhang
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Masashi Sato
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Akinori Sugaya
- Division of Gastroenterology, Ibaraki Prefectural Central Hospital, Kasama, Ibaraki 309-1793, Japan
| | - Mitsuaki Hirose
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.,Department of Gastroenterology, Tsuchiura Clinical Education and Training Center, University of Tsukuba Hospital, Tsuchiura, Ibaraki 300-8585, Japan
| | - Shinji Endo
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.,Department of Gastroenterology and Hepatology, Shinmatsudo Central General Hospital, Matsudo, Chiba 270-0034, Japan
| | | | - Toshikazu Moriwaki
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenji Yamato
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Ichinosuke Hyodo
- Department of Gastroenterology, Institute of Clinical Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.,Department of Gastrointestinal Medical Oncology, NHO Shikoku Cancer Center, Matsuyama, Ehime 791-0280, Japan
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50
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Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep 2021; 11:9460. [PMID: 33947882 PMCID: PMC8096822 DOI: 10.1038/s41598-021-88866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advances in basic research have unveiled several strategies for improving the sensitivity and specificity of cell-free DNA (cfDNA) based assays, which is a prerequisite for broadening its clinical use. Included among these strategies is leveraging knowledge of both the biogenesis and physico-chemical properties of cfDNA towards the identification of better disease-defining features and optimization of methods. While good progress has been made on this front, much of cfDNA biology remains uncharted. Here, we correlated serial measurements of cfDNA size, concentration and nucleosome histone modifications with various cellular parameters, including cell growth rate, viability, apoptosis, necrosis, and cell cycle phase in three different cell lines. Collectively, the picture emerged that temporal changes in cfDNA levels are rather irregular and not the result of constitutive release from live cells. Instead, changes in cfDNA levels correlated with intermittent cell death events, wherein apoptosis contributed more to cfDNA release in non-cancer cells and necrosis more in cancer cells. Interestingly, the presence of a ~ 3 kbp cfDNA population, which is often deemed to originate from accidental cell lysis or active release, was found to originate from necrosis. High-resolution analysis of this cfDNA population revealed an underlying DNA laddering pattern consisting of several oligo-nucleosomes, identical to those generated by apoptosis. This suggests that necrosis may contribute significantly to the pool of mono-nucleosomal cfDNA fragments that are generally interrogated for cancer mutational profiling. Furthermore, since active steps are often taken to exclude longer oligo-nucleosomes from clinical biospecimens and subsequent assays this raises the question of whether important pathological information is lost.
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Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | | | - Marielle Herzog
- Belgian Volition SRL, 22 Rue Phocas Lejeune, Parc Scientifique Crealys, 5032, Isnes, Belgium
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany.
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