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Sirajee AS, Kabiraj D, De S. Cell-free nucleic acid fragmentomics: A non-invasive window into cellular epigenomes. Transl Oncol 2024; 49:102085. [PMID: 39178576 DOI: 10.1016/j.tranon.2024.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/01/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024] Open
Abstract
Clinical genomic profiling of cell-free nucleic acids (e.g. cell-free DNA or cfDNA) from blood and other body fluids has ushered in a new era in non-invasive diagnostics and treatment monitoring strategies for health conditions and diseases such as cancer. Genomic analysis of cfDNAs not only identifies disease-associated mutations, but emerging findings suggest that structural, topological, and fragmentation characteristics of cfDNAs reveal crucial information about the location of source tissues, their epigenomes, and other clinically relevant characteristics, leading to the burgeoning field of fragmentomics. The field has seen rapid developments in computational and genomics methodologies for conducting large-scale studies on health conditions and diseases - that have led to fundamental, mechanistic discoveries as well as translational applications. Several recent studies have shown the clinical utilities of the cfDNA fragmentomics technique which has the potential to be effective for early disease diagnosis, determining treatment outcomes, and risk-free continuous patient monitoring in a non-invasive manner. In this article, we outline recent developments in computational genomic methodologies and analysis strategies, as well as the emerging insights from cfNA fragmentomics. We conclude by highlighting the current challenges and opportunities.
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Affiliation(s)
- Ahmad Salman Sirajee
- Department of Pathology and Laboratory Medicine, Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Debajyoti Kabiraj
- Department of Pathology and Laboratory Medicine, Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Subhajyoti De
- Department of Pathology and Laboratory Medicine, Rutgers Cancer Institute, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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2
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McGill MR. The Role of Mechanistic Biomarkers in Understanding Acetaminophen Hepatotoxicity in Humans. Drug Metab Dispos 2024; 52:729-739. [PMID: 37918967 PMCID: PMC11257692 DOI: 10.1124/dmd.123.001281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
Our understanding of the fundamental molecular mechanisms of acetaminophen (APAP) hepatotoxicity began in 1973 to 1974, when investigators at the US National Institutes of Health published seminal studies demonstrating conversion of APAP to a reactive metabolite that depletes glutathione and binds to proteins in the liver in mice after overdose. Since then, additional groundbreaking experiments have demonstrated critical roles for mitochondrial damage, oxidative stress, nuclear DNA fragmentation, and necrotic cell death as well. Over the years, some investigators have also attempted to translate these mechanisms to humans using human specimens from APAP overdose patients. This review presents those studies and summarizes what we have learned about APAP hepatotoxicity in humans so far. Overall, the mechanisms of APAP hepatotoxicity in humans strongly resemble those discovered in experimental mouse and cultured hepatocyte models, and emerging biomarkers also suggest similarities in liver repair. The data not only validate the first mechanistic studies of APAP-induced liver injury performed 50 years ago but also demonstrate the human relevance of numerous studies conducted since then. SIGNIFICANCE STATEMENT: Human studies using novel translational, mechanistic biomarkers have confirmed that the fundamental mechanisms of acetaminophen (APAP) hepatotoxicity discovered in rodent models since 1973 are the same in humans. Importantly, these findings have guided the development and understanding of treatments such as N-acetyl-l-cysteine and 4-methylpyrazole over the years. Additional research may improve not only our understanding of APAP overdose pathophysiology in humans but also our ability to predict and treat serious liver injury in patients.
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Affiliation(s)
- Mitchell R McGill
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health; Department of Pharmacology and Toxicology, College of Medicine; and Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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3
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Xue Y, Zhao G, Song L, Qiao L, Huang C, Wang K, Wang T. The signature of cancer methylation markers in maternal plasma: Factors influencing the development and application of cancer liquid biopsy assay. Gene 2024; 906:148261. [PMID: 38342253 DOI: 10.1016/j.gene.2024.148261] [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: 10/16/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND DNA methylation is highly correlated with cancer and embryo development, and plasma-based methylation markers have been widely used for cancer early detection. However, whether the commonly used cancer methylation markers cause "false positives" in the plasma of pregnant women has not been comprehensively evaluated. METHODS We conducted a case-control study from February 2021 to March 2023, which included 138 pregnant women and 44 control women. Plasma cell-free DNA (cfDNA) was isolated and bisulfite-converted, and then the methylation levels of eight methylated markers related to gastrointestinal cancer (SEPT9, SDC2, C9orf50, KCNQ5, CLIP4, TFPI2, ELMO1 and ZNF582) and three markers related to lung cancer (SHOX2, RASSF1A and PTGER4) were analyzed. RESULTS When comparing the plasma of pregnant women to that of control women, SEPT9, CLIP4, ZNF582, SHOX2, RASSF1A and PTGER showed significantly higher levels of methylation (p < 0.05). These positive signals originate from the placenta/fetus rather than the mother. We found no discernible difference in DNA methylation levels between fetal cfDNA fractions of < 10 % and ≥ 10 % in pregnant women (p > 0.05), while CLIP4 and PTGER4 showed high methylation levels in the assisted fertilization group compared to the natural fertilization group (p < 0.05). CONCLUSION Our study shows that cancer and fetus/placenta exhibit similar DNA methylation patterns, and some gastrointestinal cancer and lung cancer-related methylation markers also show positives in maternal plasma. This is an important consideration in the design and application of plasma-based cancer liquid biopsy assays.
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Affiliation(s)
- Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Guodong Zhao
- ZJUT Yinhu Research Institute of Innovation and Entrepreneurship Fuyang District, Hangzhou, Zhejiang 311400, China; Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China.
| | - Lishuang Song
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Chao Huang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China
| | - Kai Wang
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215000, China.
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4
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Shi T, Zhao J, Long K, Gao M, Chen F, Chen X, Zhang Y, Huang B, Shao D, Yang C, Wang L, Zhang M, Leong KW, Chen L, He K. Cationic mesoporous silica nanoparticles alleviate osteoarthritis by targeting multiple inflammatory mediators. Biomaterials 2023; 303:122366. [PMID: 37948854 DOI: 10.1016/j.biomaterials.2023.122366] [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: 03/30/2023] [Revised: 10/08/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023]
Abstract
Osteoarthritis (OA) is a common and complex inflammatory disorder that is frequently compounded by cartilage degradation, synovial inflammation, and osteophyte formation. Damaged chondrocytes release multiple danger mediators that exacerbate synovial inflammation and accelerate the progression to OA. Conventional treatments targeting only a single mediator of OA have failed to achieve a strong therapeutic effect. Addressing the crucial role of multiple danger mediators in OA progression, we prepared polyethylenimine (PEI)-functionalized diselenide-bridged mesoporous silica nanoparticles (MSN-PEI) with cell-free DNA (cfDNA)-binding and anti-oxidative properties. In models of surgery-induced and collagenase-induced arthritis, we showed that these cationic nanoparticles attenuated cartilage degradation and provided strong chondroprotection against joint damage. Mechanistically, multiple target blockades alleviated oxidative stress and dampened cfDNA-induced inflammation by suppressing the M1 polarization of macrophages. This study suggests a beneficial direction for targeting multiple danger mediators in the treatment of intractable arthritis.
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Affiliation(s)
- Tongfei Shi
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China; School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong, 511442, China; National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Jingtong Zhao
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Kongrong Long
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China; Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Mohan Gao
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Fangman Chen
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Xuenian Chen
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Yue Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Baoding Huang
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510665, China
| | - Dan Shao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong, 511442, China; National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, Guangdong, 510006, China; School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
| | - Chao Yang
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510665, China
| | - Liang Wang
- Department of Orthopedics, Academy of Orthopedics-Guangdong Province, Orthopedic Hospital of Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510665, China
| | - Ming Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Li Chen
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China; School of Nursing, Jilin University, Changchun, 130021, China.
| | - Kan He
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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5
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Wong D, Luo P, Znassi N, Arteaga DP, Gray D, Danesh A, Han M, Zhao EY, Pedersen S, Prokopec S, Sundaravadanam Y, Torti D, Marsh K, Keshavarzi S, Xu W, Krema H, Joshua AM, Butler MO, Pugh TJ. Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:267-280. [PMID: 36860651 PMCID: PMC9973415 DOI: 10.1158/2767-9764.crc-22-0456] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Uveal melanomas are rare tumors arising from melanocytes that reside in the eye. Despite surgical or radiation treatment, approximately 50% of patients with uveal melanoma will progress to metastatic disease, most often to the liver. Cell-free DNA (cfDNA) sequencing is a promising technology due to the minimally invasive sample collection and ability to infer multiple aspects of tumor response. We analyzed 46 serial cfDNA samples from 11 patients with uveal melanoma over a 1-year period following enucleation or brachytherapy (n = ∼4/patient) using targeted panel, shallow whole genome, and cell-free methylated DNA immunoprecipitation sequencing. We found detection of relapse was highly variable using independent analyses (P = 0.06-0.46), whereas a logistic regression model integrating all cfDNA profiles significantly improved relapse detection (P = 0.02), with greatest power derived from fragmentomic profiles. This work provides support for the use of integrated analyses to improve the sensitivity of circulating tumor DNA detection using multi-modal cfDNA sequencing. Significance Here, we demonstrate integrated, longitudinal cfDNA sequencing using multi-omic approaches is more effective than unimodal analysis. This approach supports the use of frequent blood testing using comprehensive genomic, fragmentomic, and epigenomic techniques.
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Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Nadia Znassi
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Diana P. Arteaga
- Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Diana Gray
- Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ming Han
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Eric Y. Zhao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Stephenie Prokopec
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | | | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sareh Keshavarzi
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Wei Xu
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Hatem Krema
- Department of Ocular Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Canada
| | - Anthony M. Joshua
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Oncology, Kinghorn Cancer Centre, St. Vincent's Hospital and Garvan Institute of Medical Research, Sydney, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Marcus O. Butler
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, Division of Medical Oncology, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Trevor J. Pugh, Princess Margaret Cancer Centre, University Health Network, MaRS Centre, 101 College Street, Princess Margaret Cancer Research Tower, Room 9-305, Toronto, Ontario M5G 1L7, Canada. Phone: 416-581-7689; E-mail: ; and Marcus Butler, Princess Margaret Cancer Centre, 610 University Avenue, OPG 7-815, Toronto, Ontario M5G 2M9. Phone: 416-946-4501 x5485;
| | - Trevor J. Pugh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada and Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Trevor J. Pugh, Princess Margaret Cancer Centre, University Health Network, MaRS Centre, 101 College Street, Princess Margaret Cancer Research Tower, Room 9-305, Toronto, Ontario M5G 1L7, Canada. Phone: 416-581-7689; E-mail: ; and Marcus Butler, Princess Margaret Cancer Centre, 610 University Avenue, OPG 7-815, Toronto, Ontario M5G 2M9. Phone: 416-946-4501 x5485;
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6
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Rabas N, Palmer S, Mitchell L, Ismail S, Gohlke A, Riley JS, Tait SW, Gammage P, Soares LL, Macpherson IR, Norman JC. PINK1 drives production of mtDNA-containing extracellular vesicles to promote invasiveness. J Cell Biol 2021; 220:e202006049. [PMID: 34623384 PMCID: PMC8641410 DOI: 10.1083/jcb.202006049] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/29/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
The cystine-glutamate antiporter, xCT, supports a glutathione synthesis program enabling cancer cells to cope with metabolically stressful microenvironments. Up-regulated xCT, in combination with glutaminolysis, leads to increased extracellular glutamate, which promotes invasive behavior by activating metabotropic glutamate receptor 3 (mGluR3). Here we show that activation of mGluR3 in breast cancer cells activates Rab27-dependent release of extracellular vesicles (EVs), which can transfer invasive characteristics to "recipient" tumor cells. These EVs contain mitochondrial DNA (mtDNA), which is packaged via a PINK1-dependent mechanism. We highlight mtDNA as a key EV cargo necessary and sufficient for intercellular transfer of invasive behavior by activating Toll-like receptor 9 in recipient cells, and this involves increased endosomal trafficking of pro-invasive receptors. We propose that an EV-mediated mechanism, through which altered cellular metabolism in one cell influences endosomal trafficking in other cells, is key to generation and dissemination of pro-invasive microenvironments during mammary carcinoma progression.
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Affiliation(s)
| | - Sarah Palmer
- Beatson Institute for Cancer Research, Glasgow, UK
| | | | | | | | - Joel S. Riley
- Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Stephen W.G. Tait
- Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Payam Gammage
- Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Leandro Lemgruber Soares
- Glasgow Imaging Facility, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Iain R. Macpherson
- Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jim C. Norman
- Beatson Institute for Cancer Research, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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7
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Underhill HR. Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology? Mol Diagn Ther 2021; 25:389-408. [PMID: 34018157 PMCID: PMC8249304 DOI: 10.1007/s40291-021-00534-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA (ccfDNA) has emerged as a promising diagnostic tool in oncology. Identification of tumour-derived ccfDNA (i.e. circulating tumour DNA [ctDNA]) provides non-invasive access to a malignancy’s molecular landscape to diagnose, inform therapeutic strategies, and monitor treatment efficacy. Current applications of ccfDNA to detect somatic mutations, however, have been largely constrained to tumour-informed searches and identification of common mutations because of the interaction between ctDNA signal and next-generation sequencing (NGS) noise. Specifically, the low allele frequency of ctDNA associated with non-metastatic and early-stage lesions may be indistinguishable from artifacts that accrue during sample preparation and NGS. Thus, using ccfDNA to achieve non-invasive and personalized molecular profiling to optimize individual patient care is a highly sought goal that remains limited in clinical practice. There is growing evidence, however, that further advances in the field of ccfDNA diagnostics may be achieved by improving detection of somatic mutations through leveraging the inherently shorter fragment lengths of ctDNA compared to non-neoplastic ccfDNA. Here, the origins and rationale for seeking to improve the mutation-based detection of ctDNA by using ccfDNA size profiling are reviewed. Subsequently, in vitro and in silico methods to enrich for a target ccfDNA fragment length are detailed to identify current practices and provide perspective into the potential of using ccfDNA size profiling to impact clinical applications in oncology.
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Affiliation(s)
- Hunter R Underhill
- Division of Medical Genetics, Department of Pediatrics, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA. .,Department of Radiology, University of Utah, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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8
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Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Nat Commun 2021; 12:2717. [PMID: 33976150 PMCID: PMC8113516 DOI: 10.1038/s41467-021-22901-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising noninvasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate the relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not require CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from cell types composing less than 1% of the total mixture. When used in two clinically-relevant situations, CelFiE correctly estimates a large placenta component in pregnant women, and an elevated skeletal muscle component in amyotrophic lateral sclerosis (ALS) patients, consistent with the occurrence of muscle wasting typical in these patients. Together, these results show how CelFiE could be a useful tool for biomarker discovery and monitoring the progression of degenerative disease. Tissue damage and turnover lead to the release of DNA in the blood and can be used to monitor changes in tissue state. Here, the authors developed a tool to accurately estimate the proportion of cell types contributing to cell-free DNA in the blood, with an application to pregnant women and ALS patients.
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9
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Hammad R, Eldosoky MAER, Fouad SH, Elgendy A, Tawfeik AM, Alboraie M, Abdelmaksoud MF. Circulating cell-free DNA, peripheral lymphocyte subsets alterations and neutrophil lymphocyte ratio in assessment of COVID-19 severity. Innate Immun 2021; 27:240-250. [PMID: 33646058 PMCID: PMC8054149 DOI: 10.1177/1753425921995577] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cell destruction results in plasma accumulation of cell-free DNA (cfDNA). Dynamic changes in circulating lymphocytes are features of COVID-19. We aimed to investigate if cfDNA level can serve in stratification of COVID-19 patients, and if cfDNA level is associated with alterations in lymphocyte subsets and neutrophil-to-lymphocyte ratio (NLR). This cross-sectional comparative study enrolled 64 SARS-CoV-2-positive patients. Patients were subdivided to severe and non-severe groups. Plasma cfDNA concentration was determined by real-time quantitative PCR. Lymphocyte subsets were assessed by flow cytometry. There was significant increase in cfDNA among severe cases when compared with non-severe cases. cfDNA showed positive correlation with NLR and inverse correlation with T cell percentage. cfDNA positively correlated with ferritin and C-reactive protein. The output data of performed ROC curves to differentiate severe from non-severe cases revealed that cfDNA at cut-off ≥17.31 ng/µl and AUC of 0.96 yielded (93%) sensitivity and (73%) specificity. In summary, excessive release of cfDNA can serve as sensitive COVID-19 severity predictor. There is an association between cfDNA up-regulation and NLR up-regulation and T cell percentage down-regulation. cfDNA level can be used in stratification and personalized monitoring strategies in COVID-19 patients.
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Affiliation(s)
- Reham Hammad
- Clinical Pathology Department, Faculty of Medicine (for Girls), Al-Azhar University, Egypt
| | | | - Shaimaa Hani Fouad
- Internal Medicine Allergy and Clinical Immunology, Ain-Shams University, Egypt
| | - Abdelaleem Elgendy
- Clinical Pathology Department, Faculty of Medicine (for Boys), Al-Azhar University, Egypt
| | - Amany M Tawfeik
- Microbiology and Immunology Department, Faculty of Medicine (for Girls), Al-Azhar University, Egypt
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10
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Hyun J, Jung Y. DNA Methylation in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2020; 21:ijms21218138. [PMID: 33143364 PMCID: PMC7662478 DOI: 10.3390/ijms21218138] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a widespread hepatic disorder in the United States and other Westernized countries. Nonalcoholic steatohepatitis (NASH), an advanced stage of NAFLD, can progress to end-stage liver disease, including cirrhosis and liver cancer. Poor understanding of mechanisms underlying NAFLD progression from simple steatosis to NASH has limited the development of effective therapies and biomarkers. An accumulating body of studies has suggested the importance of DNA methylation, which plays pivotal roles in NAFLD pathogenesis. DNA methylation signatures that can affect gene expression are influenced by environmental and lifestyle experiences such as diet, obesity, and physical activity and are reversible. Hence, DNA methylation signatures and modifiers in NAFLD may provide the basis for developing biomarkers indicating the onset and progression of NAFLD and therapeutics for NAFLD. Herein, we review an update on the recent findings in DNA methylation signatures and their roles in the pathogenesis of NAFLD and broaden people’s perspectives on potential DNA methylation-related treatments and biomarkers for NAFLD.
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Affiliation(s)
- Jeongeun Hyun
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea;
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
- Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Korea
- Cell and Matter Institute, Dankook University, Cheonan 31116, Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Pusan 46241, Korea
- Department of Biological Sciences, Pusan National University, Pusan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2262
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11
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Thakral D, Das N, Basnal A, Gupta R. Cell-free DNA for genomic profiling and minimal residual disease monitoring in Myeloma- are we there yet? AMERICAN JOURNAL OF BLOOD RESEARCH 2020; 10:26-45. [PMID: 32685257 PMCID: PMC7364270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Multiple myeloma (MM), a plasma cell neoplasm, afflicts elder individuals accounting for 10% of hematologic malignancies. The MM plasma cells largely reside within the bone marrow niche and are accessible through an invasive bone marrow biopsy, which is challenging during serial monitoring of patients. In this setting, cell free DNA (cfDNA) may have a role to ascertain the molecular aberrations at diagnosis and in assessment of residual disease during therapy. The aim of this review was to explore the utility and current status of cfDNA in MM. METHOD PubMed was searched with terms including cell-free DNA, circulating-tumor DNA, Multiple Myeloma, diagnosis, genomic profiling, Minimal Residual Disease individually or in combination to shortlist the relevant studies. RESULT cfDNA serves as a non-invasive source of tumor-specific molecular biomarker, ctDNA that has immense potential in facilitating management of cancer patients. The mutation detection platforms for ctDNA include hybrid capture and ultra-deep sequencing. Hybrid capture allows full length gene sequencing for mutation and CNV detection. The disease progression can be monitored by profiling prognostic somatic copy number alterations by ultra-low pass whole genome sequencing of ctDNA cost-effectively. Evolution of both the laboratory protocols and bioinformatics tools may further improve the sensitivity of ctDNA detection for better disease management. Only a limited number of studies were available in MM exploring the potential utility of cfDNA. CONCLUSION In this review, we discuss the nuances and challenges associated with molecular evaluation of cfDNA and its potential role in diagnosis and monitoring of treatment response in MM.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Nupur Das
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Atul Basnal
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
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