1
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Stetson D, Labrousse P, Russell H, Shera D, Abbosh C, Dougherty B, Barrett JC, Hodgson D, Hadfield J. Next-Generation Molecular Residual Disease Assays: Do We Have the Tools to Evaluate Them Properly? J Clin Oncol 2024:JCO2302301. [PMID: 38754043 DOI: 10.1200/jco.23.02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/27/2024] [Accepted: 03/05/2024] [Indexed: 05/18/2024] Open
Affiliation(s)
- Dan Stetson
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Paul Labrousse
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Hugh Russell
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - David Shera
- Oncology Biometrics, AstraZeneca, Gaithersburg, MD
| | - Chris Abbosh
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Darren Hodgson
- Cancer Biomarker Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - James Hadfield
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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2
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [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: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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3
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Caggiano C, Morselli M, Qian X, Celona B, Thompson M, Wani S, Tosevska A, Taraszka K, Heuer G, Ngo S, Steyn F, Nestor P, Wallace L, McCombe P, Heggie S, Thorpe K, McElligott C, English G, Henders A, Henderson R, Lomen-Hoerth C, Wray N, McRae A, Pellegrini M, Garton F, Zaitlen N. Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.08.24305503. [PMID: 38645132 PMCID: PMC11030489 DOI: 10.1101/2024.04.08.24305503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.
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Affiliation(s)
- C Caggiano
- Department of Neurology, UCLA, Los Angeles, California
- Institute of Genomic Health, Icahn School of Medicine at Mt Sinai, New York, New York
| | - M Morselli
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - X Qian
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - B Celona
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - M Thompson
- Department of Neurology, UCLA, Los Angeles, California
- Systems and Synthetic Biology, Centre for Genomic Regulation, Barcelona, Spain
| | - S Wani
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - A Tosevska
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Vienna, Austria
| | - K Taraszka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - G Heuer
- Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, California
| | - S Ngo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - F Steyn
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - P Nestor
- Queensland Brain Institute, Unviversity of Queensland, Brisbane, Australia
- Mater Public Hospital, Brisbane, Australia
| | - L Wallace
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - P McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - S Heggie
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - K Thorpe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | | | - G English
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A Henders
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - R Henderson
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - C Lomen-Hoerth
- Department of Neurology, UCSF, San Francisco, California
| | - N Wray
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A McRae
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - M Pellegrini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - F Garton
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - N Zaitlen
- Department of Neurology, UCLA, Los Angeles, California
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California
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4
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Penny L, Main SC, De Michino SD, Bratman SV. Chromatin- and nucleosome-associated features in liquid biopsy: implications for cancer biomarker discovery. Biochem Cell Biol 2024. [PMID: 38478957 DOI: 10.1139/bcb-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
Cell-free DNA (cfDNA) from the bloodstream has been studied for cancer biomarker discovery, and chromatin-derived epigenetic features have come into the spotlight for their potential to expand clinical applications. Methylation, fragmentation, and nucleosome positioning patterns of cfDNA have previously been shown to reveal epigenomic and inferred transcriptomic information. More recently, histone modifications have emerged as a tool to further identify tumor-specific chromatin variants in plasma. A number of sequencing methods have been developed to analyze these epigenetic markers, offering new insights into tumor biology. Features within cfDNA allow for cancer detection, subtype and tissue of origin classification, and inference of gene expression. These methods provide a window into the complexity of cancer and the dynamic nature of its progression. In this review, we highlight the array of epigenetic features in cfDNA that can be extracted from chromatin- and nucleosome-associated organization and outline potential use cases in cancer management.
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Affiliation(s)
- Lucas Penny
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Sasha C Main
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Steven D De Michino
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON M5T 1P5, Canada
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5
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Wang H, Wang Y, Zhang D, Li P. Circulating nucleosomes as potential biomarkers for cancer diagnosis and treatment monitoring. Int J Biol Macromol 2024; 262:130005. [PMID: 38331061 DOI: 10.1016/j.ijbiomac.2024.130005] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes play a crucial role in regulating gene expression through their composition and post-translational modifications. When cells die, intracellular endonucleases are activated and cleave chromatin into oligo- and mono-nucleosomes, which are then released into the body fluids. Studies have shown that the levels of nucleosomes are increased in serum and plasma in various cancer types, suggesting that analysis of circulating nucleosomes can provide an initial assessment of carcinogenesis. However, it should be noted that elevated serum nucleosome levels may not accurately diagnose certain tumor types, as increased cell death may occur in different pathological conditions. Nevertheless, detection of circulating nucleosomes and their histone modifications, along with specific tumor markers, can help diagnose certain types of cancer. Furthermore, monitoring changes in circulating nucleosome levels during chemotherapy or radiotherapy in patients with malignancies can provide valuable insights into clinical outcomes and therapeutic efficacy. The utilization of circulating nucleosomes as biomarkers is an exciting and emerging area of research, with the potential for early detection of various diseases and monitoring of treatment response. Integrating nucleosome-based biomarkers with existing ones may improve the specificity and sensitivity of current assays, offering the possibility of personalized precision medical treatment for patients.
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Affiliation(s)
- Huawei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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6
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Sridhar S, Crnjac A, Patel S, An Z, Bekdemir A, Shea D, Wang ST, Rodriguez-Aponte S, Naranjo CA, Rhoades J, Kirkpatrick JD, Fleming HE, Amini AP, Golub TR, Love JC, Bhatia SN, Adalsteinsson VA. Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies. Science 2024; 383:eadf2341. [PMID: 38236959 DOI: 10.1126/science.adf2341] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity of analytes such as cell-free DNA (cfDNA) in blood. Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. We sought to transiently augment the level of circulating tumor DNA (ctDNA) in a blood draw by attenuating its clearance in vivo. We report two intravenous priming agents given 1 to 2 hours before a blood draw to recover more ctDNA. Our priming agents consist of nanoparticles that act on the cells responsible for cfDNA clearance and DNA-binding antibodies that protect cfDNA. In tumor-bearing mice, they greatly increase the recovery of ctDNA and improve the sensitivity for detecting small tumors.
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Affiliation(s)
- Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Blewett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Andjela Crnjac
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sahil Patel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, MA 02124, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmet Bekdemir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Ting Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergio Rodriguez-Aponte
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Amini
- Microsoft Research, Cambridge, MA 02142, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Wyss Institute at Harvard University, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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7
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Maansson CT, Thomsen LS, Meldgaard P, Nielsen AL, Sorensen BS. Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies. Int J Mol Sci 2024; 25:1243. [PMID: 38279243 PMCID: PMC10815977 DOI: 10.3390/ijms25021243] [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: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene transcription. In this study, we conducted cfDNA fragmentomics evaluations using plasma from lung cancer patients (n = 12) and healthy individuals (n = 7). A personal gene expression profile was established from plasma using H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq). The genes with the highest expression displayed an enrichment of short cfDNA fragments (median = 19.99%, IQR: 16.94-27.13%, p < 0.0001) compared to the genes with low expression. Furthermore, distinct GC-rich FEMs were enriched after cfChIP. Combining the frequency of short cfDNA fragments with the presence of distinct FEMs resulted in an even further enrichment of the most expressed genes (median = 37.85%, IQR: 30.10-39.49%, p < 0.0001). An in vitro size selection of <150 bp cfDNA could isolate cfDNA representing active genes and the size-selection enrichment correlated with the cfChIP-seq enrichment (Spearman r range: 0.499-0.882, p < 0.0001). This study expands the knowledge regarding cfDNA fragmentomics and sheds new light on how gene activity is associated with both cfDNA fragment lengths and distinct FEMs.
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Affiliation(s)
- Christoffer Trier Maansson
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark;
| | - Louise Skov Thomsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark;
| | | | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
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8
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Sacdalan DB, Ul Haq S, Lok BH. Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications. Curr Oncol 2024; 31:482-500. [PMID: 38248118 PMCID: PMC10814449 DOI: 10.3390/curroncol31010033] [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: 11/24/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
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Affiliation(s)
- Danielle Benedict Sacdalan
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
| | - Sami Ul Haq
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Schulich School of Medicine & Dentistry, Western University, 1151 Richmond St, London, ON N6A 5C1, Canada
| | - Benjamin H. Lok
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, 101 College Street, Room 15-701, Toronto, ON M5G 1L7, Canada
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9
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Socol Y, Richardson A, Garali-Zineddine I, Grison S, Vares G, Klokov D. Artificial intelligence in biology and medicine, and radioprotection research: perspectives from Jerusalem. Front Artif Intell 2024; 6:1291136. [PMID: 38282906 PMCID: PMC10812117 DOI: 10.3389/frai.2023.1291136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024] Open
Abstract
While AI is widely used in biomedical research and medical practice, its use is constrained to few specific practical areas, e.g., radiomics. Participants of the workshop on "Artificial Intelligence in Biology and Medicine" (Jerusalem, Feb 14-15, 2023), both researchers and practitioners, aimed to build a holistic picture by exploring AI advancements, challenges and perspectives, as well as to suggest new fields for AI applications. Presentations showcased the potential of large language models (LLMs) in generating molecular structures, predicting protein-ligand interactions, and promoting democratization of AI development. Ethical concerns in medical decision making were also addressed. In biological applications, AI integration of multi-omics and clinical data elucidated the health relevant effects of low doses of ionizing radiation. Bayesian latent modeling identified statistical associations between unobserved variables. Medical applications highlighted liquid biopsy methods for non-invasive diagnostics, routine laboratory tests to identify overlooked illnesses, and AI's role in oral and maxillofacial imaging. Explainable AI and diverse image processing tools improved diagnostics, while text classification detected anorexic behavior in blog posts. The workshop fostered knowledge sharing, discussions, and emphasized the need for further AI development in radioprotection research in support of emerging public health issues. The organizers plan to continue the initiative as an annual event, promoting collaboration and addressing issues and perspectives in AI applications with a focus on low-dose radioprotection research. Researchers involved in radioprotection research and experts in relevant public policy domains are invited to explore the utility of AI in low-dose radiation research at the next workshop.
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Affiliation(s)
- Yehoshua Socol
- Department of Electrical and Electronics Engineering, Jerusalem College of Technology, Jerusalem, Israel
| | - Ariella Richardson
- Department of Data Mining, Jerusalem College of Technology, Jerusalem, Israel
| | - Imene Garali-Zineddine
- Health and Environnent Division, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Stephane Grison
- Health and Environnent Division, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Guillaume Vares
- Health and Environnent Division, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Dmitry Klokov
- Health and Environnent Division, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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10
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Jang MK, Markowitz TE, Andargie TE, Apalara Z, Kuhn S, Agbor-Enoh S. Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation. Life Sci Alliance 2023; 6:e202302003. [PMID: 37730434 PMCID: PMC10511822 DOI: 10.26508/lsa.202302003] [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: 02/20/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as a noninvasive proxy to define molecular gene sets and sources of tissue injury in heart transplant patients. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of relevant immune and nonimmune molecular pathways that were predominantly down-regulated in immunosuppressed heart transplant patients compared with healthy controls. cfChIP-seq also identified cell-free DNA tissue sources. Compared with healthy controls, heart transplant patients demonstrated greater cell-free DNA from tissue types associated with heart transplant complications, including the heart, hematopoietic cells, lungs, liver, and vascular endothelium. cfChIP-seq may therefore be a reliable approach to profile dynamic assessments of molecular pathways and sources of tissue injury in heart transplant patients.
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Affiliation(s)
- Moon Kyoo Jang
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Tovah E Markowitz
- https://ror.org/01cwqze88 NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Temesgen E Andargie
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
- Department of Biology, Howard University, Washington, DC, USA
| | - Zainab Apalara
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Skyler Kuhn
- https://ror.org/01cwqze88 NIAID Collaborative Bioinformatics Resource, Integrated Data Sciences Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Sean Agbor-Enoh
- https://ror.org/01cwqze88 Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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11
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Erez N, Furth N, Fedyuk V, Wadden J, Aittaleb R, Schwark K, Niculcea M, Miclea M, Mody R, Franson A, Eze A, Nourmohammadi N, Nazarian J, Venneti S, Koschmann C, Shema E. Single-molecule systems for detection and monitoring of plasma circulating nucleosomes and oncoproteins in Diffuse Midline Glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568019. [PMID: 38045418 PMCID: PMC10690213 DOI: 10.1101/2023.11.21.568019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The analysis of cell-free tumor DNA (ctDNA) and proteins in the blood of cancer patients potentiates a new generation of non-invasive diagnostics and treatment monitoring approaches. However, confident detection of these tumor-originating markers is challenging, especially in the context of brain tumors, in which extremely low amounts of these analytes circulate in the patient's plasma. Here, we applied a sensitive single-molecule technology to profile multiple histone modifications on millions of individual nucleosomes from the plasma of Diffuse Midline Glioma (DMG) patients. The system reveals epigenetic patterns that are unique to DMG, significantly differentiating this group of patients from healthy subjects or individuals diagnosed with other cancer types. We further develop a method to directly capture and quantify the tumor-originating oncoproteins, H3-K27M and mutant p53, from the plasma of children diagnosed with DMG. This single-molecule system allows for accurate molecular classification of patients, utilizing less than 1ml of liquid-biopsy material. Furthermore, we show that our simple and rapid detection strategy correlates with MRI measurements and droplet-digital PCR (ddPCR) measurements of ctDNA, highlighting the utility of this approach for non-invasive treatment monitoring of DMG patients. This work underscores the clinical potential of single-molecule-based, multi-parametric assays for DMG diagnosis and treatment monitoring.
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12
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Tao Y, Xing S, Zuo S, Bao P, Jin Y, Li Y, Li M, Wu Y, Chen S, Wang X, Zhu Y, Feng Y, Zhang X, Wang X, Xi Q, Lu Q, Wang P, Lu ZJ. Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients' blood. Cell Rep Med 2023; 4:101281. [PMID: 37992683 PMCID: PMC10694666 DOI: 10.1016/j.xcrm.2023.101281] [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: 03/27/2023] [Revised: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
During cancer progression, tumorigenic and immune signals are spread through circulating molecules, such as cell-free DNA (cfDNA) and cell-free RNA (cfRNA) in the blood. So far, they have not been comprehensively investigated in gastrointestinal cancers. Here, we profile 4 categories of cell-free omics data from patients with colorectal cancer and patients with stomach adenocarcinoma and then assay 15 types of genomic, epigenomic, and transcriptomic variations. We find that multi-omics data are more appropriate for detection of cancer genes compared with single-omics data. In particular, cfRNAs are more sensitive and informative than cfDNAs in terms of detection rate, enriched functional pathways, etc. Moreover, we identify several peripheral immune signatures that are suppressed in patients with cancer. Specifically, we establish a γδ-T cell score and a cancer-associated-fibroblast (CAF) score, providing insights into clinical statuses like cancer stage and survival. Overall, we reveal a cell-free multi-molecular landscape that is useful for blood monitoring in personalized cancer treatment.
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Affiliation(s)
- Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Shuai Zuo
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yu Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Mingyang Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingchao Wu
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China
| | - Shanwen Chen
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China
| | - Xiaojuan Wang
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China; Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China
| | - Yumin Zhu
- Medical school, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Ying Feng
- Department of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xiaohua Zhang
- Department of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xianbo Wang
- Department of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, State Key Laboratory of Molecular Oncology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qian Lu
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China; Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China.
| | - Pengyuan Wang
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China.
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China.
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13
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Moss J, Ben-Ami R, Shai E, Gal-Rosenberg O, Kalish Y, Klochendler A, Cann G, Glaser B, Arad A, Shemer R, Dor Y. Megakaryocyte- and erythroblast-specific cell-free DNA patterns in plasma and platelets reflect thrombopoiesis and erythropoiesis levels. Nat Commun 2023; 14:7542. [PMID: 37985773 PMCID: PMC10662131 DOI: 10.1038/s41467-023-43310-2] [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: 10/02/2022] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) fragments are a biological analyte with extensive utility in diagnostic medicine. Understanding the source of cfDNA and mechanisms of release is crucial for designing and interpreting cfDNA-based liquid biopsy assays. Using cell type-specific methylation markers as well as genome-wide methylation analysis, we determine that megakaryocytes, the precursors of anuclear platelets, are major contributors to cfDNA (~26%), while erythroblasts contribute 1-4% of cfDNA in healthy individuals. Surprisingly, we discover that platelets contain genomic DNA fragments originating in megakaryocytes, contrary to the general understanding that platelets lack genomic DNA. Megakaryocyte-derived cfDNA is increased in pathologies involving increased platelet production (Essential Thrombocythemia, Idiopathic Thrombocytopenic Purpura) and decreased upon reduced platelet production due to chemotherapy-induced bone marrow suppression. Similarly, erythroblast cfDNA is reflective of erythrocyte production and is elevated in patients with thalassemia. Megakaryocyte- and erythroblast-specific DNA methylation patterns can thus serve as biomarkers for pathologies involving increased or decreased thrombopoiesis and erythropoiesis, which can aid in determining the etiology of aberrant levels of erythrocytes and platelets.
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Affiliation(s)
- Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, the Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Roni Ben-Ami
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, the Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ela Shai
- Hematology Department, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ofer Gal-Rosenberg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, the Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yosef Kalish
- Hematology Department, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, the Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah University Medical Center and Faculty of Medicine, the Hebrew University, Jerusalem, Israel
| | - Ariela Arad
- Hematology Department, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, the Hebrew University-Hadassah Medical School, Jerusalem, Israel.
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, the Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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14
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Pu Y, Li L, Peng H, Liu L, Heymann D, Robert C, Vallette F, Shen S. Drug-tolerant persister cells in cancer: the cutting edges and future directions. Nat Rev Clin Oncol 2023; 20:799-813. [PMID: 37749382 DOI: 10.1038/s41571-023-00815-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Drug-tolerant persister (DTP) cell populations were originally discovered in antibiotic-resistant bacterial biofilms. Similar populations with comparable features have since been identified among cancer cells and have been linked with treatment resistance that lacks an underlying genomic alteration. Research over the past decade has improved our understanding of the biological roles of DTP cells in cancer, although clinical knowledge of the role of these cells in treatment resistance remains limited. Nonetheless, targeting this population is anticipated to provide new treatment opportunities. In this Perspective, we aim to provide a clear definition of the DTP phenotype, discuss the underlying characteristics of these cells, their biomarkers and vulnerabilities, and encourage further research on DTP cells that might improve our understanding and enable the development of more effective anticancer therapies.
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Affiliation(s)
- Yi Pu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Li
- Lung Cancer Centre, West China Hospital, Sichuan University, Chengdu, China
| | - Haoning Peng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Nantes, France
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - François Vallette
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France.
- Nantes Université, INSERM, U1307, CRCI2NA, Nantes, France.
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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15
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Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2023; 29:2737-2741. [PMID: 37865722 PMCID: PMC10695830 DOI: 10.1038/s41591-023-02605-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling.
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Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew P Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brad Fortunato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Shahabbedin Sotudian
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ikenna Madueke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manisha Thakuria
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
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16
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Andargie TE, Roznik K, Redekar N, Hill T, Zhou W, Apalara Z, Kong H, Gordon O, Meda R, Park W, Johnston TS, Wang Y, Brady S, Ji H, Yanovski JA, Jang MK, Lee CM, Karaba AH, Cox AL, Agbor-Enoh S. Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children. J Clin Invest 2023; 133:e171729. [PMID: 37651206 PMCID: PMC10617770 DOI: 10.1172/jci171729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare but life-threatening hyperinflammatory condition induced by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes pediatric COVID-19 (pCOVID-19). The relationship of the systemic tissue injury to the pathophysiology of MIS-C is poorly defined. We leveraged the high sensitivity of epigenomics analyses of plasma cell-free DNA (cfDNA) and plasma cytokine measurements to identify the spectrum of tissue injury and glean mechanistic insights. Compared with pediatric healthy controls (pHCs) and patients with pCOVID-19, patients with MIS-C had higher levels of cfDNA primarily derived from innate immune cells, megakaryocyte-erythroid precursor cells, and nonhematopoietic tissues such as hepatocytes, cardiac myocytes, and kidney cells. Nonhematopoietic tissue cfDNA levels demonstrated significant interindividual variability, consistent with the heterogenous clinical presentation of MIS-C. In contrast, adaptive immune cell-derived cfDNA levels were comparable in MIS-C and pCOVID-19 patients. Indeed, the cfDNA of innate immune cells in patients with MIS-C correlated with the levels of innate immune inflammatory cytokines and nonhematopoietic tissue-derived cfDNA, suggesting a primarily innate immunity-mediated response to account for the multisystem pathology. These data provide insight into the pathogenesis of MIS-C and support the value of cfDNA as a sensitive biomarker to map tissue injury in MIS-C and likely other multiorgan inflammatory conditions.
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Affiliation(s)
- Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
- Department of Biology, Howard University, Washington DC, USA
| | - Katerina Roznik
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Neelam Redekar
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Tom Hill
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Oren Gordon
- Infectious Diseases Unit, Department of Pediatrics, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rohan Meda
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Woojin Park
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Trevor S. Johnston
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Yi Wang
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sheila Brady
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, Maryland, USA
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jack A. Yanovski
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, Maryland, USA
| | - Moon K. Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Clarence M. Lee
- Department of Biology, Howard University, Washington DC, USA
| | - Andrew H. Karaba
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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17
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Li J, Lan X. Perspective on new cell-free DNA technologies for early cancer detection. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0159. [PMID: 37553805 PMCID: PMC10884532 DOI: 10.20892/j.issn.2095-3941.2023.0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Jie Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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18
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Chen Z, Li C, Zhou Y, Yao Y, Liu J, Wu M, Su J. Liquid biopsies for cancer: From bench to clinic. MedComm (Beijing) 2023; 4:e329. [PMID: 37492785 PMCID: PMC10363811 DOI: 10.1002/mco2.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Over the past two decades, liquid biopsy has been increasingly used as a supplement, or even, a replacement to the traditional biopsy in clinical oncological practice, due to its noninvasive and early detectable properties. The detections can be based on a variety of features extracted from tumor‑derived entities, such as quantitative alterations, genetic changes, and epigenetic aberrations, and so on. So far, the clinical applications of cancer liquid biopsy mainly aimed at two aspects, prediction (early diagnosis, prognosis and recurrent evaluation, therapeutic response monitoring, etc.) and intervention. In spite of the rapid development and great contributions achieved, cancer liquid biopsy is still a field under investigation and deserves more clinical practice. To better open up future work, here we systematically reviewed and compared the latest progress of the most widely recognized circulating components, including circulating tumor cells, cell-free circulating DNA, noncoding RNA, and nucleosomes, from their discovery histories to clinical values. According to the features applied, we particularly divided the contents into two parts, beyond epigenetics and epigenetic-based. The latter was considered as the highlight along with a brief overview of the advances in both experimental and bioinformatic approaches, due to its unique advantages and relatively lack of documentation.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Chenghao Li
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
| | - Yue Zhou
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Yinghao Yao
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Jiaqi Liu
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Min Wu
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
| | - Jianzhong Su
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
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19
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [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: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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20
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Kravitz CJ, Yan Q, Nguyen DX. Epigenetic markers and therapeutic targets for metastasis. Cancer Metastasis Rev 2023; 42:427-443. [PMID: 37286865 PMCID: PMC10595046 DOI: 10.1007/s10555-023-10109-y] [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: 01/10/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
The last few years have seen an increasing number of discoveries which collectively demonstrate that histone and DNA modifying enzyme modulate different stages of metastasis. Moreover, epigenomic alterations can now be measured at multiple scales of analysis and are detectable in human tumors or liquid biopsies. Malignant cell clones with a proclivity for relapse in certain organs may arise in the primary tumor as a consequence of epigenomic alterations which cause a loss in lineage integrity. These alterations may occur due to genetic aberrations acquired during tumor progression or concomitant to therapeutic response. Moreover, evolution of the stroma can also alter the epigenome of cancer cells. In this review, we highlight current knowledge with a particular emphasis on leveraging chromatin and DNA modifying mechanisms as biomarkers of disseminated disease and as therapeutic targets to treat metastatic cancers.
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Affiliation(s)
- Carolyn J Kravitz
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT, 06520, USA.
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21
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Fridlich O, Peretz A, Fox-Fisher I, Pyanzin S, Dadon Z, Shcolnik E, Sadeh R, Fialkoff G, Sharkia I, Moss J, Arpinati L, Nice S, Nogiec CD, Ahuno ST, Li R, Taborda E, Dunkelbarger S, Fridlender ZG, Polak P, Kaplan T, Friedman N, Glaser B, Shemer R, Constantini N, Dor Y. Elevated cfDNA after exercise is derived primarily from mature polymorphonuclear neutrophils, with a minor contribution of cardiomyocytes. Cell Rep Med 2023:101074. [PMID: 37290439 DOI: 10.1016/j.xcrm.2023.101074] [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: 02/11/2021] [Revised: 08/25/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
Strenuous physical exercise causes a massive elevation in the concentration of circulating cell-free DNA (cfDNA), which correlates with effort intensity and duration. The cellular sources and physiological drivers of this phenomenon are unknown. Using methylation patterns of cfDNA and associated histones, we show that cfDNA in exercise originates mostly in extramedullary polymorphonuclear neutrophils. Strikingly, cardiomyocyte cfDNA concentration increases after a marathon, consistent with elevated troponin levels and indicating low-level, delayed cardiac cell death. Physical impact, low oxygen levels, and elevated core body temperature contribute to neutrophil cfDNA release, while muscle contraction, increased heart rate, β-adrenergic signaling, or steroid treatment fail to cause elevation of cfDNA. Physical training reduces neutrophil cfDNA release after a standard exercise, revealing an inverse relationship between exercise-induced cfDNA release and training level. We speculate that the release of cfDNA from neutrophils in exercise relates to the activation of neutrophils in the context of exercise-induced muscle damage.
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Affiliation(s)
- Ori Fridlich
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Sheina Pyanzin
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ziv Dadon
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Eilon Shcolnik
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Ronen Sadeh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Gavriel Fialkoff
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Israa Sharkia
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ludovica Arpinati
- Institute of Pulmonary Medicine, Hadassah Medical Center and Hebrew University of Jerusalem, Israel
| | - Shachar Nice
- Heidi Rothberg Sport Medicine Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Christopher D Nogiec
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Samuel Terkper Ahuno
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rui Li
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Eddie Taborda
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Sonia Dunkelbarger
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Zvi G Fridlender
- Institute of Pulmonary Medicine, Hadassah Medical Center and Hebrew University of Jerusalem, Israel
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Naama Constantini
- Heidi Rothberg Sport Medicine Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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22
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Morganti S, Parsons HA, Lin NU, Grinshpun A. Liquid biopsy for brain metastases and leptomeningeal disease in patients with breast cancer. NPJ Breast Cancer 2023; 9:43. [PMID: 37225714 DOI: 10.1038/s41523-023-00550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
A significant subset of patients with metastatic breast cancer develops brain metastasis. As efficacy of systemic therapies has improved and patients live longer with metastatic breast cancer, the incidence of breast cancer brain metastases has increased. Brain metastases pose a clinical challenge in diagnosis, treatment, and monitoring across all breast cancer subtypes, and better tools are needed. Liquid biopsy, which enables minimally invasive sampling of a patient's cancer, has the potential to shed light on intra-cranial tumor biology and to improve patient care by enabling therapy tailoring. Here we review current evidence for the clinical validity of liquid biopsy in patients with breast cancer brain metastases, with a focus on circulating tumor cells and circulating tumor DNA.
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Affiliation(s)
- Stefania Morganti
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Heather A Parsons
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Albert Grinshpun
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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23
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Herberts C, Wyatt AW, Nguyen PL, Cheng HH. Genetic and Genomic Testing for Prostate Cancer: Beyond DNA Repair. Am Soc Clin Oncol Educ Book 2023; 43:e390384. [PMID: 37207301 DOI: 10.1200/edbk_390384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Significant progress has been made in genetic and genomic testing for prostate cancer across the disease spectrum. Molecular profiling is increasingly relevant for routine clinical management, fueled in part by advancements in testing technology and integration of biomarkers into clinical trials. In metastatic prostate cancer, defects in DNA damage response genes are now established predictors of benefit to US Food and Drug Administration-approved poly (ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors, and trials are actively investigating these and other targeted treatment strategies in earlier disease states. Excitingly, opportunities for molecularly informed management beyond DNA damage response genes are also maturing. Germline genetic variants (eg, BRCA2 or MSH2/6) and polygenic germline risk scores are being investigated to inform cancer screening and active surveillance in at-risk carriers. RNA expression tests have recently gained traction in localized prostate cancer, enabling patient risk stratification and tailored treatment intensification via radiotherapy and/or androgen deprivation therapy for localized or salvage treatment. Finally, emerging minimally invasive circulating tumor DNA technology promises to enhance biomarker testing in advanced disease pending additional methodological and clinical validation. Collectively, genetic and genomic tests are rapidly becoming indispensable tools for informing the optimal clinical management of prostate cancer.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul L Nguyen
- Harvard Medical School, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Heather H Cheng
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA
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24
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Bae M, Kim G, Lee TR, Ahn JM, Park H, Park SR, Song KB, Jun E, Oh D, Lee JW, Park YS, Song KW, Byeon JS, Kim BH, Sohn JH, Kim MH, Kim GM, Chie EK, Kang HC, Kong SY, Woo SM, Lee JE, Ryu JM, Lee J, Kim D, Ki CS, Cho EH, Choi JK. Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA. Nat Commun 2023; 14:2017. [PMID: 37037826 PMCID: PMC10085982 DOI: 10.1038/s41467-023-37768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Multi-cancer early detection remains a key challenge in cell-free DNA (cfDNA)-based liquid biopsy. Here, we perform cfDNA whole-genome sequencing to generate two test datasets covering 2125 patient samples of 9 cancer types and 1241 normal control samples, and also a reference dataset for background variant filtering based on 20,529 low-depth healthy samples. An external cfDNA dataset consisting of 208 cancer and 214 normal control samples is used for additional evaluation. Accuracy for cancer detection and tissue-of-origin localization is achieved using our algorithm, which incorporates cancer type-specific profiles of mutation distribution and chromatin organization in tumor tissues as model references. Our integrative model detects early-stage cancers, including those of pancreatic origin, with high sensitivity that is comparable to that of late-stage detection. Model interpretation reveals the contribution of cancer type-specific genomic and epigenomic features. Our methodologies may lay the groundwork for accurate cfDNA-based cancer diagnosis, especially at early stages.
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Affiliation(s)
- Mingyun Bae
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Gyuhee Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Tae-Rim Lee
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Jin Mo Ahn
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Hyunwook Park
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ki Byung Song
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunsung Jun
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dongryul Oh
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jeong-Won Lee
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young Sik Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ki-Won Song
- Division of Hepatopancreatobiliary Surgery and Liver Transplantation, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeong-Sik Byeon
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Bo Hyun Kim
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Joo Hyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- AIMA, Inc., Avison Biomedical Research Center, Seoul, Republic of Korea
| | - Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gun Min Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui Kyu Chie
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Cheol Kang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Republic of Korea
| | - Sang Myung Woo
- Center for Liver and Pancreatobiliary Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Jai Min Ryu
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Junnam Lee
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Dasom Kim
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Chang-Seok Ki
- Genome Research Center, GC Genome, Yongin, Republic of Korea
| | - Eun-Hae Cho
- Genome Research Center, GC Genome, Yongin, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.
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25
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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26
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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27
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Fisher IF, Shemer R, Dor Y. Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation. Trends Immunol 2023; 44:356-364. [PMID: 37012121 DOI: 10.1016/j.it.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Immune and inflammatory processes occurring within tissues are often undetectable by blood cell counts, standard circulating biomarkers, or imaging, representing an unmet biomedical need. Here, we outline recent advances indicating that liquid biopsies can broadly inform human immune system dynamics. Nucleosome-size fragments of cell-free DNA (cfDNA) released from dying cells into blood contain rich epigenetic information such as methylation, fragmentation, and histone mark patterns. This information allows to infer the cfDNA cell of origin, as well as pre-cell death gene expression patterns. We propose that the analysis of epigenetic features of immune cell-derived cfDNA can shed light on immune cell turnover dynamics in healthy people, and inform the study and diagnosis of cancer, local inflammation, infectious or autoimmune diseases, as well as responses to vaccination.
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28
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Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics. Nat Biotechnol 2023; 41:212-221. [PMID: 36076083 DOI: 10.1038/s41587-022-01447-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
Abstract
The analysis of cell-free DNA (cfDNA) in plasma provides information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue of origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.
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Vad-Nielsen J, Staunstrup NH, Kjeldsen ML, Dybdal N, Flandin G, De Stradis C, Daugaard TF, Vilsbøll-Larsen T, Maansson CT, Doktor TK, Sorensen BS, Nielsen AL. Genome-wide epigenetic and mRNA-expression profiling followed by CRISPR/Cas9-mediated gene-disruptions corroborate the MIR141/MIR200C-ZEB1/ZEB2-FGFR1 axis in acquired EMT-associated EGFR TKI-resistance in NSCLC cells. Transl Lung Cancer Res 2023; 12:42-65. [PMID: 36762066 PMCID: PMC9903082 DOI: 10.21037/tlcr-22-507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/12/2022] [Indexed: 01/16/2023]
Abstract
Background Epithelial-mesenchymal-transition (EMT) is an epigenetic-based mechanism contributing to the acquired treatment resistance against receptor tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) cells harboring epidermal growth factor receptor (EGFR)-mutations. Delineating the exact epigenetic and gene-expression alterations in EMT-associated EGFR TKI-resistance (EMT-E-TKI-R) is vital for improved diagnosis and treatment of NSCLC patients. Methods We characterized genome-wide changes in mRNA-expression, DNA-methylation and the histone-modification H3K36me3 in EGFR-mutated NSCLC HCC827 cells in result of acquired EMT-E-TKI-R. CRISPR/Cas9 was used to functional examine key findings from the omics analyses. Results Acquired EMT-E-TKI-R was analyzed with three omics approaches. RNA-sequencing identified 2,233 and 1,972 up- and down-regulated genes, respectively, and among these were established EMT-markers. DNA-methylation EPIC array analyses identified 14,163 and 7,999 hyper- and hypo-methylated, respectively, differential methylated positions of which several were present in EMT-markers. Finally, H3K36me3 chromatin immunoprecipitation (ChIP)-sequencing detected 2,873 and 3,836 genes with enrichment and depletion, respectively, and among these were established EMT-markers. Correlation analyses showed that EMT-E-TKI-R mRNA-expression changes correlated better with H3K36me3 changes than with DNA-methylation changes. Moreover, the omics data supported the involvement of the MIR141/MIR200C-ZEB1/ZEB2-FGFR1 signaling axis for acquired EMT-E-TKI-R. CRISPR/Cas9-mediated analyses corroborated the importance of ZEB1 in acquired EMT-E-TKI-R, MIR200C and MIR141 to be in an EMT-E-TKI-R-associated auto-regulatory loop with ZEB1, and FGFR1 to mediate cell survival in EMT-E-TKI-R. Conclusions The current study describes the synchronous genome-wide changes in mRNA-expression, DNA-methylation, and H3K36me3 in NSCLC EMT-E-TKI-R. The omics approaches revealed potential novel diagnostic markers and treatment targets. Besides, the study consolidates the functional impact of the MIR141/MIR200C-ZEB1/ZEB2-FGFR1-signaling axis in NSCLC EMT-E-TKI-R.
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Affiliation(s)
| | | | | | - Nina Dybdal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | | | | | - Christoffer Trier Maansson
- Department of Biomedicine, Aarhus University, Aarhus, Denmark;,Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark;,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark;,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Jang MK, Markowitz TE, Andargie TE, Apalara Z, Kuhn S, Agbor-Enoh S. Cell-free Chromatin Immunoprecipitation to detect molecular pathways in Physiological and Disease States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525414. [PMID: 36789421 PMCID: PMC9928031 DOI: 10.1101/2023.01.24.525414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Patient monitoring is a cornerstone in clinical practice to define disease phenotypes and guide clinical management. Unfortunately, this is often reliant on invasive and/or less sensitive methods that do not provide deep phenotype assessments of disease state to guide treatment. This paper examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) to define molecular gene sets in physiological and heart transplant patients taking immunosuppression medications. We show cfChIP-seq reliably detect gene signals that correlate with gene expression. In healthy controls and in heart transplant patients, cfChIP-seq reliably detected housekeeping genes. cfChIP-seq identified differential gene signals of the relevant immune and non-immune molecular pathways that were predominantly downregulated in immunosuppressed heart transplant patients compared to healthy controls. cfChIP-seq also identified tissue sources of cfDNA, detecting greater cell-free DNA from cardiac, hematopoietic, and other non-hematopoietic tissues such as the pulmonary, digestive, and neurological tissues in transplant patients than healthy controls. cfChIP-seq gene signals were reproducible between patient populations and blood collection methods. cfChIP-seq may therefore be a reliable approach to provide dynamic assessments of molecular pathways and tissue injury associated to disease.
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Affiliation(s)
- Moon K. Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Tovah E. Markowitz
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
| | - Skyler Kuhn
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision. Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD
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Qi T, Pan M, Shi H, Wang L, Bai Y, Ge Q. Cell-Free DNA Fragmentomics: The Novel Promising Biomarker. Int J Mol Sci 2023; 24:ijms24021503. [PMID: 36675018 PMCID: PMC9866579 DOI: 10.3390/ijms24021503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics' characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising novel biomarker. Moreover, cfDNA fragmentomics can identify tissue origins by inferring epigenetic information. Thus, further insights into the fragmentomics of plasma cfDNA shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In this review, we focus on the cfDNA fragment characteristics and its potential application, such as fragment length, end motifs, jagged ends, preferred end coordinates, as well as nucleosome footprints, open chromatin region, and gene expression inferred by the cfDNA fragmentation pattern across the genome. Furthermore, we summarize the methods for deducing the tissue of origin by cfDNA fragmentomics.
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Affiliation(s)
- Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liangying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Correspondence: ; Tel./Fax: +86-025-83792396
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Wiering L, Tacke F. Treating inflammation to combat non-alcoholic fatty liver disease. J Endocrinol 2023; 256:JOE-22-0194. [PMID: 36259984 DOI: 10.1530/joe-22-0194] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) with its more progressive form non-alcoholic steatohepatitis (NASH) has become the most common chronic liver disease, thereby representing a great burden for patients and healthcare systems. Specific pharmacological therapies for NAFLD are still missing. Inflammation is an important driver in the pathogenesis of NASH, and the mechanisms underlying inflammation in NAFLD represent possible therapeutic targets. In NASH, various intra- and extrahepatic triggers involved in the metabolic injury typically lead to the activation of different immune cells. This includes hepatic Kupffer cells, i.e. liver-resident macrophages, which can adopt an inflammatory phenotype and activate other immune cells by releasing inflammatory cytokines. As inflammation progresses, Kupffer cells are increasingly replaced by monocyte-derived macrophages with a distinct lipid-associated and scar-associated phenotype. Many other immune cells, including neutrophils, T lymphocytes - such as auto-aggressive cytotoxic as well as regulatory T cells - and innate lymphoid cells balance the progression and regression of inflammation and subsequent fibrosis. The detailed understanding of inflammatory cell subsets and their activation pathways prompted preclinical and clinical exploration of potential targets in NAFLD/NASH. These approaches to target inflammation in NASH include inhibition of immune cell recruitment via chemokine receptors (e.g. cenicriviroc), neutralization of CD44 or galectin-3 as well as agonism to nuclear factors like peroxisome proliferator-activated receptors and farnesoid X receptor that interfere with the activation of immune cells. As some of these approaches did not demonstrate convincing efficacy as monotherapies, a rational and personalized combination of therapeutic interventions may be needed for the near future.
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Affiliation(s)
- Leke Wiering
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Berlin, Germany
| | - Frank Tacke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
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Buzova D, Braghini MR, Bianco SD, Lo Re O, Raffaele M, Frohlich J, Kisheva A, Crudele A, Mosca A, Sartorelli MR, Balsano C, Cerveny J, Mazza T, Alisi A, Vinciguerra M. Profiling of cell-free DNA methylation and histone signatures in pediatric NAFLD: A pilot study. Hepatol Commun 2022; 6:3311-3323. [PMID: 36264206 PMCID: PMC9701487 DOI: 10.1002/hep4.2082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/19/2022] [Accepted: 08/10/2022] [Indexed: 01/21/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in children and adolescents, increasing the risk of its progression toward nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. There is an urgent need for noninvasive early diagnostic and prognostic tools such as epigenetic marks (epimarks), which would replace liver biopsy in the future. We used plasma samples from 67 children with biopsy-proven NAFLD, and as controls we used samples from 20 children negative for steatosis by ultrasound. All patients were genotyped for patatin-like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane bound O-acyltransferase domain containing 7 (MBOAT7), and klotho-β (KLB) gene variants, and data on anthropometric and biochemical parameters were collected. Furthermore, plasma cell-free DNA (cfDNA) methylation was quantified using a commercially available kit, and ImageStream(X) was used for the detection of free circulating histone complexes and variants. We found a significant enrichment of the levels of histone macroH2A1.2 in the plasma of children with NAFLD compared to controls, and a strong correlation between cfDNA methylation levels and NASH. Receiver operating characteristic curve analysis demonstrated that combination of cfDNA methylation, PNPLA3 rs738409 variant, coupled with either high-density lipoprotein cholesterol or alanine aminotransferase levels can strongly predict the progression of pediatric NAFLD to NASH with area under the curve >0.87. Conclusion: Our pilot study combined epimarks and genetic and metabolic markers for a robust risk assessment of NAFLD development and progression in children, offering a promising noninvasive tool for the consistent diagnosis and prognosis of pediatric NAFLD. Further studies are necessary to identify their pathogenic origin and function.
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Affiliation(s)
- Diana Buzova
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Maria Rita Braghini
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Salvatore Daniele Bianco
- Laboratory of BioinformaticsFondazione IRCCS Casa Sollievo della SofferenzaSan Giovanni Rotondo (FG)Italy
| | - Oriana Lo Re
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic,Department of Translational Stem Cell BiologyResearch Institute of the Medical University of VarnaVarnaBulgaria
| | - Marco Raffaele
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Jan Frohlich
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Antoniya Kisheva
- Department of Internal Diseases IMedical University of VarnaVarnaBulgaria
| | - Annalisa Crudele
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Antonella Mosca
- Hepatology, Gastroenterology and Nutrition UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Maria Rita Sartorelli
- Hepatology, Gastroenterology and Nutrition UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Clara Balsano
- Department of LifeHealth & Environmental Sciences‐ MESVA‐School of Emergency and Urgency Medicine, University of L'AquilaL'AquilaItaly
| | - Jan Cerveny
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Tommaso Mazza
- Laboratory of BioinformaticsFondazione IRCCS Casa Sollievo della SofferenzaSan Giovanni Rotondo (FG)Italy
| | - Anna Alisi
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Manlio Vinciguerra
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic,Department of Translational Stem Cell BiologyResearch Institute of the Medical University of VarnaVarnaBulgaria,Liverpool Center for Cardiovascular ScienceLiverpool Johns Moore UniversityLiverpoolUK
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Brusca SB, Elinoff JM, Zou Y, Jang MK, Kong H, Demirkale CY, Sun J, Seifuddin F, Pirooznia M, Valantine HA, Tanba C, Chaturvedi A, Graninger GM, Harper B, Chen LY, Cole J, Kanwar M, Benza RL, Preston IR, Agbor-Enoh S, Solomon MA. Plasma Cell-Free DNA Predicts Survival and Maps Specific Sources of Injury in Pulmonary Arterial Hypertension. Circulation 2022; 146:1033-1045. [PMID: 36004627 PMCID: PMC9529801 DOI: 10.1161/circulationaha.121.056719] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/15/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) is a noninvasive marker of cellular injury. Its significance in pulmonary arterial hypertension (PAH) is unknown. METHODS Plasma cfDNA was measured in 2 PAH cohorts (A, n=48; B, n=161) and controls (n=48). Data were collected for REVEAL 2.0 (Registry to Evaluate Early and Long-Term PAH Disease Management) scores and outcome determinations. Patients were divided into the following REVEAL risk groups: low (≤6), medium (7-8), and high (≥9). Total cfDNA concentrations were compared among controls and PAH risk groups by 1-way analysis of variance. Log-rank tests compared survival between cfDNA tertiles and REVEAL risk groups. Areas under the receiver operating characteristic curve were estimated from logistic regression models. A sample subset from cohort B (n=96) and controls (n=16) underwent bisulfite sequencing followed by a deconvolution algorithm to map cell-specific cfDNA methylation patterns, with concentrations compared using t tests. RESULTS In cohort A, median (interquartile range) age was 62 years (47-71), with 75% female, and median (interquartile range) REVEAL 2.0 was 6 (4-9). In cohort B, median (interquartile range) age was 59 years (49-71), with 69% female, and median (interquartile range) REVEAL 2.0 was 7 (6-9). In both cohorts, cfDNA concentrations differed among patients with PAH of varying REVEAL risk and controls (analysis of variance P≤0.002) and were greater in the high-risk compared with the low-risk category (P≤0.002). In cohort B, death or lung transplant occurred in 14 of 54, 23 of 53, and 35 of 54 patients in the lowest, middle, and highest cfDNA tertiles, respectively. cfDNA levels stratified as tertiles (log-rank: P=0.0001) and REVEAL risk groups (log-rank: P<0.0001) each predicted transplant-free survival. The addition of cfDNA to REVEAL improved discrimination (area under the receiver operating characteristic curve, 0.72-0.78; P=0.02). Compared with controls, methylation analysis in patients with PAH revealed increased cfDNA originating from erythrocyte progenitors, neutrophils, monocytes, adipocytes, natural killer cells, vascular endothelium, and cardiac myocytes (Bonferroni adjusted P<0.05). cfDNA concentrations derived from erythrocyte progenitor cells, cardiac myocytes, and vascular endothelium were greater in patients with PAH with high-risk versus low-risk REVEAL scores (P≤0.02). CONCLUSIONS Circulating cfDNA is elevated in patients with PAH, correlates with disease severity, and predicts worse survival. Results from cfDNA methylation analyses in patients with PAH are consistent with prevailing paradigms of disease pathogenesis.
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Affiliation(s)
- Samuel B Brusca
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
- Department of Internal Medicine, Division of Cardiology, University of California, San Francisco, CA
| | - Jason M Elinoff
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Yvette Zou
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Moon Kyoo Jang
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
| | - Hyesik Kong
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
| | - Cumhur Y Demirkale
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Junfeng Sun
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Fayaz Seifuddin
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Mehdi Pirooznia
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Hannah A Valantine
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
- Department of Internal Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Carl Tanba
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Tufts Medical Center, Boston, MA
| | - Abhishek Chaturvedi
- Pauley Heart Center, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Grace M Graninger
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Bonnie Harper
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Li-Yuan Chen
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Justine Cole
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD
| | - Manreet Kanwar
- Cardiovascular Institute at Allegheny Health Network, Pittsburgh, PA
| | - Raymond L Benza
- Departent of Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Ioana R Preston
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Tufts Medical Center, Boston, MA
| | - Sean Agbor-Enoh
- Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael A Solomon
- Pulmonary Arterial Hypertension Section of the Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
- Cardiology Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [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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Kwan EM, Wyatt AW. Androgen receptor genomic alterations and treatment resistance in metastatic prostate cancer. Prostate 2022; 82 Suppl 1:S25-S36. [PMID: 35657159 DOI: 10.1002/pros.24356] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/16/2022] [Accepted: 04/04/2022] [Indexed: 12/28/2022]
Abstract
BACKGROUND Genomic alterations to the androgen receptor (AR) are common in metastatic castration-resistant prostate cancer (mCRPC). AR copy number amplifications, ligand-binding domain missense mutations, and intronic structural rearrangements can all drive resistance to approved AR pathway inhibitors and their detection via tissue or liquid biopsy is linked to clinical outcomes. With an increasingly crowded treatment landscape, there is hope that AR genomic alterations can act as prognostic and/or predictive biomarkers to guide patient management. METHODS In this review, we evaluate the current evidence for AR genomic alterations as clinical biomarkers in mCRPC, focusing on correlative studies that have used plasma circulating tumor DNA to characterize AR genotype. RESULTS We highlight data that demonstrates the complexity of AR genotype within individual patients, and suggest that future studies should account for cancer clonal heterogeneity and variable tumor content in liquid biopsy samples. Given the potential for cooccurrence of multiple AR genomic alterations in the same or competing subclones of a patient, it is distinctly challenging to attribute blanket clinical significance to any individual alteration. This challenge is further complicated by the varied treatment exposures in contemporary patients, and the fact that AR genotype continues to evolve in the mCRPC setting across sequential lines of systemic therapy. CONCLUSIONS As treatment access and liquid biopsy technology continues to improve, we posit that real-time measures of AR biology are likely to play a key role in emerging precision oncology strategies for metastatic prostate cancer.
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Affiliation(s)
- Edmond M Kwan
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
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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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Mullen M, Wen Tan WL, Rhee JW, Wu JC. Modeling Susceptibility to Cardiotoxicity in Cancer Therapy Using Human iPSC-Derived Cardiac Cells and Systems Biology. Heart Fail Clin 2022; 18:335-347. [PMID: 35718410 DOI: 10.1016/j.hfc.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of human-induced pluripotent stem cell-derived cardiac cell types has created a new paradigm in assessing drug-induced cardiotoxicity. Advances in genomics and epigenomics have also implicated several genomic loci and biological pathways that may contribute to susceptibility to cancer therapies. In this review, we first provide a brief overview of the cardiotoxicity associated with chemotherapy. We then provide a detailed summary of systems biology approaches being applied to elucidate potential molecular mechanisms involved in cardiotoxicity. Finally, we discuss combining systems biology approaches with iPSC technology to help discover molecular mechanisms associated with cardiotoxicity.
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Affiliation(s)
- McKay Mullen
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA
| | - Wilson Lek Wen Tan
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA
| | - June-Wha Rhee
- Department of Medicine, City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA 91010, USA.
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University; Department of Radiology, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA.
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Che H, Jatsenko T, Lenaerts L, Dehaspe L, Vancoillie L, Brison N, Parijs I, Van Den Bogaert K, Fischerova D, Heremans R, Landolfo C, Testa AC, Vanderstichele A, Liekens L, Pomella V, Wozniak A, Dooms C, Wauters E, Hatse S, Punie K, Neven P, Wildiers H, Tejpar S, Lambrechts D, Coosemans A, Timmerman D, Vandenberghe P, Amant F, Vermeesch JR. Pan-Cancer Detection and Typing by Mining Patterns in Large Genome-Wide Cell-Free DNA Sequencing Datasets. Clin Chem 2022; 68:1164-1176. [PMID: 35769009 DOI: 10.1093/clinchem/hvac095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Cell-free DNA (cfDNA) analysis holds great promise for non-invasive cancer screening, diagnosis, and monitoring. We hypothesized that mining the patterns of cfDNA shallow whole-genome sequencing datasets from patients with cancer could improve cancer detection. METHODS By applying unsupervised clustering and supervised machine learning on large cfDNA shallow whole-genome sequencing datasets from healthy individuals (n = 367) and patients with different hematological (n = 238) and solid malignancies (n = 320), we identified cfDNA signatures that enabled cancer detection and typing. RESULTS Unsupervised clustering revealed cancer type-specific sub-grouping. Classification using a supervised machine learning model yielded accuracies of 96% and 65% in discriminating hematological and solid malignancies from healthy controls, respectively. The accuracy of disease type prediction was 85% and 70% for the hematological and solid cancers, respectively. The potential utility of managing a specific cancer was demonstrated by classifying benign from invasive and borderline adnexal masses with an area under the curve of 0.87 and 0.74, respectively. CONCLUSIONS This approach provides a generic analytical strategy for non-invasive pan-cancer detection and cancer type prediction.
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Affiliation(s)
- Huiwen Che
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Liesbeth Lenaerts
- Department of Oncology, Laboratory of Gynecological Oncology, KU Leuven, Leuven, Belgium
| | - Luc Dehaspe
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Daniela Fischerova
- Department of Obstetrics and Gynaecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Ruben Heremans
- Department of Development and Regeneration, Woman and Child, KU Leuven, Leuven, Belgium
| | - Chiara Landolfo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Antonia Carla Testa
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore Roma, Rome, Italy
| | | | - Lore Liekens
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Valentina Pomella
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Agnieszka Wozniak
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Christophe Dooms
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium.,Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Els Wauters
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium.,Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Sigrid Hatse
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium.,Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Kevin Punie
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium.,Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium.,Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Hans Wildiers
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium.,Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Department of Human Genetics, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Dirk Timmerman
- Department of Development and Regeneration, Woman and Child, KU Leuven, Leuven, Belgium.,Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium.,Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric Amant
- Department of Oncology, Laboratory of Gynecological Oncology, KU Leuven, Leuven, Belgium.,Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium.,Department of Surgery, Center for Gynecological Oncology Amsterdam, Academic Medical Centre Amsterdam-University of Amsterdam and the Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.,Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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Temraz S, Nasr R, Mukherji D, Kreidieh F, Shamseddine A. Liquid Biopsy Derived Circulating Tumor Cells and Circulating Tumor DNA as Novel Biomarkers in Hepatocellular Carcinoma. Expert Rev Mol Diagn 2022; 22:507-518. [PMID: 35758097 DOI: 10.1080/14737159.2022.2094706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The diagnosis of hepatocellular carcinoma (HCC) is made at a relatively advanced stage resulting in poor prognosis. Alpha-fetoprotein and liver ultrasound have limited accuracy as biomarkers in HCC. Liver biopsy provides information on tumor biology; however, it is invasive and holds high threat of tumor seeding. Thus, more accurate and less invasive approaches are needed. AREAS COVERED Highly sensitive liquid biopsy assays have made possible the detection and analysis of cells or organelles such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and tumor-derived exosomes. Here, we focus on CTCs and ctDNA components of liquid biopsy and their clinical application as diagnostic, prognostic and predictive biomarkers in HCC. Unlike tissue biopsy, liquid biopsy involves attaining a sample at several time frames in an easy and a non-invasive manner. They have been efficacious in detecting and classifying cancer, in predicting treatment response, in monitoring disease relapse and in identifying mechanisms of resistance to targeted therapies. EXPERT OPINION Although interesting and highly promising, liquid biopsy techniques still have many obstacles to overcome before their wide spread clinical application sees the light. It is expected that these techniques will be incorporated into traditional methodologies for better diagnostic, predictive and prognostic results.
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Affiliation(s)
- Sally Temraz
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiology, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Deborah Mukherji
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Firas Kreidieh
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
| | - Ali Shamseddine
- Department of internal medicine, Hematology/Oncology division, American University of Beirut Medical Center, Riad El Solh, Beirut, Lebanon
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Main SC, Cescon DW, Bratman SV. Liquid biopsies to predict CDK4/6 inhibitor efficacy and resistance in breast cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:727-748. [PMID: 36176758 PMCID: PMC9511796 DOI: 10.20517/cdr.2022.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors combined with endocrine therapy have transformed the treatment of estrogen receptor-positive (ER+) and human epidermal growth factor receptor 2 negative (HER2-) metastatic breast cancer. However, some patients do not respond to this treatment, and patients inevitably develop resistance, such that novel biomarkers are needed to predict primary resistance, monitor treatment response for acquired resistance, and personalize treatment strategies. Circumventing the spatial and temporal limitations of tissue biopsy, newly developed liquid biopsy approaches have the potential to uncover biomarkers that can predict CDK4/6 inhibitor efficacy and resistance in breast cancer patients through a simple blood test. Studies on circulating tumor DNA (ctDNA)-based liquid biopsy biomarkers of CDK4/6 inhibitor resistance have focused primarily on genomic alterations and have failed thus far to identify clear and clinically validated predictive biomarkers, but emerging epigenetic ctDNA methodologies hold promise for further discovery. The present review outlines recent advances and future directions in ctDNA-based biomarkers of CDK4/6 inhibitor treatment response.
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Affiliation(s)
- Sasha C Main
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto M5T 1P5, Ontario, Canada
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Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy. Sci Rep 2022; 12:10447. [PMID: 35729208 PMCID: PMC9213477 DOI: 10.1038/s41598-022-14675-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Dying tumor cells shed DNA fragments into the circulation that are known as circulating tumor DNA (ctDNA). Liquid biopsy tests aim to detect cancer using known markers, including genetic alterations and epigenetic profiles of ctDNA. Despite various advantages, the major limitation remains the low fraction of tumor-originating DNA fragments in a high background of normal blood-cell originating fragments in the cell-free DNA (cfDNA) pool in plasma. Deep targeted sequencing of cfDNA allows for enrichment of fragments in known cancer marker-associated regions of the genome, thus increasing the chances of detecting the low fraction variant harboring fragments. Most targeted sequencing panels are designed to include known recurrent mutations or methylation markers of cancer. Here, we propose the integration of cancer-specific chromatin accessibility states into panel designs for liquid biopsy. Using machine learning approaches, we first identify accessible and inaccessible chromatin regions specific to each major human cancer type. We then introduce a score that quantifies local chromatin accessibility in tumor relative to blood cells and show that this metric can be useful for prioritizing marker regions with higher chances of being detected in cfDNA for inclusion in future panel designs.
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43
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Cell-free DNA in lung transplantation: research tool or clinical workhorse? Curr Opin Organ Transplant 2022; 27:177-183. [PMID: 35649108 DOI: 10.1097/mot.0000000000000979] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW Recent evidence indicates that plasma donor-derived cell-free DNA (dd-cfDNA) is a sensitive biomarker for the detection of underlying allograft injury, including rejection and infection. In this review, we will cover the latest evidence revolving around dd-cfDNA in lung transplantation and its role in both advancing mechanistic insight into disease states in lung transplant recipients as well as its potential clinical utility. RECENT FINDINGS Plasma dd-cfDNA increases in the setting of allograft injury, including in primary graft dysfunction, acute cellular rejection, antibody-mediated rejection and infection. Dd-cfDNA has demonstrated good performance characteristics for the detection of various allograft injury states, most notably with a high negative-predictive value for detection of acute rejection. Elevated levels of dd-cfDNA in the early posttransplant period, reflecting molecular evidence of lung allograft injury, are associated with increased risk of chronic lung allograft dysfunction and death. SUMMARY As a quantitative, molecular biomarker of lung allograft injury, dd-cfDNA holds great promise in clinical and research settings for advancing methods of posttransplant surveillance monitoring, diagnosis of allograft injury states, monitoring adequacy of immunosuppression, risk stratification and unlocking pathophysiological mechanisms of various disease.
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Fox-Fisher I, Piyanzin S, Briller M, Oiknine-Djian E, Alfi O, Ben-Ami R, Peretz A, Neiman D, Ochana BL, Fridlich O, Drawshy Z, Klochendler A, Magenheim J, Share D, Avrahami R, Ribak Y, Talmon A, Rubin L, Milman N, Segev M, Feldman E, Tal Y, Shen-Orr SS, Glaser B, Shemer R, Wolf D, Dor Y. B-cell-derived cfDNA after primary BNT162b2 mRNA vaccination anticipates memory B-cells and SARS-CoV-2 neutralizing antibodies. MED 2022; 3:468-480.e5. [PMID: 35716665 PMCID: PMC9117261 DOI: 10.1016/j.medj.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 05/12/2022] [Indexed: 10/31/2022]
Abstract
Background Methods Findings Conclusions Funding To understand the turnover of immune cells following SARS-CoV-2 vaccination, Fox-Fisher et al. analyzed fragments of cell-free DNA (cfDNA) that are released from dying immune cells to blood. The levels of B cell cfDNA after the primary dose correlated with neutralizing antibodies and memory B cells after the booster, revealing that early B cell turnover—potentially reflecting affinity maturation—affects later development of effective antibodies. They also observed co-elevation of lymphocyte and monocyte cfDNA after the booster, underscoring the involvement of innate immune cell turnover in the development of humoral and cellular adaptive immunity. cfDNA biomarkers open a new window into human immune cell dynamics in response to perturbations.
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Vanderstichele A, Busschaert P, Landolfo C, Olbrecht S, Coosemans A, Froyman W, Loverix L, Concin N, Braicu EI, Wimberger P, Van Nieuwenhuysen E, Han SN, Van Gorp T, Venken T, Heremans R, Neven P, Bourne T, Van Calster B, Timmerman D, Lambrechts D, Vergote I. Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer. NPJ Genom Med 2022; 7:30. [PMID: 35484288 PMCID: PMC9050708 DOI: 10.1038/s41525-022-00300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals. Multinomial modeling was subsequently applied to capture these deviations in a per sample nucleosome footprint score. Validation was performed in 271 cfDNAs pre-surgically collected from women with an adnexal mass. We confirmed that nucleosome scores were elevated in invasive carcinoma patients, but not in patients with benign or borderline disease. Combining nucleosome scores with chromosomal instability scores assessed in the same cfDNA improved prediction of malignancy. Nucleosome scores were, however, more reliable to predict non-high-grade serous ovarian tumors, which are characterized by low chromosomal instability. These data highlight that compared to chromosomal instability, nucleosome footprinting provides a complementary and more generic read-out for pre-surgical diagnosis of invasive disease in women with adnexal masses.
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Affiliation(s)
- Adriaan Vanderstichele
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Pieter Busschaert
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chiara Landolfo
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Queen Charlotte's and Chelsea Hospital, Imperial College, London, UK
| | - Siel Olbrecht
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - An Coosemans
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, Immunovar Research Group, KU Leuven, Leuven, Belgium
| | - Wouter Froyman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Liselore Loverix
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Nicole Concin
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
| | - Elena Ioana Braicu
- Department of Gynecology, Campus Virchow, Charité, Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Pauline Wimberger
- National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden, Germany
| | - Els Van Nieuwenhuysen
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sileny N Han
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Toon Van Gorp
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Venken
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ruben Heremans
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Bourne
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ben Van Calster
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Dirk Timmerman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
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Furth N, Shema E. It’s all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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48
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Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12040870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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49
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Hasenleithner SO, Speicher MR. A clinician’s handbook for using ctDNA throughout the patient journey. Mol Cancer 2022; 21:81. [PMID: 35307037 PMCID: PMC8935823 DOI: 10.1186/s12943-022-01551-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The promise of precision cancer medicine presently centers around the genomic sequence of a patient’s tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption.
Main body
Owing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient’s journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome.
Conclusions
The maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care.
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50
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Abstract
Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases. Cell types affected by various diseases are inferred from cell-free RNA.
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