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Strawn M, Safranski TJ, Behura SK. Does DNA methylation in the fetal brain leave an epigenetic memory in the blood? Gene 2023; 887:147788. [PMID: 37696423 DOI: 10.1016/j.gene.2023.147788] [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: 07/11/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Epigenetic memory is an emerging concept that refers to the process in which epigenetic changes occurring early-in life can lead to long-term programs of gene regulation in time and space. By leveraging neural network regression modeling of DNA methylation data in pigs, we show that specific methylations in the adult blood can reliably predict methylation changes that occurred in the fetal brain. Genes associated with these methylations represented known markers of specific cell types of blood including bone marrow hematopoietic progenitor cells, and ependymal and oligodendrocyte cells of brain. This suggested that methylation changes that occurred in the developing brain were maintained as an epigenetic memory in the blood through the adult life.
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Affiliation(s)
- Monica Strawn
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Timothy J Safranski
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, United States; Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, United States.
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2
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Füllgrabe J, Gosal WS, Creed P, Liu S, Lumby CK, Morley DJ, Ost TWB, Vilella AJ, Yu S, Bignell H, Burns P, Charlesworth T, Fu B, Fordham H, Harding NJ, Gandelman O, Golder P, Hodson C, Li M, Lila M, Liu Y, Mason J, Mellad J, Monahan JM, Nentwich O, Palmer A, Steward M, Taipale M, Vandomme A, San-Bento RS, Singhal A, Vivian J, Wójtowicz N, Williams N, Walker NJ, Wong NCH, Yalloway GN, Holbrook JD, Balasubramanian S. Simultaneous sequencing of genetic and epigenetic bases in DNA. Nat Biotechnol 2023; 41:1457-1464. [PMID: 36747096 PMCID: PMC10567558 DOI: 10.1038/s41587-022-01652-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023]
Abstract
DNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding of biology. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete information. Methods widely used to detect epigenetic DNA bases fail to capture common C-to-T mutations or distinguish 5-methylcytosine from 5-hydroxymethylcytosine. We present a single base-resolution sequencing methodology that sequences complete genetics and the two most common cytosine modifications in a single workflow. DNA is copied and bases are enzymatically converted. Coupled decoding of bases across the original and copy strand provides a phased digital readout. Methods are demonstrated on human genomic DNA and cell-free DNA from a blood sample of a patient with cancer. The approach is accurate, requires low DNA input and has a simple workflow and analysis pipeline. Simultaneous, phased reading of genetic and epigenetic bases provides a more complete picture of the information stored in genomes and has applications throughout biomedicine.
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Affiliation(s)
- Jens Füllgrabe
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Walraj S Gosal
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Páidí Creed
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Sidong Liu
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Casper K Lumby
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - David J Morley
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Tobias W B Ost
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Albert J Vilella
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Shirong Yu
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Helen Bignell
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Philippa Burns
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Tom Charlesworth
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Beiyuan Fu
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Howerd Fordham
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Nicolas J Harding
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Olga Gandelman
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Paula Golder
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Christopher Hodson
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Mengjie Li
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Marjana Lila
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Yang Liu
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Joanne Mason
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Jason Mellad
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Jack M Monahan
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Oliver Nentwich
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Alexandra Palmer
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Michael Steward
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Minna Taipale
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Audrey Vandomme
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Rita Santo San-Bento
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Ankita Singhal
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Julia Vivian
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Natalia Wójtowicz
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Nathan Williams
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Nicolas J Walker
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Nicola C H Wong
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Gary N Yalloway
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Joanna D Holbrook
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK.
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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3
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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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Qiao L, Cao X, Tang H, Yu Z, Shi J, Xue Y, Wang T, Liang Y, Huang C, Wang J. White blood cell count affects fetal fraction and test failure rates in noninvasive prenatal screening. Front Med (Lausanne) 2023; 10:1088745. [PMID: 36817785 PMCID: PMC9932807 DOI: 10.3389/fmed.2023.1088745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Objective To investigate the effects of white blood cell (WBC) count on fetal fraction (FF), which is an essential quality control for obtaining reliable results, and on the rate of screen failures in noninvasive prenatal screening (NIPS). Methods Noninvasive prenatal screening, serum lipid and liver enzyme level measurements, and WBC count were performed for 4,281 pregnancies with male fetuses. After adjusting for confounders, including the maternal characteristics and alanine aminotransferase (ALT) levels, the effect of WBC count on FF and test failure rate was measured by linear and logistic regression analyses. Results Fetal fraction was negatively associated with BMI, ALT, IVF conceptions, and WBC count and positively correlated with gestational age in the multivariate linear regression model. Moreover, WBC count was the most important factor affecting FF after BMI according to the standardization coefficient analysis. In the 4,281 pregnancy samples with male fetuses, FF decreased with WBC count from 11.45% at ≤8 to 9.02% at >12, and FF markedly decreased to 7.40% in pregnancies with a higher WBC count (>12) and higher BMI (≥25 kg/m2). Meanwhile, the test failure rates were significantly higher in the WBC count > 12 group (4.29%) than in the WBC count ≤ 8 group (0.89%). Notably, when the BMI of pregnancies with a WBC count of >12 was >25, the rate reached 7.53%. Subsequently, multivariate logistic regression analysis further confirmed that an increased BMI and WBC count were independently and significantly associated with the test failure rates. Conclusion An increased WBC count was associated with lower FF and higher test failure rates, suggesting that these important factors should be carefully considered during genetic counseling in pregnant women who decide to undergo blood collection or resampling.
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Affiliation(s)
- Longwei Qiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - XiaoJu Cao
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Haoyu Tang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zheng Yu
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jingye Shi
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ying Xue
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ting Wang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| | - Chao Huang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
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5
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Loyfer N, Magenheim J, Peretz A, Cann G, Bredno J, Klochendler A, Fox-Fisher I, Shabi-Porat S, Hecht M, Pelet T, Moss J, Drawshy Z, Amini H, Moradi P, Nagaraju S, Bauman D, Shveiky D, Porat S, Dior U, Rivkin G, Or O, Hirshoren N, Carmon E, Pikarsky A, Khalaileh A, Zamir G, Grinbaum R, Abu Gazala M, Mizrahi I, Shussman N, Korach A, Wald O, Izhar U, Erez E, Yutkin V, Samet Y, Rotnemer Golinkin D, Spalding KL, Druid H, Arner P, Shapiro AMJ, Grompe M, Aravanis A, Venn O, Jamshidi A, Shemer R, Dor Y, Glaser B, Kaplan T. A DNA methylation atlas of normal human cell types. Nature 2023; 613:355-364. [PMID: 36599988 PMCID: PMC9811898 DOI: 10.1038/s41586-022-05580-6] [Citation(s) in RCA: 119] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/18/2022] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic mark that governs gene expression and chromatin organization, thus providing a window into cellular identity and developmental processes1. Current datasets typically include only a fraction of methylation sites and are often based either on cell lines that underwent massive changes in culture or on tissues containing unspecified mixtures of cells2-5. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing, allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell type are more than 99.5% identical, demonstrating the robustness of cell identity programmes to environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny and identifies methylation patterns retained since embryonic development. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hypermethylated loci are rare and are enriched for CpG islands, Polycomb targets and CTCF binding sites, suggesting a new role in shaping cell-type-specific chromatin looping. The atlas provides an essential resource for study of gene regulation and disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
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Affiliation(s)
- Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Merav Hecht
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tsuria Pelet
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zeina Drawshy
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | | | - Dvora Bauman
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Shveiky
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shay Porat
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri Dior
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gurion Rivkin
- Department of Orthopedics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omer Or
- Department of Orthopedics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Hirshoren
- Department of Otolaryngology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Einat Carmon
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Surgery, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Alon Pikarsky
- Surgery Division, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Abed Khalaileh
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gideon Zamir
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronit Grinbaum
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Machmud Abu Gazala
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ido Mizrahi
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noam Shussman
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Korach
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uzi Izhar
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eldad Erez
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vladimir Yutkin
- Department of Urology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Devorah Rotnemer Golinkin
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kirsty L Spalding
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Forensic Medicine, The National Board of Forensic Medicine, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine (H7) and Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - A M James Shapiro
- Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, Alberta, Canada
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alex Aravanis
- GRAIL, Inc., Menlo Park, CA, USA
- Illumina, Inc., San Diego, CA, USA
| | | | | | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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Huang E, Mengel M, Clahsen-van Groningen MC, Jackson AM. Diagnostic Potential of Minimally Invasive Biomarkers: A Biopsy-centered Viewpoint From the Banff Minimally Invasive Diagnostics Working Group. Transplantation 2023; 107:45-52. [PMID: 36508645 PMCID: PMC9746335 DOI: 10.1097/tp.0000000000004339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
With recent advances and commercial implementation of minimally invasive biomarkers in kidney transplantation, new strategies for the surveillance of allograft health are emerging. Blood and urine-based biomarkers can be used to detect the presence of rejection, but their applicability as diagnostic tests has not been studied. A Banff working group was recently formed to consider the potential of minimally invasive biomarkers for integration into the Banff classification for kidney allograft pathology. We review the existing data on donor-derived cell-free DNA, blood and urine transcriptomics, urinary protein chemokines, and next-generation diagnostics and conclude that the available data do not support their use as stand-alone diagnostic tests at this point. Future studies assessing their ability to distinguish complex phenotypes, differentiate T cell-mediated rejection from antibody-mediated rejection, and function as an adjunct to histology are needed to elevate these minimally invasive biomarkers from surveillance tests to diagnostic tests.
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Affiliation(s)
- Edmund Huang
- Division of Nephrology, Department of Medicine, Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Michael Mengel
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Marian C. Clahsen-van Groningen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Institute of Experimental and Systems Biology, RWTH Aachen University, Aachen, Germany
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Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
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8
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Epigenetic regulation of fetal brain development in pig. Gene 2022; 844:146823. [PMID: 35988784 DOI: 10.1016/j.gene.2022.146823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 02/01/2023]
Abstract
How fetal brain development is regulated at the molecular level is not well understood. Due to ethical challenges associated with research on the human fetus, large animals particularly pigs are increasingly used to study development and disorders of fetal brain. The pig fetal brain grows rapidly during the last ∼ 50 days before birth which is around day 60 (d60) of pig gestation. But what regulates the onset of accelerated growth of the brain is unknown. The current study tests the hypothesis that epigenetic alteration around d60 is involved in the onset of rapid growth of fetal brain of pig. To test this hypothesis, DNA methylation changes of fetal brain was assessed in a genome-wide manner by Enzymatic Methyl-seq (EM-seq) during two gestational periods (GP): d45 vs. d60 (GP1) and d60 vs. d90 (GP2). The cytosine-guanine (CpG) methylation data was analyzed in an integrative manner with the RNA-seq data generated from the same brain samples from our earlier study. A neural network based modeling approach was implemented to learn changes in methylation patterns of the differentially expressed genes, and then predict methylations of the brain in a genome-wide manner during rapid growth. This approach identified specific methylations that changed in a mutually informative manner during rapid growth of the fetal brain. These methylations were significantly overrepresented in specific genic as well as intergenic features including CpG islands, introns, and untranslated regions. In addition, sex-bias methylations of known single nucleotide polymorphic sites were also identified in the fetal brain ide during rapid growth.
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Xiao Y, Ju L, Qian K, Jin W, Wang G, Zhao Y, Jiang W, Liu N, Wu K, Peng M, Cao R, Li S, Shi H, Gong Y, Zheng H, Liu T, Luo Y, Ma H, Chang L, Li G, Cao X, Tian Y, Xu Z, Yang Z, Shan L, Guo Z, Yao D, Zhou X, Chen X, Guo Z, Liu D, Xu S, Ji C, Yu F, Hong X, Luo J, Cao H, Zhang Y, Wang X. Non-invasive diagnosis and surveillance of bladder cancer with driver and passenger DNA methylation in a prospective cohort study. Clin Transl Med 2022; 12:e1008. [PMID: 35968916 PMCID: PMC9377153 DOI: 10.1002/ctm2.1008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND State-of-art non-invasive diagnosis processes for bladder cancer (BLCA) harbour shortcomings such as low sensitivity and specificity, unable to distinguish between high- (HG) and low-grade (LG) tumours, as well as inability to differentiate muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). This study investigates a comprehensive characterization of the entire DNA methylation (DNAm) landscape of BLCA to determine the relevant biomarkers for the non-invasive diagnosis of BLCA. METHODS A total of 304 samples from 224 donors were enrolled in this multi-centre, prospective cohort study. BLCA-specific DNAm signature discovery was carried out with genome-wide bisulfite sequencing in 32 tumour tissues and 12 normal urine samples. A targeted sequencing assay for BLCA-specific DNAm signatures was developed to categorize tumour tissue against normal urine, or MIBC against NMIBC. Independent validation was performed with targeted sequencing of 259 urine samples in a double-blinded manner to determine the clinical diagnosis and prognosis value of DNAm-based classification models. Functions of genomic region harbouring BLCA-specific DNAm signature were validated with biological assays. Concordances of pathology to urine tumour DNA (circulating tumour DNA [ctDNA]) methylation, genomic mutations or other state-of-the-art diagnosis methods were measured. RESULTS Genome-wide DNAm profile could accurately classify LG tumour from HG tumour (LG NMIBC vs. HG NMIBC: p = .038; LG NMIBC vs. HG MIBC, p = .00032; HG NMIBC vs. HG MIBC: p = .82; Student's t-test). Overall, the DNAm profile distinguishes MIBC from NMIBC and normal urine. Targeted-sequencing-based DNAm signature classifiers accurately classify LG NMIBC tissues from HG MIBC and could detect tumours in urine at a limit of detection of less than .5%. In tumour tissues, DNAm accurately classifies pathology, thus outperforming genomic mutation or RNA expression profiles. In the independent validation cohort, pre-surgery urine ctDNA methylation outperforms fluorescence in situ hybridization (FISH) assay to detect HG BLCA (n = 54) with 100% sensitivity (95% CI: 82.5%-100%) and LG BLCA (n = 26) with 62% sensitivity (95% CI: 51.3%-72.7%), both at 100% specificity (non-BLCA: n = 72; 95% CI: 84.1%-100%). Pre-surgery urine ctDNA methylation signature correlates with pathology and predicts recurrence and metastasis. Post-surgery urine ctDNA methylation (n = 61) accurately predicts recurrence-free survival within 180 days, with 100% accuracy. CONCLUSION With the discovery of BLCA-specific DNAm signatures, targeted sequencing of ctDNA methylation outperforms FISH and DNA mutation to detect tumours, predict recurrence and make prognoses.
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Rosenheck J, Keller B, Fehringer G, Demko Z, Bohrade S, Ross D. Why Cell-Free DNA Can Be a “Game Changer” for Lung Allograft Monitoring for Rejection and Infection. CURRENT PULMONOLOGY REPORTS 2022; 11:75-85. [PMID: 35910533 PMCID: PMC9315332 DOI: 10.1007/s13665-022-00292-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2022] [Indexed: 02/06/2023]
Abstract
Purpose of Review Although there has been improvement in short-term clinical outcomes for patients following lung transplant (LT), advances have not translated into longer-term allograft survival. Furthermore, invasive biopsies are still standard of practice for monitoring LT recipients for allograft injury. We review the relevant literature supporting the role of using plasma donor-derived cell-free DNA (dd-cfDNA) as a non-invasive biomarker for LT allograft injury surveillance and discuss future research directions. Recent Findings Accumulating data has demonstrated that dd-cfDNA is associated with molecular and cellular injury due to acute (cellular and antibody-mediated) rejection, chronic lung allograft dysfunction, and relevant infectious pathogens. Strong performance in distinguishing rejection and allograft injury from stable patients has set the stage for clinical trials to assess dd-cfDNA utility for surveillance of LT patients. Research investigating the potential role of dd-cfDNA methylation signatures to map injured tissue and cell-free DNA in detecting allograft injury-related pathogens is ongoing. Summary There is an amassed breadth of clinical data to support a role for dd-cfDNA in monitoring rejection and other forms of allograft injury. Rigorously designed, robust clinical trials that encompass the diversity in patient demographics are paramount to furthering our understanding and adoption of plasma dd-cfDNA for surveillance of lung allograft health.
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Affiliation(s)
- J.P. Rosenheck
- Division of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University, Columbus, OH USA
| | - B.C. Keller
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA USA
| | - G. Fehringer
- Medical Affairs in Organ Health, Natera, Inc., San Carlos, USA
| | - Z.P. Demko
- Medical Affairs in Organ Health, Natera, Inc., San Carlos, USA
| | - S.M. Bohrade
- Medical Affairs in Organ Health, Natera, Inc., San Carlos, USA
| | - D.J. Ross
- Medical Affairs in Organ Health, Natera, Inc., San Carlos, USA
- Lung Transplant & Molecular Diagnostics, Natera, Inc, San Carlos, CA USA
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Chen M, Chan RWY, Cheung PPH, Ni M, Wong DKL, Zhou Z, Ma MJL, Huang L, Xu X, Lee WS, Wang G, Lui KO, Lam WKJ, Teoh JYC, Ng CF, Jiang P, Chan KCA, Chiu RWK, Lo YMD. Fragmentomics of urinary cell-free DNA in nuclease knockout mouse models. PLoS Genet 2022; 18:e1010262. [PMID: 35793278 PMCID: PMC9258866 DOI: 10.1371/journal.pgen.1010262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Urinary cell-free DNA (ucfDNA) is a potential biomarker for bladder cancer detection. However, the biological characteristics of ucfDNA are not well understood. We explored the roles of deoxyribonuclease 1 (DNASE1) and deoxyribonuclease 1-like 3 (DNASE1L3) in the fragmentation of ucfDNA using mouse models. The deletion of Dnase1 in mice (Dnase1-/-) caused aberrations in ucfDNA fragmentation, including a 24-fold increase in DNA concentration, and a 3-fold enrichment of long DNA molecules, with a relative decrease of fragments with thymine ends and reduction of jaggedness (i.e., the presence of single-stranded protruding ends). In contrast, such changes were not observed in mice with Dnase1l3 deletion (Dnase1l3-/-). These results suggested that DNASE1 was an important nuclease contributing to the ucfDNA fragmentation. Western blot analysis revealed that the concentration of DNASE1 protein was higher in urine than DNASE1L3. The native-polyacrylamide gel electrophoresis zymogram showed that DNASE1 activity in urine was higher than that in plasma. Furthermore, the proportion of ucfDNA fragment ends within DNase I hypersensitive sites (DHSs) was significantly increased in Dnase1-deficient mice. In humans, patients with bladder cancer had lower proportions of ucfDNA fragment ends within the DHSs when compared with participants without bladder cancer. The area under the curve (AUC) for differentiating patients with and without bladder cancer was 0.83, suggesting the analysis of ucfDNA fragmentation in the DHSs may have potential for bladder cancer detection. This work revealed the intrinsic links between the nucleases in urine and ucfDNA fragmentomics. Cell-free DNA (cfDNA) in various bodily fluids, for example blood plasma and urine, is of great importance for noninvasive cancer detection and noninvasive prenatal testing. Many emerging studies on the fragmentation of plasma DNA (i.e., fragmentomics) have received much recent interest. However, the fragmentomics in urinary cfDNA (ucfDNA) remained much less explored. In this study, we explored the biological links between ucfDNA fragmentation and DNA nucleases, using mice for which either the Dnase1 or Dnase1l3 gene was genetically inactivated. Interestingly, we found that the deletion of Dnase1, but not Dnase1l3, caused dramatic alterations of ucfDNA fragmentation patterns, including the elevation of DNA concentration, lengthening of fragment size, disruptions of ucfDNA end motifs (i.e., nucleotide sequences at fragment end) and the jagged ends (i.e., the single-stranded protruding ends). The proportion of fragment ends within DNase I hypersensitive sites (DHSs) was greatly increased in mice with the Dnase1 deletion. Such ucfDNA fragmentation pattern surrounding DHSs holds potential for classifying the human subjects with and without bladder cancer. The analysis combining various fragmentomic features could further improve the performance for bladder cancer detection, with an AUC of 0.91. This study has shed mechanistic insights into fragmentomics of ucfDNA in urine and has opened up new possibilities for applying ucfDNA fragmentomics in a clinical context.
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Affiliation(s)
- Meihui Chen
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rebecca W. Y. Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peter P. H. Cheung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Meng Ni
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Danny K. L. Wong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ze Zhou
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Mary-Jane L. Ma
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Liangbo Huang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xinzhou Xu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing-Shan Lee
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Guangya Wang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Kathy O. Lui
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - W. K. Jacky Lam
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Jeremy Y. C. Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K. C. Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W. K. Chiu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y. M. Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- * E-mail:
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12
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Shen Y, Lian D, Shi K, Gao Y, Hu X, Yu K, Zhao Q, Feng C. Cancer Risk and Mutational Patterns Following Organ Transplantation. Front Cell Dev Biol 2022; 10:956334. [PMID: 35837331 PMCID: PMC9274140 DOI: 10.3389/fcell.2022.956334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid development of medical technology and widespread application of immunosuppressive drugs have improved the success rate of organ transplantation significantly. However, the use of immunosuppressive agents increases the frequency of malignancy greatly. With the prospect of “precision medicine” for tumors and development of next-generation sequencing technology, more attention has been paid to the application of high-throughput sequencing technology in clinical oncology research, which is mainly applied to the early diagnosis of tumors and analysis of tumor-related genes. All generations of cancers carry somatic mutations, meanwhile, significant differences were observed in mutational signatures across tumors. Systematic sequencing of cancer genomes from patients after organ transplantation can reveal DNA damage and repair processes in exposed cancer cells and their precursors. In this review, we summarize the application of high-throughput sequencing and organoids in the field of organ transplantation, the mutational patterns of cancer genomes, and propose a new research strategy for understanding the mechanism of cancer following organ transplantation.
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Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuefeng Gao
- College of Applied Engineering, Henan University of Science and Technology, Sanmenxia, China
- Sanmenxia Polytechnic, Sanmenxia, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kun Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
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13
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Qian X, Shah P, Agbor-Enoh S. Noninvasive biomarkers in heart transplant: 2020-2021 year in review. Curr Opin Organ Transplant 2022; 27:7-14. [PMID: 34939959 PMCID: PMC8711631 DOI: 10.1097/mot.0000000000000945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE OF REVIEW Endomyocardial biopsy (EMB), the current gold standard for cardiac allograft monitoring is invasive, may have a low sensitivity and is associated with significant variability in histopathologic interpretation. Fortunately, on-going research is identifying noninvasive biomarkers that address some of these limitations. This review provides an update on noninvasive blood-based methods for rejection surveillance and diagnosis in heart transplantation. RECENT FINDINGS Recent studies highlight good test performance to detect acute rejection for donor-derived cell-free DNA (dd-cfDNA) and microRNAs (miR). dd-cfDNA is sensitive, nonspecific, and has a high negative predictive value for acute cellular and antibody-mediated rejection. Clinical utility trials are being planned to test its role as a rule-out test for acute rejection as compared to the EMB. miRs may have an added advantage as it may phenotype the subtypes of rejection alleviating the need for an EMB or permitting the initiation of targeted therapy while awaiting the results of the EMB. SUMMARY In this review, we discuss recent advances in the field of noninvasive biomarkers to detect allograft rejection after heart transplant. We provide a perspective of additional studies needed to prove their clinical utility and bring these biomarkers to widescale clinical use.
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Affiliation(s)
- Xiaoxiao Qian
- Cardiovascular Medicine, Inova Heart and Vascular Institute, Falls Church VA
| | - Palak Shah
- Heart Failure, MCS and Transplant, Inova Heart and Vascular Institute, Falls Church VA
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT), Bethesda, MD
- Laboratory of Applied Precision Omics, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
- Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD
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14
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Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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15
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Fearon WF, Valantine HA. Can We Predict Rejection Early After Heart Transplantation? Circulation 2021; 144:1473-1475. [PMID: 34723641 DOI: 10.1161/circulationaha.121.056808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- William F Fearon
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, CA (W.F.F., H.A.V.)
- VA Palo Alto Health Care System, CA (W.F.F.)
| | - Hannah A Valantine
- Division of Cardiovascular Medicine and Cardiovascular Institute, Stanford University, CA (W.F.F., H.A.V.)
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Lo YMD. Noninvasive prenatal testing: Advancing through a virtuous circle of science, technology and clinical applications. Prenat Diagn 2021; 41:1190-1192. [PMID: 34585773 DOI: 10.1002/pd.5978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Since the discovery of cell-free fetal DNA in maternal blood in 1997, the interplay of basic scientific observations and technological developments have continued to drive new clinical applications in the field. AIMS This commentary discusses a number of examples in this virtuous circle of science, technology and clinical applications. MATERIALS & METHODS: Commentary and literature review. RESULTS One example of technological developments is the detection technologies for detecting circulating DNA, moving from conventional PCR, to real-time PCR, to massively parallel sequencing. One example of basic scientific understanding is the size and fragmentation patterns of circulating DNA. DISCUSSION Beyond creating a global paradigm in prenatal medicine, the development of noninvasive prenatal testing has also impacted other areas such as cancer screening and transplantation monitoring. Finally, the commentary looks forward to what might be in store in the next decade.
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Affiliation(s)
- Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, New Territories, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
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