Skip to main content

2020 | OriginalPaper | Buchkapitel

Estimating the Rate of Cell Type Degeneration from Epigenetic Sequencing of Cell-Free DNA

verfasst von : Christa Caggiano, Barbara Celona, Fleur Garton, Joel Mefford, Brian Black, Catherine Lomen-Hoerth, Andrew Dahl, Noah Zaitlen

Erschienen in: Research in Computational Molecular Biology

Verlag: Springer International Publishing

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

Cells die at different rates as a function of disease state, age, environmental exposure, and behavior [8, 10]. Knowing the rate at which cells die is a fundamental scientific question, with direct translational applicability. A quantifiable indication of cell death could facilitate disease diagnosis and prognosis, prioritize patients for admission into clinical trials, and improve evaluations of treatment efficacy and disease progression [1, 4, 14, 16]. Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising non-invasive biomarker for cell death.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literatur
1.
Zurück zum Zitat Bowser, R., Turner, M.R., Shefner, J.: Biomarkers in amyotrophic lateral sclerosis: opportunities and limitations. Nat. Rev. Neurol. 7, 631–8 (2011)CrossRef Bowser, R., Turner, M.R., Shefner, J.: Biomarkers in amyotrophic lateral sclerosis: opportunities and limitations. Nat. Rev. Neurol. 7, 631–8 (2011)CrossRef
2.
Zurück zum Zitat Houseman, E.A., Molitor, J., Marsit, C.J.: Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 30, 1431–1439 (2014)CrossRef Houseman, E.A., Molitor, J., Marsit, C.J.: Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 30, 1431–1439 (2014)CrossRef
4.
Zurück zum Zitat Joka, D., et al.: Prospective biopsy-controlled evaluation of cell death biomarkers for prediction of liver fibrosis and nonalcoholic steatohepatitis. Hepatology 55, 455–64 (2012)CrossRef Joka, D., et al.: Prospective biopsy-controlled evaluation of cell death biomarkers for prediction of liver fibrosis and nonalcoholic steatohepatitis. Hepatology 55, 455–64 (2012)CrossRef
5.
Zurück zum Zitat Lehmann-Werman, R., et al.: Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc. Natl. Acad. Sci. 113, E1826–E1834 (2016)CrossRef Lehmann-Werman, R., et al.: Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc. Natl. Acad. Sci. 113, E1826–E1834 (2016)CrossRef
6.
Zurück zum Zitat Liu, X., et al.: Comprehensive DNA methylation analysis of tissue of origin of plasma cell-free DNA by methylated CpG tandem amplification and sequencing (MCTA-Seq). Clin. Epigenetics 11, 93 (2019)CrossRef Liu, X., et al.: Comprehensive DNA methylation analysis of tissue of origin of plasma cell-free DNA by methylated CpG tandem amplification and sequencing (MCTA-Seq). Clin. Epigenetics 11, 93 (2019)CrossRef
8.
Zurück zum Zitat Meier, P., Finch, A., Evan, G.: Apoptosis in development. Nature 407, 796–801 (2000)CrossRef Meier, P., Finch, A., Evan, G.: Apoptosis in development. Nature 407, 796–801 (2000)CrossRef
9.
Zurück zum Zitat Moss, J., et al.: Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat. Commun. 9, 1–12 (2018)CrossRef Moss, J., et al.: Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat. Commun. 9, 1–12 (2018)CrossRef
10.
11.
Zurück zum Zitat Rahmani, E., Schweiger, R., Shenhav, L., Eskin, E., Halperin, E.: A Bayesian framework for estimating cell type composition from DNA methylation without the need for methylation reference. In: Sahinalp, S.C. (ed.) RECOMB 2017. LNCS, vol. 10229, pp. 207–223. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-56970-3_13CrossRef Rahmani, E., Schweiger, R., Shenhav, L., Eskin, E., Halperin, E.: A Bayesian framework for estimating cell type composition from DNA methylation without the need for methylation reference. In: Sahinalp, S.C. (ed.) RECOMB 2017. LNCS, vol. 10229, pp. 207–223. Springer, Cham (2017). https://​doi.​org/​10.​1007/​978-3-319-56970-3_​13CrossRef
12.
Zurück zum Zitat Rahmani, E., et al.: Sparse PCA corrects for cell-type heterogeneity in epigenome-wide association studies. Nat. Methods 13, 443–445 (2016)CrossRef Rahmani, E., et al.: Sparse PCA corrects for cell-type heterogeneity in epigenome-wide association studies. Nat. Methods 13, 443–445 (2016)CrossRef
13.
Zurück zum Zitat Snyder, M.W., Kircher, M., Hill, A.J., Daza, R.M., Shendure, J.: Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164, 57–68 (2016)CrossRef Snyder, M.W., Kircher, M., Hill, A.J., Daza, R.M., Shendure, J.: Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164, 57–68 (2016)CrossRef
14.
Zurück zum Zitat Turner, M.R., et al.: Mechanisms, models and biomarkers in amyotrophic lateral sclerosis. Amyotroph. Lateral Scler. Frontotemporal Degener. 14, 19–32 (2013)CrossRef Turner, M.R., et al.: Mechanisms, models and biomarkers in amyotrophic lateral sclerosis. Amyotroph. Lateral Scler. Frontotemporal Degener. 14, 19–32 (2013)CrossRef
15.
Zurück zum Zitat Verber, N.S., et al.: Biomarkers in motor neuron disease: a state of the art review. Front. Neurol. 10, 291 (2019)CrossRef Verber, N.S., et al.: Biomarkers in motor neuron disease: a state of the art review. Front. Neurol. 10, 291 (2019)CrossRef
16.
Zurück zum Zitat Vila, M., Przedborski, S.: Targeting programmed cell death in neurodegenerative diseases. Nat. Rev. Neurosci. 4, 365–375 (2003)CrossRef Vila, M., Przedborski, S.: Targeting programmed cell death in neurodegenerative diseases. Nat. Rev. Neurosci. 4, 365–375 (2003)CrossRef
Metadaten
Titel
Estimating the Rate of Cell Type Degeneration from Epigenetic Sequencing of Cell-Free DNA
verfasst von
Christa Caggiano
Barbara Celona
Fleur Garton
Joel Mefford
Brian Black
Catherine Lomen-Hoerth
Andrew Dahl
Noah Zaitlen
Copyright-Jahr
2020
DOI
https://doi.org/10.1007/978-3-030-45257-5_21