Annals of the New York Academy of Sciences, Circulating Nucleic Acids in Plasma and Serum V / Edition 1

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DNA and RNA fractions have been isolated from whole blood, serum, plasma, the surface of blood cells, and urine from both healthy persons and patients. Specific fragments have been identified as being related to particular disorders, for example, diabetes, cancer, myocardial infarction, and stroke. The ability to isolate these fractions and assess their relationship to specific diseases makes early noninvasive diagnosis possible. This volume reports on the most recent progress in this field, including chapters on developing protocols for nucleic acid extraction, determining the origin of the circulating nucleic acids, the capacity of these nucleic acids to enter cells and exhibit biological activity, isolating and testing fetal cells from maternal blood, and discussing the clinical implications of these discoveries and developing the techniques that will bring them into clinical application.

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Table of Contents

Preface: Peter B. Gahan and R. Swaminathan.

Circulating Nucleic Acids in Plasma and Serum: RecentDevelopments: Peter B. Gahan and R. Swaminathan.

Part I. Basic Research:.

1. Metabolic DNA as the Origin of Spontaneously Released DNA?:Peter Gahan, Philippe Anker, and Maurice Stroun.

2. Circulating DNA: Its Origin and Fluctuation: Maniesh van derVaart and Piet J. Pretorius.

3. The Origin of Elevated Levels of Circulating DNA in BloodPlasma of Premature Newborns: N. O. Tuaeva, Z.I. Abramova and V. V.Sofronov.

4. The Effect of Protein Transport Inhibitors on the Productionof Extracellular DNA: Evgeniy S. Morozkin, Tatyana I. Babochkina,Valentin V. Vlassov, and Pavel P. Laktionov.

5. Binding and Penetration of Methylated DNA into Primary andTransformed Human Cells: Tatyana E. Skvortsova, Valentin V.Vlassov, and Pavel P. Laktionov.

6. Extracellular DNA Fragments: Factors of Stress Signallingbetween X-irradiated and Non-irradiated Human Lymphocytes: AlekseiV. Ermakov, Svetlana V. Kostyuk, Marina S. Konkova, Natalya A.Egolina, Elena M. Malinovskaya, and Natalya N. Veiko.

7. Isolation and Sequencing of Short Cell-Surface-Bound DNA:Vera S. Mal’shakova, Dmitry V. Pyshnyi, Alexander A. Bondar,Valentin V. Vlassov, and Pavel P. Laktionov.

8. Extracellular RNA Spontaneously Internalized by Human CellsUndergo Deamination of Adenosines: Elena V. Kuligina, Oksana V.Vratskih, Dmitry V. Semenov, Vera A. Matveea, and Vladimir A.Richter.

9. Circulating Nucleic Acids in the Assessment of EndogenousGrowth Hormone Production: H. Thakkar, A.N. Butt, J. Powrie, R.Holt, and R. Swaminathan.

10. The Involvement of Different Mobile Line Copies of BloodPlasma and Extrachromosomal DNA of Liver Cells in Systemic AdaptiveResponse: Sophiya S. Sherlina and Viktor G. Vladimirov.

Part II. Methodology:.

11. Transrenal Nucleic Acids from Proof-of-Principle to ClinicalTests: Problems and Solutions: Hovsep S. Melkonyan, W. John Feaver,Erik Meyer, Vladimir Scheinker, Eugene M. Shekhtman, Zhenghan Xin,and Samuil R. Umansky.

12. Removal of High Molecular Weight DNA by CarboxylatedMagnetic Beads Enhances the Detection of Mutated K-ras DNA inUrine: Ying-Hsiu Su, Janet Song, Zhili Wang, Xiao-He Wang, MengjunWang, Dean E. Brenner, and Timothy M. Block.

13. A Method for Characterization of Total Circulating DNA:Maniesh van der Vaart and Piet J. Pretorius.

14. Isolation and Extraction of Circulating Tumour DNA fromPatients with Small Cell Lung Cancer: Ruth E Board, Victoria SWilliams, Lucy Knight , Jacqueline Shaw, Alastair Greystoke,Malcolm Ranson, Caroline Dive, Fiona H Blackhall, and AndrewHughes.

15. Stability of β–Actin mRNA in Plasma: N.C.Holford, H.S. Sandhu, H. Thakkar, A.N. Butt, and R.Swaminathan.

16. Normalization of Circulating Nucleic Acid Results. Should WeUse β-Actin?: N.C. Holford, A. Ramoutar, A.N. Butt, and R.Swaminathan.

17. Artificial BOX C/D RNA Targeted to Branch Point AdenosineImpairs Splicing by Exon Exclusion: Dmitry V. Semenov, Oksana V.Vratskih, Elena V. Kuligina, and Vladimir A. Richter.

18. Optimization of Purification of Human Cell-free mRNA fromPlasma: Tadeja Dovc-Drnovsek, Barbara Emersic, Primoz Rozman, DarkoCerne, and Jana Lukac-Bajalo.

19. Fragments of Non-coding RNA in Plasma of Human Blood: DmitryV. Semenov, Dmitry N. Baryakin, Tatyana P. Kamynina, Elena V.Kuligina, and Vladimir A. Richter.

20. An Improved Method for the Isolation of Free-circulatingPlasma DNA and Cell-free DNA from Other Body Fluids: ChristophKirsch, Sabine Weickmann, Bernd Schmidt, and MichaelFleischhacker.

Part III. Fetal Nucleic Acids:.

21. Fetal Nucleic Acids in Maternal Plasma: Towards theDevelopment of Noninvasive Prenatal Diagnosis of Fetal ChromosomalAneuploidies: Y.M. Dennis Lo.

22. Phenotype and mRNA Expression of SyncytiotrophoblastMicroparticles Isolated from Human Placenta: Belinda Kumpel,May-Jean King, Suren Sooranna,Dave Jackson, Jane Eastlake, RongCheng, and Mark Johnson.

23. Fetal Sex Identification in Maternal Plasma Using DhortTandem Repeats on Chromosome X: Gennaro Vecchione, MichelaTomaiuolo, Michelina Sarno, Donatella Colaizzo,Rosella Petraroli,Maria Matteo, Pantaleo Greco, Elvira Grandone, and MaurizioMargaglione.

24. A New Y-chromosome Marker for Noninvasive Fetal GenderDetermination: Olga B. Vainer, Aleksey V. Katokhin, Sergey M.Kustov , Valentin V. Vlassov, and Pavel P. Laktionov.

Part IV. Circulating Nucleic Acids and Cancer:.

25. DNA Integrity in Plasma and Serum of Patients with Malignantand Benign Diseases: Stefan Holdenrieder, Alexander Burges, OliverReich, Fritz W. Spelsberg, and Petra Stieber.

26. Quantification of LINE1 in Circulating DNA as a MolecularBiomarker of Breast Cancer: Eiji Sunami, Anh-Thu Vu, Sandy L.Nguyen, Armando E Giuliano, and Dave S. B. Hoo.

27. Effect of Adjuvant Chemotherapy on Integrity of Free SerumDNA in Patients with Breast Cancer: Ugur Deligezer, Yesim Eralp,Elif Z. Akisik, Ebru E. Akisik, Pinar Saip,Erkan Topuz, and NejatDalay.

28. Clinical Relevance of Circulating Nucleosomes in CancerDisease: Stefan Holdenrieder, Dorothea Nagel, Andreas Schalhorn,Volker Heinemann, Ralf Wilkowski, Joachim von Pawel, HanneloreRaith, Knut Feldmann, Andreas E Kremer, Susanne Müller, SandraGeiger, Gerhard F Hamann, Dietrich Seidel, and Petra Stieber.

29. Detection and Monitoring of Cell-Free DNA in Blood ofPatients with Colorectal Cancer: Heidi Schwarzenbach, JanStoehlmacher, Klaus Pantel, and Eray Goekkurt.

30. Detection of Mutated K-ras DNA in Urine, Plasma and Serumfrom Patients with Colorectal Carcinoma or Adenomatous Polyps:Ying-Hsiu Su, Mengjun Wang, Dean E. Brenner, Pamela A. Norton, andTimothy M. Block.

31. Integrity of Cell-free Plasma DNA in Patients with LungCancer and Non-malignant Lung Disease: Bernd Schmidt, SabineWeickmann, Christian Witt, and Michael Fleischhacker.

32. Cell-surface-bound Circulating DNA as A Prognostic Factor ofLung Cancer: Svetlana N. Tamkovich, Nikolai V. Litviakov, Olga E.Bryzgunova, Aleksey Yu. Dobrodeev, Elena Yu. Rykova, Sergey A.Tuzikov, Aleksandr A. Zav’ialov, Valentin V. Vlassov,Nadezhda V. Cherdyntseva, and Pavel P. Laktionov.

33. Deoxyribonuclease Activity and Circulating DNA Concentrationin Blood Plasma of Prostate Tumor Patients: Anna V. Cherepanova,Svetlana N. Tamkovich, Olga E. Bryzgunova, Valentin V. Vlassov, andPavel P. Laktionov.

34. Methylation–specific Sequencing of GSTP1 Gene Promoterin Circulating/Extracellular DNA from Blood and Urine of HealthyDonors and Prostate Cancer Patients: Olga E. Bryzgunova, Evgeniy S.Morozkin, Sergey V. Yarmoschuk, Valentin V. Vlassov, and Pavel P.Laktionov.

35. Circulating DNA in the Blood of Gastric Cancer Patients:Elena V. Kolesnikova, Svetlana N. Tamkovicha, Olga E. Bryzgunova,Petr I. Shelestyuk, Valentina I. Permyakova, Aleksandr S. Tuzikovd,Valentin V. Vlassov, Pavel P. Laktionov, and Elena Y. Rykova.

36. Methylation-based Analysis of Circulating DNA for BreastTumors Screening: Elena Y. Rykova, Galina A. Tsvetovskaya, GalinaI. Sergeeva, Valentin V. Vlassov, and Pavel P. Laktionov.

Part V. Circulating Nucleic Acids and Other Diseases:.

37. Overview of Circulating Nucleic Acids in Plasma/Serum:Update on Potential Prognostic and Diagnostic Value in PathologyExcluding Fetal Medicine and Oncology: Asif N. Butt and R.Swaminathan.

38. Effect of Hypoxia on Circulating Levels of Retina SpecificMessenger RNA in Type 2 Diabetes Mellitus: Amy Wong, Simon Merritt,Asif N. Butt, AdrianWilliams, and R. Swaminathan.

39. Retinal Specific mRNA in the Assessment of DiabeticRetinopathy: Z. Shalchi, H. S. Sandhu, A.N. Butt, S. Smith, J.Powrie, and R. Swaminathan.

40. Measurement of circulating Neuron Specific Enolase mRNA inDiabetes Mellitus: H. S. Sandhu, A.N. Butt, J. Powrie, and R.Swaminathan.

41. Hepatitis B Virus X-DNA: A Serum Marker for Early Detectionof Resistance Development during Lamivudine Therapy: Wei Zhang,Yan-Hong Li, Shao-Jun Zhu, Yan Zhang, Li Gong, Shu-Mei Wang, HansJörg Hacker, Claus Hobe Schröder, Dong-Sheng Cheng, andYing-Ming Feng.

42. Cell - free DNA of Patients with Cardiomyopathy and rDNAAlone Change the Frequency of Contraction of the Electrically PacedNeonatal Rat Ventricular Myocytes in Culture: N. Bulicheva, O.Fidelina, N. Mkrtumova, M. Neverova, A. Bogush, M. Bogush, O.Roginko, and N. Veiko.

43. Influence of Plasma DNA on Acid-base Balance, Blood GasMeasurement, and Oxygen Transport in Health and Stroke: Irina L.Konorova, Natalya N. Veiko, and Viktor E. Novikov.

44. Circulating 11β-Hydroxysteroid Dehydrogenase Type 1mRNA and Cardiovascular Risk Factors: Maise Al Bakir, Asif Butt,and R. Swaminathan.

45. Hypertension and circulating mRNA for11β-Hydroxysteroid Dehydrogenase Type II: S. Agalou, A. Butt,Phil Chowienczyk, and R. Swaminathan.

46. Cell-free Plasma DNA during Peritoneal Dialysis,Hemodialysis, and in Patients with Chronic Kidney Disease: MarieKorabecna, Sylvie Opatrna, Jan Wirth, Kamila Rulcova, Jan Eiselt,Frantisek Sefrna, and Ales Horinek.

47. Arrayed Primer EXtension (APEX) for the Non-InvasivePrenatal Diagnosis of β-thalassaemia Based on Detection ofSingle Nucleotide Polymorphisms: Thessalia Papasavva, IoannisKalikas, Andreanni Kyrri, and Marina Kleanthous.

48. The Housekeeping Gene (ga3pdh) and the Long InterspersedNuclear Element (line) in the Blood and Organs of the Rats Treatedwith Cocaine: Anatoliy M. Voskresenskiy and Lena S. Sun.

49. Extracellular Functional Non-Coding Nucleic Acid Bioaptamersand Angiotropin RNP Ribokines in Vascularization andSelf-Tolerance: 3D-Episcripts on Domains Shared in RegulatorProteins of the Vascular and Cancer Epigenome: Josef H. Wissler,Joerg E. Wissler, and Enno Logemann.

Index of Contributors

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