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

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Overview

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.

NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit www.blackwellpublishing.com/nyas.

ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to the Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Join.aspx for more information about becoming a member

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Table of Contents

Preface: Peter B. Gahan and R. Swaminathan.

Circulating Nucleic Acids in Plasma and Serum: Recent Developments: 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 der Vaart and Piet J. Pretorius.

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

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

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

6. Extracellular DNA Fragments: Factors of Stress Signalling between X-irradiated and Non-irradiated Human Lymphocytes: Aleksei V. 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 Cells Undergo 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 Endogenous Growth Hormone Production: H. Thakkar, A.N. Butt, J. Powrie, R. Holt, and R. Swaminathan.

10. The Involvement of Different Mobile Line Copies of Blood Plasma and Extrachromosomal DNA of Liver Cells in Systemic Adaptive Response: Sophiya S. Sherlina and Viktor G. Vladimirov.

Part II. Methodology:.

11. Transrenal Nucleic Acids from Proof-of-Principle to Clinical Tests: 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 Carboxylated Magnetic Beads Enhances the Detection of Mutated K-ras DNA in Urine: Ying-Hsiu Su, Janet Song, Zhili Wang, Xiao-He Wang, Mengjun Wang, 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 from Patients with Small Cell Lung Cancer: Ruth E Board, Victoria S Williams, Lucy Knight , Jacqueline Shaw, Alastair Greystoke, Malcolm Ranson, Caroline Dive, Fiona H Blackhall, and Andrew Hughes.

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 We Use β-Actin?: N.C. Holford, A. Ramoutar, A.N. Butt, and R. Swaminathan.

17. Artificial BOX C/D RNA Targeted to Branch Point Adenosine Impairs 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 from Plasma: Tadeja Dovc-Drnovsek, Barbara Emersic, Primoz Rozman, Darko Cerne, and Jana Lukac-Bajalo.

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

20. An Improved Method for the Isolation of Free-circulating Plasma DNA and Cell-free DNA from Other Body Fluids: Christoph Kirsch, Sabine Weickmann, Bernd Schmidt, and Michael Fleischhacker.

Part III. Fetal Nucleic Acids:.

21. Fetal Nucleic Acids in Maternal Plasma: Towards the Development of Noninvasive Prenatal Diagnosis of Fetal Chromosomal Aneuploidies: Y.M. Dennis Lo.

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

23. Fetal Sex Identification in Maternal Plasma Using Dhort Tandem Repeats on Chromosome X: Gennaro Vecchione, Michela Tomaiuolo, Michelina Sarno, Donatella Colaizzo,Rosella Petraroli, Maria Matteo, Pantaleo Greco, Elvira Grandone, and Maurizio Margaglione.

24. A New Y-chromosome Marker for Noninvasive Fetal Gender Determination: 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 Malignant and Benign Diseases: Stefan Holdenrieder, Alexander Burges, Oliver Reich, Fritz W. Spelsberg, and Petra Stieber.

26. Quantification of LINE1 in Circulating DNA as a Molecular Biomarker 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 Serum DNA in Patients with Breast Cancer: Ugur Deligezer, Yesim Eralp, Elif Z. Akisik, Ebru E. Akisik, Pinar Saip,Erkan Topuz, and Nejat Dalay.

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

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

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

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

32. Cell-surface-bound Circulating DNA as A Prognostic Factor of Lung 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 Concentration in Blood Plasma of Prostate Tumor Patients: Anna V. Cherepanova, Svetlana N. Tamkovich, Olga E. Bryzgunova, Valentin V. Vlassov, and Pavel P. Laktionov.

34. Methylation–specific Sequencing of GSTP1 Gene Promoter in Circulating/Extracellular DNA from Blood and Urine of Healthy Donors 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 Breast Tumors Screening: Elena Y. Rykova, Galina A. Tsvetovskaya, Galina I. 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 Pathology Excluding Fetal Medicine and Oncology: Asif N. Butt and R. Swaminathan.

38. Effect of Hypoxia on Circulating Levels of Retina Specific Messenger 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 Diabetic Retinopathy: Z. Shalchi, H. S. Sandhu, A.N. Butt, S. Smith, J. Powrie, and R. Swaminathan.

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

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

42. Cell - free DNA of Patients with Cardiomyopathy and rDNA Alone Change the Frequency of Contraction of the Electrically Paced Neonatal 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 Gas Measurement, and Oxygen Transport in Health and Stroke: Irina L. Konorova, Natalya N. Veiko, and Viktor E. Novikov.

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

45. Hypertension and circulating mRNA for 11β-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: Marie Korabecna, Sylvie Opatrna, Jan Wirth, Kamila Rulcova, Jan Eiselt, Frantisek Sefrna, and Ales Horinek.

47. Arrayed Primer EXtension (APEX) for the Non-Invasive Prenatal Diagnosis of β-thalassaemia Based on Detection of Single Nucleotide Polymorphisms: Thessalia Papasavva, Ioannis Kalikas, Andreanni Kyrri, and Marina Kleanthous.

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

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

Index of Contributors

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