Current directions in development of postgenomic medical technologies
Keywords:
postgenomic technologies, biotechnology, biopharmaceuticals, personalized medicine
Abstract
The aim of this study was to analyze key expected postgenomic technologies as a part of priority in scientific and technological development defined in item 20 of the Strategy for Scientific and Technological Development of the Russian Federation, «Transition to personalized medicine, high-tech health care and health saving technologies through the rational use of medicines (primarily antibacterial)». Results. The most promising areas of further research were identified. The international level of postgenomic technologies (PGT) allows to move from research and development to implementation in medical practice. Presently, industrial biotechnology, biopharmaceuticals, including development of gene editing methods for treatment of oncological and orphan diseases and molecular profiling methods for individualized medicine, nutrition, and prolonging the active life are considered the main directions for successful practical use of PGT in Russia and other countries. Conclusion. Rapid development of high-performance postgenomic technologies and computer systems has expedited studying biological systems. Individual and integrative postgenomic profiles are useful for monitoring the state of human health, taking preventive measures, and selecting effective drug therapy.
Downloads
Download data is not yet available.
References
1. Berestyanaya A.N. Methylation as the most important mechanism of epigenetic regulation in eukaryotes. Uspekhi sovremennoy biologii. 2014; 134: 363-76. (in Russian)
2. Chen R., Snyder M. Promise of Personalized Omics to Precision Medicine. Wiley Interdiscip Rev Syst Biol Med. 2013; 5: 73-82.
3. Snyder M., Du J., Gerstein M. Personal genome sequencing: current approaches and challenges. Genes & development. 2010; 24: 423-31.
4. Chen R., Mias G.I., Li-Pook-Than J., Jiang L., Lam H.Y., et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012; 148: 1293-307.
5. Lee H.Y., Lee S.D., Shin K.J. Forensic DNA methylation profiling from evidence material for investigative leads. BMB Rep. 2016; 49: 359-69.
6. Gokhman D., Lavi E., Prufer K., Fraga M.F., Riancho J.A., et al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science. 2014; 344: 523-27.
7. Briggs A.W., Stenzel U., Meyer M., Krause J., Kircher M. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2010; 38: e87.
8. Fulka H., Mrazek M., Tepla O., Fulka J.Jr. DNA methylation pattern in human zygotes and developing embryos. Reproduction. 2004; 128 (6): 703-8.
9. Karan R., DeLeon T., Biradar H., Subudhi P.K. Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes. PLoS One. 2012; 7 (6): e40203.
10. Stewart L., Evans N., Bexon K.J., van der Meer D.J., Williams G. Differentiating between monozygotic twins through DNA methylation-specific high-resolution melt curve analysis. Anal Biochem. 2010; 476: 36-9.
11. Pohlers M., Calabrese J.M., Magnuson T. Small RNA expression from the human macrosatellite DXZ4. G3 (Bethesda). 2010; 4: 1981-9.
12. Lee H.Y., Park M.J., Choi A., An J.H., Yang W.I. et al. Potential forensic application of DNA methylation. Int J Legal Med. 2012; 126: 55-62.
13. Xu C., Qu H., Wang G. et al. A novel strategy for forensic age prediction by DNA methylation and support vector regression model. Sci Rep. 2015; 5: 17788.
14. Chan A., Broaddus R.R., Houlihan P.S., Issa J-P.J., Hamilton S.R. et al. CpG Island Methylation in Aberrant Crypt Foci of the Colorectum. Am J Pathol. 2002; 160 (5): 1823-30.
15. Baylin S.B., Herman J.G., Graff J.R., Vertino P.M., Issa J.P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res. 1998; 72; 141-96.
16. Grishin D.V. Relationship between the Duration of G1 Period of the Eukaryotic Cell Cycle and Age-Associated Changes in the Expression of Cyclin D1 and Nuclear Receptors, Bulleten of Experimental Biology and Medicine. 2012; 154: 80-3.
17. Grishin D.V. Molecular-genetic inversion of the cell cycle: the concept of R/K-aging of higher eukaryotes. Uspekhi sovremennoy biologii. 2013; 133: 323-32. (in Russian)
18. Witkowski J.M., Bryl E. Paradoxical age-related cell cycle, quickening of human CD4 (+) lymphocytes: a role for cyclin D1 and calpain. Exp Gerontol. 2004; 39: 577-85.
19. Quadri R.A., Arbogast A., Phelouzat M.A., Boutet S., Plastre O., Proust J.J. Age-Associated Decline in cdk1 Activity Delays Cell Cycle Progression of Human T Lymphocytes. J Immunol. 1999; 161: 5203-9.
20. Chkhotua A.B., Gabusi E., Altimari A., D’Errico A., Yakubovich M. et al. Increased expression of p16 (INK4a) and p27 (Kip1) cyclin-dependent kinase inhibitor genes in aging human kidney and chronic allograft nephropathy. Am J Kidney Dis. 2003; 41: 1303-13.
21. Suska M., Brucka-Jastrzebska E., Kawczuga D. Na+, K(+)-ATPase activity and ATP concentration in the Wielkopolski breed in relation to age. Pol J Vet Sci. 2011; 14: 635-42.
22. Sabbah M., Courilleau D., Mester J., Redeuilh G. Estrogen induction of the cyclin D1 promoter: involvement of a cAMP response-like element. PNAS. 1999; 96: 11217-22.
23. Kamiya K., Sakakibara K., Ryer E.J., Hom R.P., Leof E.B. et al. Phosphorylation of the cyclic AMP response element binding protein mediates transforming growth factor beta-induced downregulation of cyclin A in a vascular smooth muscle cells. Mol Cell Biol. 2007; 27: 3489-98.
24. Karigane D., Kobayashi H., Morikawa T., Ootomo Y. et al. P38a Activates Purine Metabolism to Initiate Hematopoietic Stem / Progenitor Cell Cycling in Response to Stress. Stem Cell. 2016; 19: 192-204.
25. Siegfried Z., Simon I. DNA methylation and gene expression. Wiley Interdiscip Rev Syst Biol Med. 2010; 2: 362-71.
26. Moarii M., Boeva V., Vert J.-P., Reyal F. Changes in the correlation between promoter methylation and gene expression in cancer. BMC Genomics. 2015; 16: 873.
27. Vinnichuk Yu.D., Gunina L.M. Predictors and markers of the functional condition of athletes during training in the middle reaches. Health for All. 2014; 2: 3-10. (in Russian)
28. Mikhailov S.S. Sports Biochemistry. Textbook for high schools and colleges of physical culture. 2nd ed. In: Moscow: Soviet Sport. 2004. (in Russian)
29. Rogozkin V.A. Decoding of the human genome and sport. Theory and Practice of Physical Culture. 2001; 6: 60-3. (in Russian)
30. Rogozkin V.A. Sport Genetics: Status and Prospects. VII International Scientific Congress «Modern Olympic Sport and Sport for All». 2003; 3: 265-9. (in Russian)
31. Nazarov I., Woods D., Montgomery H., Schneider O., Kazakov V. et al. The angiotensin converting enzyme 1/D polymorphism in Russian athletes. Eur J Hum Genet. 2001; 9: 797-801.
32. Lim U.U., Song M.A. Dietary and lifestyle factors of DNA methylation. Methods Mol Biol. 2012; 863: 359-76.
33. Acevedo N., Reinius L.E., Vitezic M. et al. Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes. Clin Epigenetics. 2015; 26: 34.
34. Wahl S., Drong A., Lehne B. et al. Epigenome-wide association study of the body mass index, and the adverse outcome of adiposity. Nature. 2017; 541: 81-6.
35. Lalani R., Bhasin S., Byhover F. et al. Myostatin and insulin-like growth factor-I and -II expression in the muscle of rats exposed to the microgravity environment of the NeuroLab space shuttle flight. J Endocrinol. 2000; 167: 417-28.
36. Izumikawa M., Hayashi K. et al. Effects of Amelogenin on Proliferation, Differentiation, and Mineralization of Rat Bone Marrow Mesenchymal Stem Cells In Vitro. Scientific World Journal. 2012; 2012: 8.
37. Grishin D.V., Nikitin A.V. Perspectives of prevention and treatment of malabsorption syndrome. Antibiotiki i khimioterapiya. 2009; 3: 49-51. (in Russian)
38. Waterland R.A., Dolinoy D.C., Lin J.R., Smith C.A., Shi X. et al. Maternal methyl supplements increase offspring DNA methylation at Axin Fused. Genesis. 2006; 44 (9): 401-6.
39. Anderson O.S., Sant K.E., Dolinoy D.C. Nutrition and epigenetics: An interplay of dietary methyl donors, one-carbon metabolism, and DNA methylation. J Nutr Biochem. 2012; 23(8): 853-9.
40. O’Neill R.J., Vrana P.B., Rosenfeld C.S. Maternal methyl supplemented diets and effects on offspring health. Front Genet. 2014; 26: 289.
41. Bansal A.K., Shetty D.C., Bindal R., Pathak A. Amelogenin: A novel protein with diverse applications in genetic and molecular profiling. J Oral Maxillofac Pathol. 2012; 16: 395-9.
42. Moch H., Blank P.R., Dietel M., Elmberger G., Kerr K.M. et al. Personalized cancer medicine and the future of pathology. Virchows Archiv: an international journal of pathology. 2012; 460: 3-8.
43. Berman D.M., Bosenberg M.W., Orwant R.L., Thurberg B.L., Draetta G.F., Fletcher C.D., Loda M. Investigative pathology: leading the post-genomic revolution, Laboratory investigation; a journal of technical methods and pathology. 2012; 92: 4-8.
44. Khan F.A., Pandupuspitasari N.S., Chun-Jie H., Ao Z., Jamal M. et al. CRISPR/Cas9 therapeutics: a cure for cancer and other genetic diseases. Oncotarget. 2016; 7: 52541-52.
45. Hindorff L.A., MacArthur J., Wise A., Junkins H.A., Hall P.N. et al. A Catalog of Published Genome-Wide Association Studies. 2012.
46. Antman E., Weiss S., Loscalzo J. Systems pharmacology, pharmacogenetics, and clinical trial design in network medicine. Wiley interdisciplinary reviews Systems biology and medicine. 2012; 4: 367-83.
47. Puente X.S., Pinyol M., Quesada V., Conde L., Ordonez G.R. et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 2011; 475: 101-5.
48. Bainbridge M.N., Wiszniewski W., Murdock D.R., Friedman J., Gonzaga-Jauregui C. et al. Whole-genome sequencing for optimized patient management. Science translational medicine. 2011; 3: 87re83.
49. Kaysheva A.L., Kopylov A.T., Ponomarenko E.A., Kiseleva O.I., Teryaeva A.A. et al. Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia. J. Mol. Neurosci. 2018.
50. Kaysheva A.L., Kopylov A.T., Pleshakova T.O., Iourov I.Y., Vorsanova S.G. et al. Proteomic analysis of serum. Biotecnologia Aplicada. 2017; 34(2): 2211-4.
51. Kaysheva A.L., Kopylov A.T., Yurov I.Y., Archakov A.I., Ivanov Y.D. Proteomic analysis of serum protein profiles in children with autism. Voprosy Prakticheskoy Pediatrii. 2016; 11 (5): 12-7. (in Russian)
52. Khramova T.V., Kaysheva A.L., Ivanov Y.D., Pleshakova T.O., Iourov I.Y. et al. Serologic Markers of Autism Spectrum Disorder. J Mol Neurosci. 2017; 62(3-4): 420-9.
53. Lisitsa A.V., Ponomarenko E.A., Lokhov P.G., Archakov A.I. Postgenomic Medicine: Alternative to Biomarkers. Vestn Ross Akad Med Nauk. 2016; 71(3): 255-60. (in Russian)
2. Chen R., Snyder M. Promise of Personalized Omics to Precision Medicine. Wiley Interdiscip Rev Syst Biol Med. 2013; 5: 73-82.
3. Snyder M., Du J., Gerstein M. Personal genome sequencing: current approaches and challenges. Genes & development. 2010; 24: 423-31.
4. Chen R., Mias G.I., Li-Pook-Than J., Jiang L., Lam H.Y., et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012; 148: 1293-307.
5. Lee H.Y., Lee S.D., Shin K.J. Forensic DNA methylation profiling from evidence material for investigative leads. BMB Rep. 2016; 49: 359-69.
6. Gokhman D., Lavi E., Prufer K., Fraga M.F., Riancho J.A., et al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science. 2014; 344: 523-27.
7. Briggs A.W., Stenzel U., Meyer M., Krause J., Kircher M. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2010; 38: e87.
8. Fulka H., Mrazek M., Tepla O., Fulka J.Jr. DNA methylation pattern in human zygotes and developing embryos. Reproduction. 2004; 128 (6): 703-8.
9. Karan R., DeLeon T., Biradar H., Subudhi P.K. Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes. PLoS One. 2012; 7 (6): e40203.
10. Stewart L., Evans N., Bexon K.J., van der Meer D.J., Williams G. Differentiating between monozygotic twins through DNA methylation-specific high-resolution melt curve analysis. Anal Biochem. 2010; 476: 36-9.
11. Pohlers M., Calabrese J.M., Magnuson T. Small RNA expression from the human macrosatellite DXZ4. G3 (Bethesda). 2010; 4: 1981-9.
12. Lee H.Y., Park M.J., Choi A., An J.H., Yang W.I. et al. Potential forensic application of DNA methylation. Int J Legal Med. 2012; 126: 55-62.
13. Xu C., Qu H., Wang G. et al. A novel strategy for forensic age prediction by DNA methylation and support vector regression model. Sci Rep. 2015; 5: 17788.
14. Chan A., Broaddus R.R., Houlihan P.S., Issa J-P.J., Hamilton S.R. et al. CpG Island Methylation in Aberrant Crypt Foci of the Colorectum. Am J Pathol. 2002; 160 (5): 1823-30.
15. Baylin S.B., Herman J.G., Graff J.R., Vertino P.M., Issa J.P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res. 1998; 72; 141-96.
16. Grishin D.V. Relationship between the Duration of G1 Period of the Eukaryotic Cell Cycle and Age-Associated Changes in the Expression of Cyclin D1 and Nuclear Receptors, Bulleten of Experimental Biology and Medicine. 2012; 154: 80-3.
17. Grishin D.V. Molecular-genetic inversion of the cell cycle: the concept of R/K-aging of higher eukaryotes. Uspekhi sovremennoy biologii. 2013; 133: 323-32. (in Russian)
18. Witkowski J.M., Bryl E. Paradoxical age-related cell cycle, quickening of human CD4 (+) lymphocytes: a role for cyclin D1 and calpain. Exp Gerontol. 2004; 39: 577-85.
19. Quadri R.A., Arbogast A., Phelouzat M.A., Boutet S., Plastre O., Proust J.J. Age-Associated Decline in cdk1 Activity Delays Cell Cycle Progression of Human T Lymphocytes. J Immunol. 1999; 161: 5203-9.
20. Chkhotua A.B., Gabusi E., Altimari A., D’Errico A., Yakubovich M. et al. Increased expression of p16 (INK4a) and p27 (Kip1) cyclin-dependent kinase inhibitor genes in aging human kidney and chronic allograft nephropathy. Am J Kidney Dis. 2003; 41: 1303-13.
21. Suska M., Brucka-Jastrzebska E., Kawczuga D. Na+, K(+)-ATPase activity and ATP concentration in the Wielkopolski breed in relation to age. Pol J Vet Sci. 2011; 14: 635-42.
22. Sabbah M., Courilleau D., Mester J., Redeuilh G. Estrogen induction of the cyclin D1 promoter: involvement of a cAMP response-like element. PNAS. 1999; 96: 11217-22.
23. Kamiya K., Sakakibara K., Ryer E.J., Hom R.P., Leof E.B. et al. Phosphorylation of the cyclic AMP response element binding protein mediates transforming growth factor beta-induced downregulation of cyclin A in a vascular smooth muscle cells. Mol Cell Biol. 2007; 27: 3489-98.
24. Karigane D., Kobayashi H., Morikawa T., Ootomo Y. et al. P38a Activates Purine Metabolism to Initiate Hematopoietic Stem / Progenitor Cell Cycling in Response to Stress. Stem Cell. 2016; 19: 192-204.
25. Siegfried Z., Simon I. DNA methylation and gene expression. Wiley Interdiscip Rev Syst Biol Med. 2010; 2: 362-71.
26. Moarii M., Boeva V., Vert J.-P., Reyal F. Changes in the correlation between promoter methylation and gene expression in cancer. BMC Genomics. 2015; 16: 873.
27. Vinnichuk Yu.D., Gunina L.M. Predictors and markers of the functional condition of athletes during training in the middle reaches. Health for All. 2014; 2: 3-10. (in Russian)
28. Mikhailov S.S. Sports Biochemistry. Textbook for high schools and colleges of physical culture. 2nd ed. In: Moscow: Soviet Sport. 2004. (in Russian)
29. Rogozkin V.A. Decoding of the human genome and sport. Theory and Practice of Physical Culture. 2001; 6: 60-3. (in Russian)
30. Rogozkin V.A. Sport Genetics: Status and Prospects. VII International Scientific Congress «Modern Olympic Sport and Sport for All». 2003; 3: 265-9. (in Russian)
31. Nazarov I., Woods D., Montgomery H., Schneider O., Kazakov V. et al. The angiotensin converting enzyme 1/D polymorphism in Russian athletes. Eur J Hum Genet. 2001; 9: 797-801.
32. Lim U.U., Song M.A. Dietary and lifestyle factors of DNA methylation. Methods Mol Biol. 2012; 863: 359-76.
33. Acevedo N., Reinius L.E., Vitezic M. et al. Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes. Clin Epigenetics. 2015; 26: 34.
34. Wahl S., Drong A., Lehne B. et al. Epigenome-wide association study of the body mass index, and the adverse outcome of adiposity. Nature. 2017; 541: 81-6.
35. Lalani R., Bhasin S., Byhover F. et al. Myostatin and insulin-like growth factor-I and -II expression in the muscle of rats exposed to the microgravity environment of the NeuroLab space shuttle flight. J Endocrinol. 2000; 167: 417-28.
36. Izumikawa M., Hayashi K. et al. Effects of Amelogenin on Proliferation, Differentiation, and Mineralization of Rat Bone Marrow Mesenchymal Stem Cells In Vitro. Scientific World Journal. 2012; 2012: 8.
37. Grishin D.V., Nikitin A.V. Perspectives of prevention and treatment of malabsorption syndrome. Antibiotiki i khimioterapiya. 2009; 3: 49-51. (in Russian)
38. Waterland R.A., Dolinoy D.C., Lin J.R., Smith C.A., Shi X. et al. Maternal methyl supplements increase offspring DNA methylation at Axin Fused. Genesis. 2006; 44 (9): 401-6.
39. Anderson O.S., Sant K.E., Dolinoy D.C. Nutrition and epigenetics: An interplay of dietary methyl donors, one-carbon metabolism, and DNA methylation. J Nutr Biochem. 2012; 23(8): 853-9.
40. O’Neill R.J., Vrana P.B., Rosenfeld C.S. Maternal methyl supplemented diets and effects on offspring health. Front Genet. 2014; 26: 289.
41. Bansal A.K., Shetty D.C., Bindal R., Pathak A. Amelogenin: A novel protein with diverse applications in genetic and molecular profiling. J Oral Maxillofac Pathol. 2012; 16: 395-9.
42. Moch H., Blank P.R., Dietel M., Elmberger G., Kerr K.M. et al. Personalized cancer medicine and the future of pathology. Virchows Archiv: an international journal of pathology. 2012; 460: 3-8.
43. Berman D.M., Bosenberg M.W., Orwant R.L., Thurberg B.L., Draetta G.F., Fletcher C.D., Loda M. Investigative pathology: leading the post-genomic revolution, Laboratory investigation; a journal of technical methods and pathology. 2012; 92: 4-8.
44. Khan F.A., Pandupuspitasari N.S., Chun-Jie H., Ao Z., Jamal M. et al. CRISPR/Cas9 therapeutics: a cure for cancer and other genetic diseases. Oncotarget. 2016; 7: 52541-52.
45. Hindorff L.A., MacArthur J., Wise A., Junkins H.A., Hall P.N. et al. A Catalog of Published Genome-Wide Association Studies. 2012.
46. Antman E., Weiss S., Loscalzo J. Systems pharmacology, pharmacogenetics, and clinical trial design in network medicine. Wiley interdisciplinary reviews Systems biology and medicine. 2012; 4: 367-83.
47. Puente X.S., Pinyol M., Quesada V., Conde L., Ordonez G.R. et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 2011; 475: 101-5.
48. Bainbridge M.N., Wiszniewski W., Murdock D.R., Friedman J., Gonzaga-Jauregui C. et al. Whole-genome sequencing for optimized patient management. Science translational medicine. 2011; 3: 87re83.
49. Kaysheva A.L., Kopylov A.T., Ponomarenko E.A., Kiseleva O.I., Teryaeva A.A. et al. Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia. J. Mol. Neurosci. 2018.
50. Kaysheva A.L., Kopylov A.T., Pleshakova T.O., Iourov I.Y., Vorsanova S.G. et al. Proteomic analysis of serum. Biotecnologia Aplicada. 2017; 34(2): 2211-4.
51. Kaysheva A.L., Kopylov A.T., Yurov I.Y., Archakov A.I., Ivanov Y.D. Proteomic analysis of serum protein profiles in children with autism. Voprosy Prakticheskoy Pediatrii. 2016; 11 (5): 12-7. (in Russian)
52. Khramova T.V., Kaysheva A.L., Ivanov Y.D., Pleshakova T.O., Iourov I.Y. et al. Serologic Markers of Autism Spectrum Disorder. J Mol Neurosci. 2017; 62(3-4): 420-9.
53. Lisitsa A.V., Ponomarenko E.A., Lokhov P.G., Archakov A.I. Postgenomic Medicine: Alternative to Biomarkers. Vestn Ross Akad Med Nauk. 2016; 71(3): 255-60. (in Russian)
Published
2018-10-05
How to Cite
Kaysheva A. L., Grishin D. V., Kamenski P. A., Fedoronchuk T. V., Choynzonov E. L., Lisitsa A. V., . Current directions in development of postgenomic medical technologies // Patologicheskaya Fiziologiya i Eksperimental’naya Terapiya (Pathological physiology and experimental therapy). 2018. VOL. 62. № 3. PP. 95–105.
Issue
Section
Reviews
