Building digital life systems for future biology and medicine

Abstract

The rapid development of biological technology (BT) and information technology (IT) especially of genomics and artificial intelligence (AI) is bringing great potential for revolutionizing future medicine. We propose the concept and framework of Digital Life Systems or dLife as a new paradigm to unleash this potential. It includes the multi-scale and multi-granule measure and representation of life in the digital space, the mathematical and/or computational modeling of the biology behind physiological and pathological processes, and ultimately cyber twins of healthy or diseased human body in the virtual space that can be used to simulate complex biological processes and deduce effects of medical treatments. We advocate that dLife is the route toward future AI precision medicine and should be the new paradigm for future biological and medical research.

Graphical abstract

Keywords

digital life systems / digital twin / aritificial intelligence / precision medicine

References

[1] Loukas, M., Hanna, M., Alsaiegh, N., Shoja, M. M. Tubbs, R. (2011). Clinical anatomy as practiced by ancient Egyptians. Clin. Anat., 24: 409–415

[2] Ford, B. (1982). Bacteria and cells of human origin on van Leeuwenhoek’s sections of 1674. Trans. Am. Microsc. Soc., 101: 1–9

[3] Kligfield, P. (2016). The Bicentennial of the Stethoscope: 1816 to 2016. Am. J. Cardiol., 118: 1601–1602

[4] Mould, R. (1995). The early history of X-ray diagnosis with emphasis on the contributions of physics 1895–1915. Phys. Med. Biol., 40: 1741–1787

[5] Fye, W. (1994). A history of the origin, evolution, and impact of electrocardiography. Am. J. Cardiol., 73: 937–949

[6] Stone, J. L. Hughes, J. (2013). Early history of electroencephalography and establishment of the American Clinical Neurophysiology Society. J. Clin. Neurophysiol., 30: 28–44

[7] Edler, I. Hertz, C. (2004). The use of ultrasonic reflectoscope for the continuous recording of the movements of heart walls. Clin. Physiol. Funct. Imaging, 24: 118–136

[8] Beckmann, E. (2006). CT scanning the early days. Br. J. Radiol., 79: 5–8

[9] Ai, T., Morelli, J. N., Hu, X., Hao, D., Goerner, F. L., Ager, B. Runge, V. (2012). A historical overview of magnetic resonance imaging, focusing on technological innovations. Invest. Radiol., 47: 725–741

[10] Riley, J. (2005). Estimates of regional and global life expectancy, 1800–2001. Popul. Dev. Rev., 31: 537–543

[11] Ellis, T. H. N., Hofer, J. M. I., Timmerman-Vaughan, G. M., Coyne, C. J. Hellens, R. (2011). Mendel, 150 years on. Trends Plant Sci., 16: 590–596

[12] Dahm, R. Discovering, D. N. (2008). Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum. Genet., 122: 565–581

[13] Thess, A., Hoerr, I., Panah, B. Y., Jung, G. (2021). Historic nucleic acids isolated by Friedrich Miescher contain RNA besides DNA. Biol. Chem., 402: 1179–1185

[14] Hartley, H. (1951). Origin of the word “protein”. Nature, 168: 244

[15] Watson, J. D. Crick, F. H. (1953). Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171: 737–738

[16] Wu, R. (1970). Nucleotide sequence analysis of DNA. I. Partial sequence of the cohesive ends of bacteriophage lambda and 186 DNA. J. Mol. Biol., 51: 501–521

[17] Collins, F. S., Morgan, M. (2003). The Human Genome Project: lessons from large-scale biology. Science, 300: 286–290

[18] RegevA.,TeichmannS. A.,LanderE. S.,AmitI.,BenoistC.,BirneyE.,BodenmillerB.,CampbellP.,CarninciP.,ClatworthyM.,, (2017) The Human Cell Atlas. eLife, 6, e27041

[19] HuBMAPConsortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature, 574,187–192

[20] Chen, S., Luo, Y., Gao, H., Li, F., Chen, Y., Li, J., You, R., Hao, M., Bian, H., Xi, X. . (2022). hECA: the cell-centric assembly of a cell atlas. iScience, 25: 104318

[21] Vaduganathan, M., Mensah, G. A., Turco, J. V., Fuster, V. Roth, G. (2022). The global burden of cardiovascular diseases and risk: a compass for future health. J. Am. Coll. Cardiol., 80: 2361–2371

[22] Siegel, R. L., Miller, K. D., Fuchs, H. E. (2022). Cancer statistics, 2022. CA Cancer J. Clin., 72: 7–33

[23] Moor, M., Banerjee, O., Abad, Z. S. H., Krumholz, H. M., Leskovec, J., Topol, E. J. (2023). Foundation models for generalist medical artificial intelligence. Nature, 616: 259–265

[24] Committeeon the Learning Health Care System in America & Institute of Medicine. (2013) Best Care at Lower Cost: The Path to Continuously Learning Health Care in America. Washington (DC): National Academies Press

[25] Li, J., Qiu, Z., Zhang, C., Chen, S., Wang, M., Meng, Q., Lu, H., Wei, L., Lv, H., Zhong, W. . (2022). ITHscore: comprehensive quantification of intra-tumor heterogeneity in NSCLC by multi-scale radiomic features. Eur. Radiol., 33: 893–903

[26] Yuan, Y., Liu, B., Xie, P., Zhang, M. Q., Li, Y., Xie, Z. (2015). Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. Proc. Natl. Acad. Sci. USA, 112: 3158–3163

[27] Wei, L., Yuan, Y., Hu, T., Li, S., Cheng, T., Lei, J., Xie, Z., Zhang, M. Q. (2019). Regulation by competition: a hidden layer of gene regulatory network. Quant. Biol., 7: 110–121

[28] Huang, H., Liu, Y., Liao, W., Cao, Y., Liu, Q., Guo, Y., Lu, Y. (2019). Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy. Nat. Commun., 10: 4801

[29] Wei, L., Li, S., Zhang, P., Hu, T., Zhang, M. Q., Xie, Z. (2021). Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits. Cell Rep., 36: 109573

[30] Demirel, H. O., Ahmed, S. Duffy, V. (2022). Digital human modeling: a review and reappraisal of origins, present, and expected future methods for representing humans computationally. Int. J. Hum. Comput. Interact., 38: 897–937

[31] Campbell, M. (2022). Digital self: the next evolution of the digital human. Computer, 55: 82–86

[32] Morris, R. W., Bean, C. A., Farber, G. K., Gallahan, D., Jakobsson, E., Liu, Y., Lyster, P. M., Peng, G. C. Y., Roberts, F. S., Twery, M. . (2005). Digital biology: an emerging and promising discipline. Trends Biotechnol., 23: 113–117

[33] Corral-Acero, J., Margara, F., Marciniak, M., Rodero, C., Loncaric, F., Feng, Y., Gilbert, A., Fernandes, J. F., Bukhari, H. A., Wajdan, A. . (2020). The “digital twin” to enable the vision of precision cardiology. Eur. Heart J., 41: 4556–4564

[34] Subramanian, K. (2020). Digital twin for drug discovery and development—the virtual liver. J. Indian Inst. Sci., 100: 653–662

[35] Masison, J., Beezley, J., Mei, Y., Ribeiro, H., Knapp, A. C., Sordo Vieira, L., Adhikari, B., Scindia, Y., Grauer, M., Helba, B. . (2021). A modular computational framework for medical digital twins. Proc. Natl. Acad. Sci. USA, 118: e2024287118

[36] Mussomeli, A., Parrott, A., Umbenhauer, B. (2020). Deloitte. TechTrends, 2020: 70–71

ACKNOWLEDGEMENTS

This work was partially supported by the National Natural Science Foundation of China (NSFC) (Nos. 61721003 and 62250005), the National Key R&D Program of China (No. 2021YFF1200900), and Tsinghua-Fuzhou Institute for Data Technology (No. TFIDT2021005).

COMPLIANCE WITH ETHICS GUIDELINES

Conflicts of interest The authors Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, and Hairong Lv declare that they have no conflict of interest or financial conflicts to disclose.

This article is a perspective article and does not contain any human or animal subjects performed by any of the authors.

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