Parkinson’s Disease: Bioinspired Optimization Algorithms for Omics Datasets Monitoring

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Handbook of Computational Neurodegeneration

Abstract

Omics data create several computational challenges related to their volume, high dimensionality, and complexity. A subfield of the computational intelligence area that can address part of this complexity is bioinspired algorithms. These methods are gaining importance by strategies upon modeling the behavior of living organisms to create an algorithmic process that solves optimization problems. There is a remarkable progress in the application of bioinspired algorithms in neurodegeneration diseases from omics data, such as in Parkinson’s disease, a progressive disorder that affects the nervous system and the parts of the body controlled by the nerves. In this chapter, we address the main cutting-edge bioinspired optimization methods applied to PD omics datasets driven by high-throughput analytical workflows offering a significant clinical contribution and providing a more comprehensive outcome across multiple biological layers.

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References

  • Atmar W (1994) Notes on the simulation of evolution. IEEE Trans Neural Netw 5:130–147

    Article  CAS  PubMed  Google Scholar 

  • Barkovits K, Kruse N, Linden A, Tönges L, Pfeiffer K, Mollenhauer B, Marcus K (2020) Blood contamination in CSF and its impact on quantitative analysis of alpha-synuclein. Cells 9:370

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Botta-Orfila T, Sànchez-Pla A, Fernández M, Carmona F, Ezquerra M, Tolosa E (2012) Brain transcriptomic profiling in idiopathic and LRRK2-associated Parkinson’s disease. Brain Res 1466:152–157

    Article  CAS  PubMed  Google Scholar 

  • Clerc M, Kennedy J (2002) The particle swarm-explosion, stability, and convergence in a multidimensional complex space. IEEE Trans Evol Comput 6:58–73

    Article  Google Scholar 

  • Dafsari HS, Weiß L, Silverdale M, Rizos A, Reddy P, Ashkan K, Evans J, Reker P, Petry-Schmelzer JN, Samuel M, Visser-Vandewalle V, Antonini A, Martinez-Martin P, Ray-Chaudhuri K, Timmermann L, EUROPAR and the IPMDS Non Motor PD Study Group (2018) Short-term quality of life after subthalamic stimulation depends on non-motor symptoms in Parkinson’s disease. Brain Stimul 11:867–874

    Article  PubMed  Google Scholar 

  • Dong W, Qiu C, Gong D, Jiang X, Liu W, Liu W, Zhang L, Zhang W (2019) Proteomics and bioinformatics approaches for the identification of plasma biomarkers to detect Parkinson’s disease. Exp Ther Med 18:2833–2842

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eiben AE, Smith JE (2015) What is an evolutionary algorithm? In: Introduction to evolutionary computing. Springer, Berlin/Heidelberg, pp 25–48

    Chapter  Google Scholar 

  • Fernandes HJR, Patikas N, Foskolou S, Field SF, Park JE, Byrne ML, Bassett AR, Metzakopian E (2020) Single-cell transcriptomics of Parkinson’s disease human in vitro models reveals dopamine neuron-specific stress responses. Cell Rep 33:108263

    Article  CAS  PubMed  Google Scholar 

  • Figura M, Sitkiewicz E, Świderska B, Milanowski Ł, Szlufik S, Koziorowski D, Friedman A (2021) Proteomic profile of saliva in Parkinson’s disease patients: a proof of concept study. Brain Sci 11:661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ganguly U, Singh S, Pal S, Prasad S, Agrawal BK, Saini RV, Chakrabarti S (2021) Alpha-synuclein as a biomarker of Parkinson’s disease: good, but not good enough. Front Aging Neurosci 13:702639

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glaab E, Trezzi JP, Greuel A, Jäger C, Hodak Z, Drzezga A, Timmermann L, Tittgemeyer M, Diederich NJ, Eggers C (2019) EIntegrative analysis of blood metabolomics and PET brain neuroimaging data for Parkinson’s disease. Neurobiol Dis 124:555–562

    Article  CAS  PubMed  Google Scholar 

  • Haldar S (2016) Particle swarm optimization supported artificial neural network in detection of Parkinson’s disease. J Comput Eng 18:24

    Google Scholar 

  • Ham SJ, Lee D, Xu WJ, Cho E, Choi S, Min S, Park S, Chung J (2021) Loss of UCHL1 rescues the defects related to Parkinson’s disease by suppressing glycolysis. Sci Adv 7:eabg4574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He R, Yan X, Guo J, Xu Q, Tang B, Sun Q (2018) Recent advances in biomarkers for Parkinson’s disease. Front Aging Neurosci 10:305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holland JH (1992) Genetic algorithms. Sci Am 267:66–73

    Article  Google Scholar 

  • Horst R, Tuy H (2013) Global optimization: deterministic approaches. Springer Science & Business Media, Berlin/Heidelberg

    Google Scholar 

  • Hu L, Dong MX, Huang YL, Lu CQ, Qian Q, Zhang CC, Xu XM, Liu Y, Chen GH, Wei YD (2020) Integrated metabolomics and proteomics analysis reveals plasma lipid metabolic disturbance in patients with Parkinson’s disease. Front Mol Neurosci 13:80

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kennedy J (2006) Swarm intelligence. In: Handbook of nature-inspired and innovative computing. Springer, Boston, pp 187–219

    Chapter  Google Scholar 

  • Kennedy J, Eberhart R (1995) Particle swarm optimization. In: Proceedings of ICNN’95-international conference on neural networks, vol 4, pp 1942–1948

    Chapter  Google Scholar 

  • Keo A, Mahfouz A, Ingrassia AMT, Meneboo JP, Villenet C, Mutez E, Comptdaer T, Lelieveldt BPF, Figeac M, Chartier-Harlin MC, van de Berg WDJ, van Hilten JJ, Reinders MJT (2020) Transcriptomic signatures of brain regional vulnerability to Parkinson’s disease. Commun Biol 3:101

    Article  PubMed  PubMed Central  Google Scholar 

  • Kukurba KR, Montgomery SB (2015) RNA sequencing and analysis. Cold Spring Harb Protoc 11:951–969

    Google Scholar 

  • Kurvits L, Lättekivi F, Reimann E, Kadastik-Eerme L, Kasterpalu KM, Kõks S, Taba P, Planken A (2021) Transcriptomic profiles in Parkinson’s disease. Exp Biol Med (Maywood) 246:584–595

    Article  CAS  PubMed  Google Scholar 

  • Lang C, Campbell KR, Ryan BJ, Carling P, Attar M, Vowles J, Perestenko OV, Bowden R, Baig F, Kasten M, Hu MT, Cowley SA, Webber C, Wade-Martins R (2019) Single-cell sequencing of iPSC-dopamine neurons reconstructs disease progression and identifies HDAC4 as a regulator of Parkinson cell phenotypes. Cell Stem Cell 24:93–106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Q, Chen H, Huang H, Zhao X, Cai Z, Tong C, Liu W, Tian X (2017) An enhanced grey wolf optimization based feature selection wrapped kernel extreme learning machine for medical diagnosis. Comput Math Methods Med 2017:9512741

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu X, Li N, Liu S, Wang J, Zhang N, Zheng X, Leung K, Cheng L (2019) Normalization methods for the analysis of unbalanced transcriptome data: a review. Front Bioeng Biotechnol 7:358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lokhov PG, Trifonova OP, Maslov DL, Lichtenberg S, Balashova EE (2020) Diagnosis of Parkinson’s disease by a metabolomics-based laboratory-developed test (LDT). Diagnostics (Basel) 10:332

    Article  CAS  PubMed  Google Scholar 

  • Marsili L, Rizzo G, Colosimo C (2018) Diagnostic criteria for Parkinson’s disease: from James Parkinson to the concept of prodromal disease. Front Neurol 9:156

    Article  PubMed  PubMed Central  Google Scholar 

  • Morenas-Rodríguez E, Alcolea D, Suárez-Calvet M, Muñoz-Llahuna L, Vilaplana E, Sala I, Subirana A, Querol-Vilaseca M, Carmona-Iragui M, Illán-Gala I, Ribosa-Nogué R, Blesa R, Haass C, Fortea J, Lleó A (2019) Different pattern of CSF glial markers between dementia with Lewy bodies and Alzheimer’s disease. Sci Rep 9:1–10

    Article  Google Scholar 

  • Nido GS, Dick F, Toker L, Petersen K, Alves G, Tysnes OB, Jonassen I, Haugarvoll K, Tzoulis C (2020) Common gene expression signatures in Parkinson’s disease are driven by changes in cell composition. Acta Neuropathol Commun 8:55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nocedal J, Wright S (2006) Numerical optimization. Springer Science & Business Media, Berlin/Heidelberg

    Google Scholar 

  • Parsopoulos KE, Vrahatis MN (2002) Recent approaches to global optimization problems through particle swarm optimization. Nat Comput 1:235–306

    Article  Google Scholar 

  • Pasha A, Latha PH (2020) Bio-inspired dimensionality reduction for Parkinson’s disease (PD) classification. Health Inf Sci Syst 8:1–22

    Article  Google Scholar 

  • Picillo M, Pivonello R, Santangelo G, Pivonello C, Savastano R, Auriemma R, Amboni M, Scannapieco S, Pierro A, Colao A, Barone P, Pellecchia MT (2017) Serum IGF-1 is associated with cognitive functions in early, drug-naïve Parkinson’s disease. PLoS One 12:e0186508

    Article  PubMed  PubMed Central  Google Scholar 

  • Planken A, Kurvits L, Reimann E, Kadastik-Eerme L, Kingo K, Kõks S, Taba P (2017) Looking beyond the brain to improve the pathogenic understanding of Parkinson’s disease: implications of whole transcriptome profiling of patients’ skin. BMC Neurol 17:6

    Article  PubMed  PubMed Central  Google Scholar 

  • Posavi M, Diaz-Ortiz M, Liu B, Swanson CR, Skrinak RT, Hernandez-Con P, Amado DA, Fullard M, Rick J, Siderowf A, Weintraub D, McCluskey L, Trojanowski JQ, Dewey Jr RB, Huang X, Chen-Plotkin AS (2019) Characterization of Parkinson’s disease using blood-based biomarkers: a multicohort proteomic analysis. PLoS Med 16:e1002931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Redenšek S, Dolžan V, Kunej T (2018) From genomics to omics landscapes of Parkinson’s disease: revealing the molecular mechanisms. Omics: J Integr Biol 22:1–16

    Article  Google Scholar 

  • Repici M, Straatman KR, Balduccio N, Enguita FJ, Outeiro TF, Giorgini F (2013) Parkinson’s disease-associated mutations in DJ-1 modulate its dimerization in living cells. J Mol Med 91:599–611

    Article  CAS  PubMed  Google Scholar 

  • Rotunno MS, Lane M, Zhang W, Wolf P, Oliva P, Viel C, Wills AM, Alcalay RN, Scherzer CR, Shihabuddin LS, Zhang K, Sardi SP (2020) Cerebrospinal fluid proteomics implicates the granin family in Parkinson’s disease. Sci Rep 10:2479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roverato ND, Sailer C, Catone N, Aichem A, Stengel F, Groettrup M (2021) Parkin is an E3 ligase for the ubiquitin-like modifier FAT10, which inhibits Parkin activation and mitophagy. Cell Rep 34:108857

    Article  CAS  PubMed  Google Scholar 

  • Rowe JE, Sudholt D (2014) The choice of the offspring population size in the (1, λ) evolutionary algorithm. Theor Comput Sci 545:20–38

    Article  Google Scholar 

  • Salmanpour MR, Shamsaei M, Saberi A, Klyuzhin IS, Tang J, Sossi V, Rahmim A (2020) Machine learning methods for optimal prediction of outcome in Parkinson’s disease. Phys Med 69:233–240

    Article  PubMed  Google Scholar 

  • Shi X, Zheng J, Ma J, Wang Z, Sun W, Li M, Huang S, Hu S (2022) Insulin-like growth factor in Parkinson’s disease is related to nonmotor symptoms and the volume of specific brain areas. Neurosci Lett 783:136735

    Article  CAS  PubMed  Google Scholar 

  • Sinha A, Malo P, Deb K (2017) Evolutionary algorithm for bilevel optimization using approximations of the lower level optimal solution map**. Eur J Oper Res 257:395–411

    Article  Google Scholar 

  • Storn R, Price K (1997) Differential evolution–a simple and efficient heuristic for global optimization over continuous spaces. J Glob Optim 11:341–359

    Article  Google Scholar 

  • Tolosa E, Garrido A, Scholz SW, Poewe W (2021) Challenges in the diagnosis of Parkinson’s disease. Lancet Neurol 20:385–397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Dijk KD, Bidinosti M, Weiss A, Raijmakers P, Berendse HW, van de Berg WDJ (2014) Reduced α-synuclein levels in cerebrospinal fluid in Parkinson’s disease are unrelated to clinical and imaging measures of disease severity. Eur J Neurol 21:388–394

    Article  PubMed  Google Scholar 

  • Vázquez-Vélez GE, Zoghbi HY (2021) Parkinson’s disease genetics and pathophysiology. Annu Rev Neurosci 44:87–108

    Article  PubMed  Google Scholar 

  • Verger A, Grimaldi S, Ribeiro MJ, Frismand S, Guedj E (2021) Single photon emission computed tomography/positron emission tomography molecular imaging for parkinsonism: a fast-develo** field. Ann Neurol 90:711–719

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The research work was supported by the Hellenic Foundation for Research and Innovation (HFRI) under the 3rd Call for HFRI PhD Fellowships (Fellowship Number: 6620).

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Correspondence to Konstantina Skolariki .

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Skolariki, K., Krokidis, M.G., Vrahatis, A.G., Exarchos, T.P., Vlamos, P. (2023). Parkinson’s Disease: Bioinspired Optimization Algorithms for Omics Datasets Monitoring. In: Vlamos, P., Kotsireas, I.S., Tarnanas, I. (eds) Handbook of Computational Neurodegeneration. Springer, Cham. https://doi.org/10.1007/978-3-319-75479-6_46-1

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  • DOI: https://doi.org/10.1007/978-3-319-75479-6_46-1

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