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Procopio A, Cesarelli G, Donisi L, Merola A, Amato F, Cosentino C. Combined mechanistic modeling and machine-learning approaches in systems biology - A systematic literature review. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 240:107681. [PMID: 37385142 DOI: 10.1016/j.cmpb.2023.107681] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND AND OBJECTIVE Mechanistic-based Model simulations (MM) are an effective approach commonly employed, for research and learning purposes, to better investigate and understand the inherent behavior of biological systems. Recent advancements in modern technologies and the large availability of omics data allowed the application of Machine Learning (ML) techniques to different research fields, including systems biology. However, the availability of information regarding the analyzed biological context, sufficient experimental data, as well as the degree of computational complexity, represent some of the issues that both MMs and ML techniques could present individually. For this reason, recently, several studies suggest overcoming or significantly reducing these drawbacks by combining the above-mentioned two methods. In the wake of the growing interest in this hybrid analysis approach, with the present review, we want to systematically investigate the studies available in the scientific literature in which both MMs and ML have been combined to explain biological processes at genomics, proteomics, and metabolomics levels, or the behavior of entire cellular populations. METHODS Elsevier Scopus®, Clarivate Web of Science™ and National Library of Medicine PubMed® databases were enquired using the queries reported in Table 1, resulting in 350 scientific articles. RESULTS Only 14 of the 350 documents returned by the comprehensive search conducted on the three major online databases met our search criteria, i.e. present a hybrid approach consisting of the synergistic combination of MMs and ML to treat a particular aspect of systems biology. CONCLUSIONS Despite the recent interest in this methodology, from a careful analysis of the selected papers, it emerged how examples of integration between MMs and ML are already present in systems biology, highlighting the great potential of this hybrid approach to both at micro and macro biological scales.
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Affiliation(s)
- Anna Procopio
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italia
| | - Giuseppe Cesarelli
- Department of Electrical Engineering and Information Technology, Università degli Studi di Napoli Federico II, Napoli, 80125, Italy
| | - Leandro Donisi
- Department of Advanced Medical and Surgical Sciences, Università della Campania Luigi Vanvitelli, Napoli, 80138, Italy
| | - Alessio Merola
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italia
| | - Francesco Amato
- Department of Electrical Engineering and Information Technology, Università degli Studi di Napoli Federico II, Napoli, 80125, Italy.
| | - Carlo Cosentino
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italia.
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He B, Zhang Z, Huang Z, Duan X, Wang Y, Cao J, Li L, He K, Nice EC, He W, Gao W, Shen Z. Protein persulfidation: Rewiring the hydrogen sulfide signaling in cell stress response. Biochem Pharmacol 2023; 209:115444. [PMID: 36736962 DOI: 10.1016/j.bcp.2023.115444] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
The past few decades have witnessed significant progress in the discovery of hydrogen sulfide (H2S) as a ubiquitous gaseous signaling molecule in mammalian physiology, akin to nitric oxide and carbon monoxide. As the third gasotransmitter, H2S is now known to exert a wide range of physiological and cytoprotective functions in the biological systems. However, endogenous H2S concentrations are usually low, and its potential biologic mechanisms responsible have not yet been fully clarified. Recently, a growing body of evidence has demonstrated that protein persulfidation, a posttranslational modification of cysteine residues (RSH) to persulfides (RSSH) elicited by H2S, is a fundamental mechanism of H2S-mediated signaling pathways. Persulfidation, as a biological switch for protein function, plays an important role in the maintenance of cell homeostasis in response to various internal and external stress stimuli and is also implicated in numerous diseases, such as cardiovascular and neurodegenerative diseases and cancer. In this review, the biological significance of protein persulfidation by H2S in cell stress response is reviewed providing a framework for understanding the multifaceted roles of H2S. A mechanism-guided perspective can help open novel avenues for the exploitation of therapeutics based on H2S-induced persulfidation in the context of diseases.
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Affiliation(s)
- Bo He
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Zhe Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Zhao Huang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Xirui Duan
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Jiangjun Cao
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Lei Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Kai He
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Weifeng He
- Institute of Burn Research, Southwest Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Military Medical University, Chongqing 400038, China.
| | - Wei Gao
- Clinical Genetics Laboratory, Affiliated Hospital & Clinical Medical College of Chengdu University, Chengdu 610081, China.
| | - Zhisen Shen
- Department of Otorhinolaryngology and Head and Neck Surgery, Affiliated Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China.
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Kardynska M, Kogut D, Pacholczyk M, Smieja J. Mathematical modeling of regulatory networks of intracellular processes - Aims and selected methods. Comput Struct Biotechnol J 2023; 21:1523-1532. [PMID: 36851915 PMCID: PMC9958294 DOI: 10.1016/j.csbj.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract knowledge from existing databases. This review is focused on mathematical modeling used to analyze dynamics and robustness of these networks. This paper presents a review of selected modeling methods that facilitate advances in molecular biology.
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Affiliation(s)
- Malgorzata Kardynska
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland
| | - Daria Kogut
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Marcin Pacholczyk
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Jaroslaw Smieja
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
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Srinivasan M, Clarke R, Kraikivski P. Mathematical Models of Death Signaling Networks. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1402. [PMID: 37420422 PMCID: PMC9602293 DOI: 10.3390/e24101402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 07/09/2023]
Abstract
This review provides an overview of the progress made by computational and systems biologists in characterizing different cell death regulatory mechanisms that constitute the cell death network. We define the cell death network as a comprehensive decision-making mechanism that controls multiple death execution molecular circuits. This network involves multiple feedback and feed-forward loops and crosstalk among different cell death-regulating pathways. While substantial progress has been made in characterizing individual cell death execution pathways, the cell death decision network is poorly defined and understood. Certainly, understanding the dynamic behavior of such complex regulatory mechanisms can be only achieved by applying mathematical modeling and system-oriented approaches. Here, we provide an overview of mathematical models that have been developed to characterize different cell death mechanisms and intend to identify future research directions in this field.
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Affiliation(s)
- Madhumita Srinivasan
- College of Architecture, Arts, and Design, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Pavel Kraikivski
- Academy of Integrated Science, Division of Systems Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Gulhane P, Singh S. MicroRNA-520c-3p impacts sphingolipid metabolism mediating PI3K/AKT signaling in NSCLC: Systems perspective. J Cell Biochem 2022; 123:1827-1840. [PMID: 35977046 DOI: 10.1002/jcb.30319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/09/2022]
Abstract
Increasing research suggests that sphingolipid metabolism is essential for the progression and metastasis of cancer. The underlying mechanistic insight into the dysregulation of sphingolipid metabolism affecting pathways is poorly investigated. As a result, the goal of the current study was to glean knowledge from the systems biology approach to investigate how the sphingolipid metabolism affects the signal transduction network in non-small cell lung cancer (NSCLC), the most common type of cancer in terms of occurrence and death globally. Our paper includes system-level models representing the diseased and healthy states elucidating that sphingolipids and its enzymes mediate PI3K/AKT pathway. Notably, its activation of downstream signaling mediators has led to cancer growth. Considering the critical role of sphingolipids in NSCLC, our study advocates the target CERS6 which can be potentially inhibited using hsa-miR-520c-3p to combat NSCLC for future precision medicine.
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Affiliation(s)
- Pooja Gulhane
- Department of Pathogenesis and Cellular Response, Computational and Systems Biology Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Shailza Singh
- Department of Pathogenesis and Cellular Response, Computational and Systems Biology Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
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Bhavani GS, Palanisamy A. SNAIL driven by a feed forward loop motif promotes TGF βinduced epithelial to mesenchymal transition. Biomed Phys Eng Express 2022; 8. [PMID: 35700712 DOI: 10.1088/2057-1976/ac7896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022]
Abstract
Epithelial to Mesenchymal Transition (EMT) plays an important role in tissue regeneration, embryonic development, and cancer metastasis. Several signaling pathways are known to regulate EMT, among which the modulation of TGFβ(Transforming Growth Factor-β) induced EMT is crucial in several cancer types. Several mathematical models were built to explore the role of core regulatory circuit of ZEB/miR-200, SNAIL/miR-34 double negative feedback loops in modulating TGFβinduced EMT. Different emergent behavior including tristability, irreversible switching, existence of hybrid EMT states were inferred though these models. Some studies have explored the role of TGFβreceptor activation, SMADs nucleocytoplasmic shuttling and complex formation. Recent experiments have revealed that MDM2 along with SMAD complex regulates SNAIL expression driven EMT. Encouraged by this, in the present study we developed a mathematical model for p53/MDM2 dependent TGFβinduced EMT regulation. Inclusion of p53 brings in an additional mechanistic perspective in exploring the EM transition. The network formulated comprises a C1FFL moderating SNAIL expression involving MDM2 and SMAD complex, which functions as a noise filter and persistent detector. The C1FFL was also observed to operate as a coincidence detector driving the SNAIL dependent downstream signaling into phenotypic switching decision. Systems modelling and analysis of the devised network, displayed interesting dynamic behavior, systems response to various inputs stimulus, providing a better understanding of p53/MDM2 dependent TGF-βinduced Epithelial to Mesenchymal Transition.
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Jeong EM, Song YM, Kim JK. Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations. Interface Focus 2022; 12:20210084. [PMID: 35450279 PMCID: PMC9010851 DOI: 10.1098/rsfs.2021.0084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/24/2022] [Indexed: 12/14/2022] Open
Abstract
Transcriptional repression can occur via various mechanisms, such as blocking, sequestration and displacement. For instance, the repressors can hold the activators to prevent binding with DNA or can bind to the DNA-bound activators to block their transcriptional activity. Although the transcription can be completely suppressed with a single mechanism, multiple repression mechanisms are used together to inhibit transcriptional activators in many systems, such as circadian clocks and NF-κB oscillators. This raises the question of what advantages arise if seemingly redundant repression mechanisms are combined. Here, by deriving equations describing the multiple repression mechanisms, we find that their combination can synergistically generate a sharply ultrasensitive transcription response and thus strong oscillations. This rationalizes why the multiple repression mechanisms are used together in various biological oscillators. The critical role of such combined transcriptional repression for strong oscillations is further supported by our analysis of formerly identified mutations disrupting the transcriptional repression of the mammalian circadian clock. The hitherto unrecognized source of the ultrasensitivity, the combined transcriptional repressions, can lead to robust synthetic oscillators with a previously unachievable simple design.
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Affiliation(s)
- Eui Min Jeong
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Yun Min Song
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
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Mathematical Modelling of p53 Signalling during DNA Damage Response: A Survey. Int J Mol Sci 2021; 22:ijms221910590. [PMID: 34638930 PMCID: PMC8508851 DOI: 10.3390/ijms221910590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023] Open
Abstract
No gene has garnered more interest than p53 since its discovery over 40 years ago. In the last two decades, thanks to seminal work from Uri Alon and Ghalit Lahav, p53 has defined a truly synergistic topic in the field of mathematical biology, with a rich body of research connecting mathematic endeavour with experimental design and data. In this review we survey and distill the extensive literature of mathematical models of p53. Specifically, we focus on models which seek to reproduce the oscillatory dynamics of p53 in response to DNA damage. We review the standard modelling approaches used in the field categorising them into three types: time delay models, spatial models and coupled negative-positive feedback models, providing sample model equations and simulation results which show clear oscillatory dynamics. We discuss the interplay between mathematics and biology and show how one informs the other; the deep connections between the two disciplines has helped to develop our understanding of this complex gene and paint a picture of its dynamical response. Although yet more is to be elucidated, we offer the current state-of-the-art understanding of p53 response to DNA damage.
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p53: A Key Protein That Regulates Pulmonary Fibrosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6635794. [PMID: 33312337 PMCID: PMC7721501 DOI: 10.1155/2020/6635794] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Pulmonary fibrosis is a progressively aggravating lethal disease that is a serious public health concern. Although the incidence of this disease is increasing, there is a lack of effective therapies. In recent years, the pathogenesis of pulmonary fibrosis has become a research hotspot. p53 is a tumor suppressor gene with crucial roles in cell cycle, apoptosis, tumorigenesis, and malignant transformation. Previous studies on p53 have predominantly focused on its role in neoplastic disease. Following in-depth investigation, several studies have linked it to pulmonary fibrosis. This review covers the association between p53 and pulmonary fibrosis, with the aim of providing novel ideas to improve the clinical diagnosis, treatment, and prognosis of pulmonary fibrosis.
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