1
|
Itoh T, Kondo Y, Aoki K, Saito N. Revisiting the evolution of bow-tie architecture in signaling networks. NPJ Syst Biol Appl 2024; 10:70. [PMID: 38951549 PMCID: PMC11217396 DOI: 10.1038/s41540-024-00396-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
Bow-tie architecture is a layered network structure that has a narrow middle layer with multiple inputs and outputs. Such structures are widely seen in the molecular networks in cells, suggesting that a universal evolutionary mechanism underlies the emergence of bow-tie architecture. The previous theoretical studies have implemented evolutionary simulations of the feedforward network to satisfy a given input-output goal and proposed that the bow-tie architecture emerges when the ideal input-output relation is given as a rank-deficient matrix with mutations in network link intensities in a multiplicative manner. Here, we report that the bow-tie network inevitably appears when the link intensities representing molecular interactions are small at the initial condition of the evolutionary simulation, regardless of the rank of the goal matrix. Our dynamical system analysis clarifies the mechanisms underlying the emergence of the bow-tie structure. Further, we demonstrate that the increase in the input-output matrix reduces the width of the middle layer, resulting in the emergence of bow-tie architecture, even when evolution starts from large link intensities. Our data suggest that bow-tie architecture emerges as a side effect of evolution rather than as a result of evolutionary adaptation.
Collapse
Affiliation(s)
- Thoma Itoh
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Yohei Kondo
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Kazuhiro Aoki
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Nen Saito
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, 739-8511, Japan.
| |
Collapse
|
2
|
Ortega OO, Ozen M, Wilson BA, Pino JC, Irvin MW, Ildefonso GV, Garbett SP, Lopez CF. Signal execution modes emerge in biochemical reaction networks calibrated to experimental data. iScience 2024; 27:109989. [PMID: 38846004 PMCID: PMC11154230 DOI: 10.1016/j.isci.2024.109989] [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: 10/30/2023] [Revised: 02/29/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
Mathematical models of biomolecular networks are commonly used to study cellular processes; however, their usefulness to explain and predict dynamic behaviors is often questioned due to the unclear relationship between parameter uncertainty and network dynamics. In this work, we introduce PyDyNo (Python dynamic analysis of biochemical networks), a non-equilibrium reaction-flux based analysis to identify dominant reaction paths within a biochemical reaction network calibrated to experimental data. We first show, in a simplified apoptosis execution model, that despite the thousands of parameter vectors with equally good fits to experimental data, our framework identifies the dynamic differences between these parameter sets and outputs three dominant execution modes, which exhibit varying sensitivity to perturbations. We then apply our methodology to JAK2/STAT5 network in colony-forming unit-erythroid (CFU-E) cells and provide previously unrecognized mechanistic explanation for the survival responses of CFU-E cell population that would have been impossible to deduce with traditional protein-concentration based analyses.
Collapse
Affiliation(s)
- Oscar O. Ortega
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37212, USA
| | - Mustafa Ozen
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Multiscale Modeling Group, Comp. Bio. Hub, Altos Laboratories, Redwood City, CA 94065, USA
| | - Blake A. Wilson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
| | - James C. Pino
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
| | - Michael W. Irvin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
| | - Geena V. Ildefonso
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37212, USA
| | - Shawn P. Garbett
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Carlos F. Lopez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Multiscale Modeling Group, Comp. Bio. Hub, Altos Laboratories, Redwood City, CA 94065, USA
| |
Collapse
|
3
|
Reisman EG, Hawley JA, Hoffman NJ. Exercise-Regulated Mitochondrial and Nuclear Signalling Networks in Skeletal Muscle. Sports Med 2024; 54:1097-1119. [PMID: 38528308 PMCID: PMC11127882 DOI: 10.1007/s40279-024-02007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2024] [Indexed: 03/27/2024]
Abstract
Exercise perturbs energy homeostasis in skeletal muscle and engages integrated cellular signalling networks to help meet the contraction-induced increases in skeletal muscle energy and oxygen demand. Investigating exercise-associated perturbations in skeletal muscle signalling networks has uncovered novel mechanisms by which exercise stimulates skeletal muscle mitochondrial biogenesis and promotes whole-body health and fitness. While acute exercise regulates a complex network of protein post-translational modifications (e.g. phosphorylation) in skeletal muscle, previous investigations of exercise signalling in human and rodent skeletal muscle have primarily focused on a select group of exercise-regulated protein kinases [i.e. 5' adenosine monophosphate-activated protein kinase (AMPK), protein kinase A (PKA), Ca2+/calmodulin-dependent protein kinase (CaMK) and mitogen-activated protein kinase (MAPK)] and only a small subset of their respective protein substrates. Recently, global mass spectrometry-based phosphoproteomic approaches have helped unravel the extensive complexity and interconnection of exercise signalling pathways and kinases beyond this select group and phosphorylation and/or translocation of exercise-regulated mitochondrial and nuclear protein substrates. This review provides an overview of recent advances in our understanding of the molecular events associated with acute endurance exercise-regulated signalling pathways and kinases in skeletal muscle with a focus on phosphorylation. We critically appraise recent evidence highlighting the involvement of mitochondrial and nuclear protein phosphorylation and/or translocation in skeletal muscle adaptive responses to an acute bout of endurance exercise that ultimately stimulate mitochondrial biogenesis and contribute to exercise's wider health and fitness benefits.
Collapse
Affiliation(s)
- Elizabeth G Reisman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia
| | - Nolan J Hoffman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Level 5, 215 Spring Street, Melbourne, VIC, 3000, Australia.
| |
Collapse
|
4
|
Bhardwaj S, Bulluss M, D'Aubeterre A, Derakhshani A, Penner R, Mahajan M, Mahajan VB, Dufour A. Integrating the analysis of human biopsies using post-translational modifications proteomics. Protein Sci 2024; 33:e4979. [PMID: 38533548 DOI: 10.1002/pro.4979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.
Collapse
Affiliation(s)
- Sonali Bhardwaj
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mitchell Bulluss
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ana D'Aubeterre
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Afshin Derakhshani
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Regan Penner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - MaryAnn Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
5
|
Rodosy FB, Azad MAK, Halder SK, Limon MBH, Jaman S, Lata NA, Sarker M, Riya AI. The potential of phytochemicals against epidermal growth factor receptor tyrosine kinase (EGFRK): an insight from molecular dynamic simulations. J Biomol Struct Dyn 2024; 42:2482-2493. [PMID: 37154806 DOI: 10.1080/07391102.2023.2207656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/16/2023] [Indexed: 05/10/2023]
Abstract
Cancer is an umbrella term used to define various diseases with abnormal cell proliferation at the focal point. According to the WHO, cancer is the leading cause of death worldwide, with lung cancer being the second most common perpetrator after breast cancer. There are several proteins acting in harmony that lead to cancer. EGFR has been identified as one of the proteins that is linked to cell division, even when it is cancerous in nature. Cancer can be treated using therapeutic agents that target EGFR or their signaling networks. Available drugs that could inhibit EGFR have acquired resistance in most cases and multiple side effects on the human body. That is why phytochemicals are being studied for their role in this case. Around 8000 compounds were retrieved from our previously created phytochemdb database for their drug activity, and the 3D protein structure was collected from the protein data bank. The selected dataset of ligands was virtually screened through HTVS, SP, and XP to retain the top 4 hits. Molecular dynamics revealed the stability and flexibility of protein-(selected)ligand interactions. The non-bond interactions of each of the compounds with EGFR, such as Gossypetin interacting with active site MET769 and ASP831; Muxiangrine III interacting with MET769 and ASP831; Quercetagetin showing non-bonded interactions with GLU738, GLN767, and MET769 for >100% of the simulation timeframe These findings suggest further research into these compounds, which can yield a potential phytochemical drug against cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fabliha Bashashat Rodosy
- Department of Microbiology, Bhashasoinik Gaziul Haque Institute of Bioscience, Bogura, Bangladesh
| | - Md Abul Kalam Azad
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong, Foy's Lake, Bangladesh
| | - Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar university, Dhaka, Bangladesh
| | | | - Sadia Jaman
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Nure Asma Lata
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Mohua Sarker
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Ananna Islam Riya
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| |
Collapse
|
6
|
Can AT, Mitchell JS, Dutton M, Bennett M, Hermens DF, Lagopoulos J. Insights into the neurobiology of suicidality: explicating the role of glutamatergic systems through the lens of ketamine. Psychiatry Clin Neurosci 2023; 77:513-529. [PMID: 37329495 DOI: 10.1111/pcn.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/16/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Suicidality is a prevalent mental health condition, and managing suicidal patients is one of the most challenging tasks for health care professionals due to the lack of rapid-acting, effective psychopharmacological treatment options. According to the literature, suicide has neurobiological underpinnings that are not fully understood, and current treatments for suicidal tendencies have considerable limitations. To treat suicidality and prevent suicide, new treatments are required; to achieve this, the neurobiological processes underlying suicidal behavior must be thoroughly investigated. Although multiple neurotransmitter systems, particularly serotonergic systems, have been studied in the past, less has been reported in relation to disruptions in glutamatergic neurotransmission, neuronal plasticity, and neurogenesis that result from stress-related abnormalities of the hypothalamic-pituitary-adrenal system. Informed by the literature, which reports robust antisuicidal and antidepressive properties of subanaesthetic doses of ketamine, this review aims to provide an examination of the neurobiology of suicidality (and relevant mood disorders) with implications of pertinent animal, clinical, and postmortem studies. We discuss dysfunctions in the glutamatergic system, which may play a role in the neuropathology of suicidality and the role of ketamine in restoring synaptic connectivity at the molecular levels.
Collapse
Affiliation(s)
- Adem Tevfik Can
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | - Jules Shamus Mitchell
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | - Megan Dutton
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | - Maxwell Bennett
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | | | - Jim Lagopoulos
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| |
Collapse
|
7
|
Mazloom-Farsibaf H, Zou Q, Hsieh R, Danuser G, Driscoll MK. Cellular harmonics for the morphology-invariant analysis of molecular organization at the cell surface. NATURE COMPUTATIONAL SCIENCE 2023; 3:777-788. [PMID: 38177778 PMCID: PMC10840993 DOI: 10.1038/s43588-023-00512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/08/2023] [Indexed: 01/06/2024]
Abstract
The spatiotemporal organization of membrane-associated molecules is central to the regulation of cellular signals. Powerful new microscopy techniques enable the three-dimensional visualization of localization and activation of these molecules; however, the quantitative interpretation and comparison of molecular organization on the three-dimensional cell surface remains challenging because cells themselves vary greatly in morphology. Here we introduce u-signal3D, a framework to assess the spatial scales of molecular organization at the cell surface in a cell-morphology-invariant manner. We validated the framework by analyzing synthetic signaling patterns painted onto observed cell morphologies, as well as measured distributions of cytoskeletal and signaling molecules. To demonstrate the framework's versatility, we further compared the spatial organization of cell surface signals both within, and between, cell populations, and powered an upstream machine-learning-based analysis of signaling motifs.
Collapse
Affiliation(s)
- Hanieh Mazloom-Farsibaf
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rebecca Hsieh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Meghan K Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
8
|
Mandal S, Jana D, Dolai J, Sarkar AK, Ghorai BK, Jana NR. Biodegradable Poly(trehalose) Nanoparticle for Preventing Amyloid Beta Aggregation and Related Neurotoxicity. ACS APPLIED BIO MATERIALS 2023. [PMID: 37167565 DOI: 10.1021/acsabm.2c00771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Trehalose is a disaccharide that is capable of inhibiting protein aggregation and activating cellular autophagy. It has been shown that a polymer or nanoparticle form, terminated with multiple trehalose units, can significantly enhance the anti-amyloidogenic performance and is suitable for the treatment of neurodegenerative diseases. Here, we report a trehalose-conjugated polycarbonate-co-lactide polymer and formulation of its nanoparticles having multiple numbers of trehalose exposed on the surface. The resultant poly(trehalose) nanoparticle inhibits the aggregation of amyloid beta peptides and disintegrates matured amyloid fibrils into smaller fragments. Moreover, the poly(trehalose) nanoparticle lowers extracellular amyloid β oligomer-driven cellular stress and enhances cell viability. The presence of biodegradable polycarbonate components in the poly(trehalose) nanoparticle would enhance their application potential as an anti-amyloidogenic material.
Collapse
Affiliation(s)
- Suman Mandal
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003, United States
| | - Debabrata Jana
- Department of Chemistry, Ramakrishna Mission Vivekananda Centenary College, Rahara, West Bengal 700118, India
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, India
| | - Jayanta Dolai
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Ankan Kumar Sarkar
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Binay K Ghorai
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, India
| | - Nikhil R Jana
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| |
Collapse
|
9
|
Pandey AK, Loscalzo J. Network medicine: an approach to complex kidney disease phenotypes. Nat Rev Nephrol 2023:10.1038/s41581-023-00705-0. [PMID: 37041415 DOI: 10.1038/s41581-023-00705-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
Scientific reductionism has been the basis of disease classification and understanding for more than a century. However, the reductionist approach of characterizing diseases from a limited set of clinical observations and laboratory evaluations has proven insufficient in the face of an exponential growth in data generated from transcriptomics, proteomics, metabolomics and deep phenotyping. A new systematic method is necessary to organize these datasets and build new definitions of what constitutes a disease that incorporates both biological and environmental factors to more precisely describe the ever-growing complexity of phenotypes and their underlying molecular determinants. Network medicine provides such a conceptual framework to bridge these vast quantities of data while providing an individualized understanding of disease. The modern application of network medicine principles is yielding new insights into the pathobiology of chronic kidney diseases and renovascular disorders by expanding the understanding of pathogenic mediators, novel biomarkers and new options for renal therapeutics. These efforts affirm network medicine as a robust paradigm for elucidating new advances in the diagnosis and treatment of kidney disorders.
Collapse
Affiliation(s)
- Arvind K Pandey
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
10
|
Toledano M, Osorio E, Osorio MT, Aguilera FS, Toledano R, Romero EF, Osorio R. Dexamethasone-doped nanoparticles improve mineralization, crystallinity and collagen structure of human dentin. J Dent 2023; 130:104447. [PMID: 36754111 DOI: 10.1016/j.jdent.2023.104447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/09/2023] Open
Abstract
OBJECTIVES Bioactive materials have been used for functionalization of adhesives to promote dentin remineralization. This study aims to evaluate bonding ability and both mechanical and chemical behavior of demineralized dentin infiltrated with polymeric nanoparticles doped with dexamethasone (Dex-NPs). METHODS Dentin conditioned surfaces were infiltrated with NPs, Dex-NPs or Dex-Zn-NPs. Bonded interfaces were also created and stored for 24 h or 21d, and then submitted to microtensile bond strength testing. Dentin remineralization was analyzed by Nanohardness, Young's modulus and Raman analysis. RESULTS At 21d of storage, dentin treated with undoped-NPs attained the lowest nanohardness and Young's modulus. Dex-NPs and Zn-Dex-NPs increased dentin nanohardness and Young's modulus after 21d Raman analysis showed high remineralization, crystallinity, crosslinking and better structure of collagen when functionalized Dex-NPs were present at the dentin interface. CONCLUSIONS Infiltration of dentin with Dex-NPs promoted functional remineralization as proved by nanomechanical and morpho-chemical evaluation tests. Dexamethasone in dentin facilitated crystallographic maturity, crystallinity and improved maturity and secondary structure of dentin collagen. CLINICAL SIGNIFICANCE Using dexamethasone-functionalized NPs before resin infiltration is a clear option to obtain dentin remineralization, as these NPs produce the reinforcement of the dentin structure, which will lead to the improvement of the longevity of resin restorations.
Collapse
Affiliation(s)
- Manuel Toledano
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain
| | - Estrella Osorio
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain
| | - María T Osorio
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain
| | - Fátima S Aguilera
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain.
| | - Raquel Toledano
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain
| | - Enrique Fernández- Romero
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain
| | - Raquel Osorio
- Faculty of Dentistry, Dental Materials Section, Colegio Máximo de Cartuja s/n, University of Granada, Granada 18071, Spain
| |
Collapse
|
11
|
He H, Duo H, Hao Y, Zhang X, Zhou X, Zeng Y, Li Y, Li B. Computational drug repurposing by exploiting large-scale gene expression data: Strategy, methods and applications. Comput Biol Med 2023; 155:106671. [PMID: 36805225 DOI: 10.1016/j.compbiomed.2023.106671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
De novo drug development is an extremely complex, time-consuming and costly task. Urgent needs for therapies of various diseases have greatly accelerated searches for more effective drug development methods. Luckily, drug repurposing provides a new and effective perspective on disease treatment. Rapidly increased large-scale transcriptome data paints a detailed prospect of gene expression during disease onset and thus has received wide attention in the field of computational drug repurposing. However, how to efficiently mine transcriptome data and identify new indications for old drugs remains a critical challenge. This review discussed the irreplaceable role of transcriptome data in computational drug repurposing and summarized some representative databases, tools and strategies. More importantly, it proposed a practical guideline through establishing the correspondence between three gene expression data types and five strategies, which would facilitate researchers to adopt appropriate strategies to deeply mine large-scale transcriptome data and discover more effective therapies.
Collapse
Affiliation(s)
- Hao He
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, PR China
| | - Hongrui Duo
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Xiaoxi Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Xinyi Zhou
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Yinghong Li
- The Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China.
| |
Collapse
|
12
|
Wu CC, Huang SJ, Fu TY, Lin FL, Wang XY, Tan KT. Small-Molecule Modulated Affinity-Tunable Semisynthetic Protein Switches. ACS Sens 2022; 7:2691-2700. [PMID: 36084142 DOI: 10.1021/acssensors.2c01211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Engineered protein switches have been widely applied in cell-based protein sensors and point-of-care diagnosis for the rapid and simple analysis of a wide variety of proteins, metabolites, nucleic acids, and enzymatic activities. Currently, these protein switches are based on two main types of switching mechanisms to transduce the target binding event to a quantitative signal, through a change in the optical properties of fluorescent molecules and the activation of enzymatic activities. In this paper, we introduce a new affinity-tunable protein switch strategy in which the binding of a small-molecule target with the protein activates the streptavidin-biotin interaction to generate a readout signal. In the absence of a target, the biotinylated protein switch forms a closed conformation where the biotin is positioned in close proximity to the protein, imposing a large steric hindrance to prevent the effective binding with streptavidin. In the presence of the target molecule, this steric hindrance is removed, thereby exposing the biotin for streptavidin binding to produce strong fluorescent signals. With this modular sensing concept, various sulfonamide, methotrexate, and trimethoprim drugs can be selectively detected on the cell surface of native and genetically engineered cells using different fluorescent dyes and detection techniques.
Collapse
Affiliation(s)
- Chien-Chi Wu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Shao-Jie Huang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Tsung-Yu Fu
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Fang-Ling Lin
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Xin-You Wang
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, Republic of China
| |
Collapse
|
13
|
Ludwig RJ, Welch MG. Wired to Connect: The Autonomic Socioemotional Reflex Arc. Front Psychol 2022; 13:841207. [PMID: 35814106 PMCID: PMC9268160 DOI: 10.3389/fpsyg.2022.841207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/04/2022] [Indexed: 01/10/2023] Open
Abstract
We have previously proposed that mothers and infants co-regulate one another’s autonomic state through an autonomic conditioning mechanism, which starts during gestation and results in the formation of autonomic socioemotional reflexes (ASRs) following birth. Theoretically, autonomic physiology associated with the ASR should correlate concomitantly with behaviors of mother and infant, although the neuronal pathway by which this phenomenon occurs has not been elucidated. In this paper, we consider the neuronal pathway by which sensory stimuli between a mother and her baby/child affect the physiology and emotional behavior of each. We divide our paper into two parts. In the first part, to gain perspective on current theories on the subject, we conduct a 500-year narrative history of scientific investigations into the human nervous system and theories that describe the neuronal pathway between sensory stimulus and emotional behavior. We then review inconsistencies between several currently accepted theories and recent data. In the second part, we lay out a new theory of emotions that describes how sensory stimuli between mother and baby unconsciously control the behavior and physiology of both. We present a theory of mother/infant emotion based on a set of assumptions fundamentally different from current theories. Briefly, we propose that mother/infant sensory stimuli trigger conditional autonomic socioemotional reflexes (ASRs), which drive cardiac function and behavior without the benefit of the thalamus, amygdala or cortex. We hold that the ASR is shaped by an evolutionarily conserved autonomic learning mechanism (i.e., functional Pavlovian conditioning) that forms between mother and fetus during gestation and continues following birth. We highlight our own and others research findings over the past 15 years that support our contention that mother/infant socioemotional behavior is driven by mutual autonomic state plasticity, as opposed to cortical trait plasticity. We review a novel assessment tool designed to measure the behaviors associated with the ASR phenomenon. Finally, we discuss the significance of our theory for the treatment of mothers and infants with socioemotional disorders.
Collapse
Affiliation(s)
- Robert J. Ludwig
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, United States
- *Correspondence: Robert J. Ludwig,
| | - Martha G. Welch
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, United States
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, United States
- Department of Anatomy and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
| |
Collapse
|
14
|
Jones RD, Qian Y, Ilia K, Wang B, Laub MT, Del Vecchio D, Weiss R. Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles. Nat Commun 2022; 13:1720. [PMID: 35361767 PMCID: PMC8971529 DOI: 10.1038/s41467-022-29338-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Engineered signaling networks can impart cells with new functionalities useful for directing differentiation and actuating cellular therapies. For such applications, the engineered networks must be tunable, precisely regulate target gene expression, and be robust to perturbations within the complex context of mammalian cells. Here, we use bacterial two-component signaling proteins to develop synthetic phosphoregulation devices that exhibit these properties in mammalian cells. First, we engineer a synthetic covalent modification cycle based on kinase and phosphatase proteins derived from the bifunctional histidine kinase EnvZ, enabling analog tuning of gene expression via its response regulator OmpR. By regulating phosphatase expression with endogenous miRNAs, we demonstrate cell-type specific signaling responses and a new strategy for accurate cell type classification. Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. Our work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
Collapse
Affiliation(s)
- Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yili Qian
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Benjamin Wang
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Michael T Laub
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
15
|
Transcriptome-Guided Identification of Drugs for Repurposing to Treat Age-Related Hearing Loss. Biomolecules 2022; 12:biom12040498. [PMID: 35454087 PMCID: PMC9028743 DOI: 10.3390/biom12040498] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/13/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Age-related hearing loss (ARHL) or presbycusis is a prevalent condition associated with social isolation, cognitive impairment, and dementia. Age-related changes in the cochlea, the auditory portion of the inner ear, are the primary cause of ARHL. Unfortunately, there are currently no pharmaceutical approaches to treat ARHL. To examine the biological processes underlying age-related changes in the cochlea and identify candidate drugs for rapid repurposing to treat ARHL, we utilized bulk RNA sequencing to obtain transcriptomes from the functional substructures of the cochlea—the sensorineural structures, including the organ of Corti and spiral ganglion neurons (OC/SGN) and the stria vascularis and spiral ligament (SV/SL)—in young (6-week-old) and old (2-year-old) C57BL/6 mice. Transcriptomic analyses revealed both overlapping and unique patterns of gene expression and gene enrichment between substructures and with ageing. Based on these age-related transcriptional changes, we queried the protein products of genes differentially expressed with ageing in DrugBank and identified 27 FDA/EMA-approved drugs that are suitable to be repurposed to treat ARHL. These drugs target the protein products of genes that are differentially expressed with ageing uniquely in either the OC/SGN or SV/SL and that interrelate diverse biological processes. Further transcriptomic analyses revealed that most genes differentially expressed with ageing in both substructures encode protein products that are promising drug target candidates but are, nevertheless, not yet linked to approved drugs. Thus, with this study, we apply a novel approach to characterize the druggable genetic landscape for ARHL and propose a list of drugs to test in pre-clinical studies as potential treatment options for ARHL.
Collapse
|
16
|
Yan X, Chen Q, Huo Z, Zhang N, Ma M. Programmable Multistimuli-Responsive and Multimodal Polymer Actuator Based on a Designed Energy Transduction Network. ACS APPLIED MATERIALS & INTERFACES 2022; 14:13768-13777. [PMID: 35262326 DOI: 10.1021/acsami.2c01549] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A polymer actuator typically responds to only one or two types of stimuli, where sensing and actuation are simultaneously exerted by the same responsive polymer. In cells, sensing and actuation are exerted separately by different biomolecules, which are integrated into nanoscale assemblies to construct the signaling network, making cells a multistimuli responsive and multimodal system. Inspired by the structure-function relationship of the signaling network in cells, we have developed a strategy to select and assemble proper functional polymers into assemblies, where sensing and actuation are exerted by different polymers, and the assemblies can present novel functions beyond that of each polymer component. Three polymers [polyaniline, PANi; poly(N-isopropylacrylamide), PNIPAm; and polydimethylsiloxane, PDMS] are integrated as nodes into a simple energy transduction network, which can be regulated by three molecular factors (pH, kosmotropic anions, and polyethylene glycol). PANi converts the light or electric stimulus into heat, which triggers the actuation of PNIPAm and PDMS. Relying on this energy transduction network, the polymer assembly can respond to six types of stimuli (light, electricity, temperature, water, ions, and organic solvents) and perform different actuation modes, serving as a powerful actuator. Programmable complex deformation upon multiple simultaneous or sequential stimuli has also been achieved by this actuator. An adaptive gripper to catch thin objects and a self-regulating switch to maintain environmental humidity illustrate the wide potential of this actuator for next-generation smart materials and soft robots.
Collapse
Affiliation(s)
- Xiunan Yan
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qing Chen
- Deutsches Elektronen-Synchrotron, Hamburg 22607, Germany
| | - Ziyu Huo
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ning Zhang
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui 230601, China
| | - Mingming Ma
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| |
Collapse
|
17
|
Fu Q, Li Y, Zhang H, Cao M, Zhang L, Gao C, Cai X, Chen D, Yang Z, Li J, Yang N, Li C. Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:97-115. [PMID: 35084599 PMCID: PMC8792528 DOI: 10.1007/s10126-021-10089-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Aeromonas salmonicida is a global fish pathogen. Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and caused huge losses to salmonid industry in China. Hence, it is of great significance to develop ASM vaccine and explore its protection mechanism in salmonids. In this regard, we conducted RNA-seq analysis with spleen tissue of Atlantic salmon after ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. In our results, a total of 441.63 million clean reads were obtained, and 389.37 million reads were mapped onto the Atlantic salmon reference genome. In addition, 1125, 2126, 1098, 820, and 1351 genes were significantly up-regulated, and 747, 2626, 818, 254, and 908 genes were significantly down-regulated post-ASM vaccination at 12 h, 24 h, 1 month, 2 months, and 3 months, respectively. Subsequent pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cytokine-cytokine receptor interaction (TNFRSF11b, IL-17RA, CCR9, and CXCL11), HTLV-I infection (MR1 and HTLV-1), MAPK signaling pathway (MAPK, IL8, and TNF-α-1), PI3K-Akt signaling pathway (PIK3R3, THBS4, and COL2A1), and TNF signaling pathway (PTGS2, TNFRSF21-l, and CXCL10). Finally, the results of qRT-PCR showed a significant correlation with RNA-seq results, suggesting the reliability of RNA-seq for gene expression analysis. This study provided insights into regulation of gene expression and their involved pathways in Atlantic salmon spleen in responses to vaccine, and set the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species.
Collapse
Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hao Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Zhang
- Shandong Sinder Technology Co., Ltd, Zhucheng, 262200, China
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Defeng Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ziying Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Li
- Key Laboratory of Maricultural Organism Disease Control, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
18
|
Vandermeulen MD, Cullen PJ. Gene by Environment Interactions reveal new regulatory aspects of signaling network plasticity. PLoS Genet 2022; 18:e1009988. [PMID: 34982769 PMCID: PMC8759647 DOI: 10.1371/journal.pgen.1009988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/14/2022] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Phenotypes can change during exposure to different environments through the regulation of signaling pathways that operate in integrated networks. How signaling networks produce different phenotypes in different settings is not fully understood. Here, Gene by Environment Interactions (GEIs) were used to explore the regulatory network that controls filamentous/invasive growth in the yeast Saccharomyces cerevisiae. GEI analysis revealed that the regulation of invasive growth is decentralized and varies extensively across environments. Different regulatory pathways were critical or dispensable depending on the environment, microenvironment, or time point tested, and the pathway that made the strongest contribution changed depending on the environment. Some regulators even showed conditional role reversals. Ranking pathways' roles across environments revealed an under-appreciated pathway (OPI1) as the single strongest regulator among the major pathways tested (RAS, RIM101, and MAPK). One mechanism that may explain the high degree of regulatory plasticity observed was conditional pathway interactions, such as conditional redundancy and conditional cross-pathway regulation. Another mechanism was that different pathways conditionally and differentially regulated gene expression, such as target genes that control separate cell adhesion mechanisms (FLO11 and SFG1). An exception to decentralized regulation of invasive growth was that morphogenetic changes (cell elongation and budding pattern) were primarily regulated by one pathway (MAPK). GEI analysis also uncovered a round-cell invasion phenotype. Our work suggests that GEI analysis is a simple and powerful approach to define the regulatory basis of complex phenotypes and may be applicable to many systems.
Collapse
Affiliation(s)
- Matthew D. Vandermeulen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Paul J. Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| |
Collapse
|
19
|
Boehi F, Manetsch P, Hottiger MO. Interplay between ADP-ribosyltransferases and essential cell signaling pathways controls cellular responses. Cell Discov 2021; 7:104. [PMID: 34725336 PMCID: PMC8560908 DOI: 10.1038/s41421-021-00323-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Signaling cascades provide integrative and interactive frameworks that allow the cell to respond to signals from its environment and/or from within the cell itself. The dynamic regulation of mammalian cell signaling pathways is often modulated by cascades of protein post-translational modifications (PTMs). ADP-ribosylation is a PTM that is catalyzed by ADP-ribosyltransferases and manifests as mono- (MARylation) or poly- (PARylation) ADP-ribosylation depending on the addition of one or multiple ADP-ribose units to protein substrates. ADP-ribosylation has recently emerged as an important cell regulator that impacts a plethora of cellular processes, including many intracellular signaling events. Here, we provide an overview of the interplay between the intracellular diphtheria toxin-like ADP-ribosyltransferase (ARTD) family members and five selected signaling pathways (including NF-κB, JAK/STAT, Wnt-β-catenin, MAPK, PI3K/AKT), which are frequently described to control or to be controlled by ADP-ribosyltransferases and how these interactions impact the cellular responses.
Collapse
Affiliation(s)
- Flurina Boehi
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Cancer Biology PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Patrick Manetsch
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
20
|
Viacava Follis A. Centrality of drug targets in protein networks. BMC Bioinformatics 2021; 22:527. [PMID: 34715787 PMCID: PMC8555226 DOI: 10.1186/s12859-021-04342-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023] Open
Abstract
Background In the pharmaceutical industry, competing for few validated drug targets there is a drive to identify new ways of therapeutic intervention. Here, we attempted to define guidelines to evaluate a target’s ‘fitness’ based on its node characteristics within annotated protein functional networks to complement contingent therapeutic hypotheses. Results We observed that targets of approved, selective small molecule drugs exhibit high node centrality within protein networks relative to a broader set of investigational targets spanning various development stages. Targets of approved drugs also exhibit higher centrality than other proteins within their respective functional class. These findings expand on previous reports of drug targets’ network centrality by suggesting some centrality metrics such as low topological coefficient as inherent characteristics of a ‘good’ target, relative to other exploratory targets and regardless of its functional class. These centrality metrics could thus be indicators of an individual protein’s ‘fitness’ as potential drug target. Correlations between protein nodes’ network centrality and number of associated publications underscored the possibility of knowledge bias as an inherent limitation to such predictions. Conclusions Despite some entanglement with knowledge bias, like structure-oriented ‘druggability’ assessments of new protein targets, centrality metrics could assist early pharmaceutical discovery teams in evaluating potential targets with limited experimental proof of concept and help allocate resources for an effective drug discovery pipeline. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04342-x.
Collapse
Affiliation(s)
- Ariele Viacava Follis
- EMD Serono Research and Development Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA.
| |
Collapse
|
21
|
Alveolar Regeneration in COVID-19 Patients: A Network Perspective. Int J Mol Sci 2021; 22:ijms222011279. [PMID: 34681944 PMCID: PMC8538208 DOI: 10.3390/ijms222011279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
A viral infection involves entry and replication of viral nucleic acid in a host organism, subsequently leading to biochemical and structural alterations in the host cell. In the case of SARS-CoV-2 viral infection, over-activation of the host immune system may lead to lung damage. Albeit the regeneration and fibrotic repair processes being the two protective host responses, prolonged injury may lead to excessive fibrosis, a pathological state that can result in lung collapse. In this review, we discuss regeneration and fibrosis processes in response to SARS-CoV-2 and provide our viewpoint on the triggering of alveolar regeneration in coronavirus disease 2019 (COVID-19) patients.
Collapse
|
22
|
Shetty A, Bhosale SD, Tripathi SK, Buchacher T, Biradar R, Rasool O, Moulder R, Galande S, Lahesmaa R. Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells. ACS OMEGA 2021; 6:24834-24847. [PMID: 34604665 PMCID: PMC8482465 DOI: 10.1021/acsomega.1c03681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 05/10/2023]
Abstract
Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among the latter, FOSL1 and FOSL2 modulate the effector functions of Th17 cells. However, the molecular mechanisms underlying these effects are unclear, owing to the poorly characterized protein interaction networks of FOSL factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a significant fraction of these interactors to be associated with RNA-binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17 fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL proteins that potentially govern Th17 cell differentiation and associated pathologies.
Collapse
Affiliation(s)
- Ankitha Shetty
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Santosh D. Bhosale
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- Protein
Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Subhash Kumar Tripathi
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
| | - Tanja Buchacher
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Rahul Biradar
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Riitta Lahesmaa
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| |
Collapse
|
23
|
Gong C, Qiao Z, Zhu S, Wang W, Chen YC. Self-Assembled Biophotonic Lasing Network Driven by Amyloid Fibrils in Microcavities. ACS NANO 2021; 15:15007-15016. [PMID: 34533023 DOI: 10.1021/acsnano.1c05266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-assembled biological structures have played a significant role in many living systems for its functionality and distinctiveness. Here, we experimentally demonstrate that the random dynamic behavior of strong light-matter interactions in complex biological structures can provide hidden information on optical coupling in a network. The concept of biophotonic lasing network is therefore introduced, where a self-assembled human amyloid fibril network was confined in a Fabry-Perot optical cavity. Distinctive lasing patterns were discovered from self-assembled amyloids with different structural dimensions (0D, 1D, 2D, and 3D) confined in a microcavity. Network laser emission exhibiting evidence of light coupling at different wavelengths and locations was spectrally resolved. Dynamic changes of lasing patterns can therefore be interpreted into a graph to reveal the optical correlation in biophotonic networks. Our findings indicate that each graph represents the highly unclonable features of a self-assembled network which can sensitively respond to environmental stimulus. This study offers the potential for studying dynamic biological networks through amplified interactions, shedding light on the development of biologically controlled photonic devices, biosensing, and information encryption.
Collapse
Affiliation(s)
- Chaoyang Gong
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Zhen Qiao
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Song Zhu
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Wenjie Wang
- Key Lab of Advanced Transducers and Intelligent Control System of Ministry of Education, Taiyuan University of Technology, 79 Yingze Street, Taiyuan 030024, PR China
| | - Yu-Cheng Chen
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| |
Collapse
|
24
|
Toledano-Osorio M, Aguilera FS, Muñoz-Soto E, Osorio E, Toledano M, Escames G, Medina-Castillo AL, Osorio MT, López-López MT, Vallecillo-Rivas M, Osorio R. Melatonin-doped polymeric nanoparticles induce high crystalline apatite formation in root dentin. Dent Mater 2021; 37:1698-1713. [PMID: 34544591 DOI: 10.1016/j.dental.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/04/2021] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To investigate the effect of novel polymeric nanoparticles (NPs) doped with melatonin (ML) on nano-hardness, crystallinity and ultrastructure of the formed hydroxyapatite after endodontic treatment. METHODS Undoped-NPs and ML-doped NPs (ML-NPs) were tested at radicular dentin, after 24 h and 6 m. A control group without NPs was included. Radicular cervical and apical dentin surfaces were studied by nano-hardness measurements, X-ray diffraction and transmission electron microscopy. Mean and standard deviation were analyzed by ANOVA and Student-Newman-Keuls multiple comparisons (p < 0.05). RESULTS Cervical dentin treated with undoped NPs maintained its nano-hardness values after 6 m of storage being [24 h: 0.29 (0.01); 6 m: 0.30 (0.02) GPa], but it decreased at apical dentin [24 h: 0.36 (0.01); 6 m: 0.28 (0.02) GPa]. When ML-NPs were used, nano-hardness was similar over time [24h: 0.31 (0.02); 6 m: 0.28 (0.03) GPa], at apical dentin. Root dentin treated with ML-NPs produced, in general, high crystallinity of new minerals and thicker crystals than those produced in the rest of the groups. After 6 m, crystals became organized in randomly oriented polyhedral, square polygonal block-like apatite or drop-like apatite polycrystalline lattices when ML-NPs were used. Undoped NPs generated poor crystallinity, with preferred orientation of small crystallite and increased microstrain. SIGNIFICANCE New polycrystalline formations encountered in dentin treated with ML-NPs may produce structural dentin stability and high mechanical performance at the root. The decrease of mechanical properties over time in dentin treated without NPs indicates scarce remineralization potential, dentin demineralization and further potential degradation. The amorphous stage may provide high hydroxyapatite solubility and remineralizing activity.
Collapse
Affiliation(s)
- Manuel Toledano-Osorio
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain
| | - Fátima S Aguilera
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain
| | - Esther Muñoz-Soto
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain
| | - Estrella Osorio
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain
| | - Manuel Toledano
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain.
| | - Germaine Escames
- Faculty of Medicine, Department of Physiology, Biomedical Research Center, CIBERFES, Ibs. San Cecilio University Hospital, University of Granada, Granada, Spain
| | - Antonio L Medina-Castillo
- University of Granada, NanoMyP, Spin-Off Enterprise, Edificio BIC-Granada, Av. Innovación 1, 18016, Armilla, Granada, Spain
| | | | - Modesto T López-López
- University of Granada, Faculty of Science, Applied Physics Department, Av. Fuente Nueva s/n, 18071 Granada, Spain
| | - Marta Vallecillo-Rivas
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain
| | - Raquel Osorio
- University of Granada, Department of Stomatology, Colegio Máximo de Cartuja s/n, Granada 18071, Spain
| |
Collapse
|
25
|
Prabhakar A, González B, Dionne H, Basu S, Cullen PJ. Spatiotemporal control of pathway sensors and cross-pathway feedback regulate a differentiation MAPK pathway in yeast. J Cell Sci 2021; 134:jcs258341. [PMID: 34347092 PMCID: PMC8353523 DOI: 10.1242/jcs.258341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways control cell differentiation and the response to stress. In Saccharomyces cerevisiae, the MAPK pathway that controls filamentous growth (fMAPK) shares components with the pathway that regulates the response to osmotic stress (HOG). Here, we show that the two pathways exhibit different patterns of activity throughout the cell cycle. The different patterns resulted from different expression profiles of genes encoding mucin sensors that regulate the pathways. Cross-pathway regulation from the fMAPK pathway stimulated the HOG pathway, presumably to modulate fMAPK pathway activity. We also show that the shared tetraspan protein Sho1p, which has a dynamic localization pattern throughout the cell cycle, induced the fMAPK pathway at the mother-bud neck. A Sho1p-interacting protein, Hof1p, which also localizes to the mother-bud neck and regulates cytokinesis, also regulated the fMAPK pathway. Therefore, spatial and temporal regulation of pathway sensors, and cross-pathway regulation, control a MAPK pathway that regulates cell differentiation in yeast.
Collapse
Affiliation(s)
| | | | | | | | - Paul J. Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260-1300, USA
| |
Collapse
|
26
|
Das D, Wang J, Hong J. Next-Generation Kinase Inhibitors Targeting Specific Biomarkers in Non-Small Cell Lung Cancer (NSCLC): A Recent Overview. ChemMedChem 2021; 16:2459-2479. [PMID: 33929777 DOI: 10.1002/cmdc.202100166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/27/2021] [Indexed: 12/25/2022]
Abstract
Lung cancer causes many deaths globally. Mutations in regulatory genes, irregularities in specific signal transduction events, or alterations of signalling pathways are observed in cases of non-small cell lung cancer (NSCLC). Over the past two decades, a few kinases have been identified, validated, and studied as biomarkers for NSCLC. Among them, EGFR, ALK, ROS1, MET, RET, NTRK, and BRAF are regarded as targetable biomarkers to cure and/or control the disease. In recent years, the US Food and Drug Administration (FDA) approved more than 15 kinase inhibitors targeting these NSCLC biomarkers. The kinase inhibitors significantly improved the progression-free survival (PFS) of NSCLC patients. Challenges still remain for metastatic diseases and advanced NSCLC cases. New discoveries of potent kinase inhibitors and rapid development of modern medical technologies will help to control NSCLC cases. This article provides an overview of the discoveries of various types of kinase inhibitors against NSCLC, along with medicinal chemistry aspects and related developments in next-generation kinase inhibitors that have been reported in recent years.
Collapse
Affiliation(s)
- Debasis Das
- Discovery Chemistry Research, Arromax Pharmatech Co., Ltd., Sangtiandao Innovation Park, No. 1 Huayun Road, SIP, Suzhou, 215123, China
| | - Jingbing Wang
- Discovery Chemistry Research, Arromax Pharmatech Co., Ltd., Sangtiandao Innovation Park, No. 1 Huayun Road, SIP, Suzhou, 215123, China
| | - Jian Hong
- Discovery Chemistry Research, Arromax Pharmatech Co., Ltd., Sangtiandao Innovation Park, No. 1 Huayun Road, SIP, Suzhou, 215123, China
| |
Collapse
|
27
|
Anene CA, Khan F, Bewicke-Copley F, Maniati E, Wang J. ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles. PATTERNS (NEW YORK, N.Y.) 2021; 2:100270. [PMID: 34179848 PMCID: PMC8212143 DOI: 10.1016/j.patter.2021.100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/10/2021] [Accepted: 04/28/2021] [Indexed: 11/01/2022]
Abstract
Determining the tissue- and disease-specific circuit of biological pathways remains a fundamental goal of molecular biology. Many components of these biological pathways still remain unknown, hindering the full and accurate characterization of biological processes of interest. Here we describe ACSNI, an algorithm that combines prior knowledge of biological processes with a deep neural network to effectively decompose gene expression profiles (GEPs) into multi-variable pathway activities and identify unknown pathway components. Experiments on public GEP data show that ACSNI predicts cogent components of mTOR, ATF2, and HOTAIRM1 signaling that recapitulate regulatory information from genetic perturbation and transcription factor binding datasets. Our framework provides a fast and easy-to-use method to identify components of signaling pathways as a tool for molecular mechanism discovery and to prioritize genes for designing future targeted experiments (https://github.com/caanene1/ACSNI).
Collapse
Affiliation(s)
- Chinedu Anthony Anene
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Faraz Khan
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Findlay Bewicke-Copley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Eleni Maniati
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| |
Collapse
|
28
|
Sommariva S, Caviglia G, Piana M. Gain and loss of function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells. J Math Biol 2021; 82:55. [PMID: 33945019 PMCID: PMC8096774 DOI: 10.1007/s00285-021-01607-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/20/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found in cancer cells. More specifically, from a theoretical perspective, our approach focuses on the determination of moiety conservation laws for the system and their relation with the corresponding stoichiometric surfaces. Then we show that Loss of Function mutations can be implemented in the model via modification of the initial conditions in the system, while Gain of Function mutations can be implemented by eliminating specific reactions. Finally, the model is utilized to examine in detail the G1-S phase of a colorectal cancer cell.
Collapse
Affiliation(s)
- Sara Sommariva
- Dipartimento di Matematica, Universitá di Genova, Via Dodecaneso, 35 16146, Genoa, Italy
| | - Giacomo Caviglia
- Dipartimento di Matematica, Universitá di Genova, Via Dodecaneso, 35 16146, Genoa, Italy
| | - Michele Piana
- Dipartimento di Matematica, Universitá di Genova, Via Dodecaneso, 35 16146, Genoa, Italy. .,CNR - SPIN GENOVA, Via Dodecaneso, 35 16146, Genoa, Italy.
| |
Collapse
|
29
|
Harris MJ, Fuyal M, James JR. Quantifying persistence in the T-cell signaling network using an optically controllable antigen receptor. Mol Syst Biol 2021; 17:e10091. [PMID: 33988299 PMCID: PMC8120804 DOI: 10.15252/msb.202010091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022] Open
Abstract
T cells discriminate between healthy and infected cells with remarkable sensitivity when mounting an immune response, which is hypothesized to depend on T cells combining stimuli from multiple antigen-presenting cell interactions into a more potent response. To quantify the capacity for T cells to accomplish this, we have developed an antigen receptor that is optically tunable within cell conjugates, providing control over the duration, and intensity of intracellular T-cell signaling. We observe limited persistence within the T-cell intracellular network on disruption of receptor input, with signals dissipating entirely in ~15 min, and directly show sustained proximal receptor signaling is required to maintain gene transcription. T cells thus primarily accumulate the outputs of gene expression rather than integrate discrete intracellular signals. Engineering optical control in a clinically relevant chimeric antigen receptor (CAR), we show that this limited signal persistence can be exploited to increase CAR-T cell activation threefold using pulsatile stimulation. Our results are likely to apply more generally to the signaling dynamics of other cellular networks.
Collapse
Affiliation(s)
- Michael J Harris
- Molecular Immunity UnitDepartment of MedicineMRC‐LMBUniversity of CambridgeCambridgeUK
| | - Muna Fuyal
- Division of Biomedical SciencesWarwick Medical SchoolUniversity of WarwickCoventryUK
| | - John R James
- Molecular Immunity UnitDepartment of MedicineMRC‐LMBUniversity of CambridgeCambridgeUK
- Division of Biomedical SciencesWarwick Medical SchoolUniversity of WarwickCoventryUK
| |
Collapse
|
30
|
Hernández-Vega AM, Camacho-Arroyo I. Crosstalk between 17β-Estradiol and TGF-β Signaling Modulates Glioblastoma Progression. Brain Sci 2021; 11:brainsci11050564. [PMID: 33925221 PMCID: PMC8145480 DOI: 10.3390/brainsci11050564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/30/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is an essential mechanism contributing to glioblastoma multiforme (GBM) progression, the most common and malignant brain tumor. EMT is induced by signaling pathways that crosstalk and regulate an intricate regulatory network of transcription factors. It has been shown that downstream components of 17β-estradiol (E2) and transforming growth factor β (TGF-β) signaling pathways crosstalk in estrogen-sensitive tumors. However, little is known about the interaction between the E2 and TGF-β signaling components in brain tumors. We have investigated the relationship between E2 and TGF-β signaling pathways and their effects on EMT induction in human GBM-derived cells. Here, we showed that E2 and TGF-β negatively regulated the expression of estrogen receptor α (ER-α) and Smad2/3. TGF-β induced Smad2 phosphorylation and its subsequent nuclear translocation, which E2 inhibited. Both TGF-β and E2 induced cellular processes related to EMT, such as morphological changes, actin filament reorganization, and mesenchymal markers (N-cadherin and vimentin) expression. Interestingly, we found that the co-treatment of E2 and TGF-β blocked EMT activation. Our results suggest that E2 and TGF-β signaling pathways interact through ER-α and Smad2/3 mediators in cells derived from human GBM and inhibit EMT activation induced by both factors alone.
Collapse
|
31
|
Geilfus CM, Zhang X, Mithöfer A, Burgel L, Bárdos G, Zörb C. Leaf apoplastic alkalization promotes transcription of the ABA-synthesizing enzyme Vp14 and stomatal closure in Zea mays. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2686-2695. [PMID: 33345268 PMCID: PMC8006549 DOI: 10.1093/jxb/eraa589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The chloride component of NaCl salinity causes the leaf apoplast to transiently alkalinize. This transition in pH reduces stomatal aperture. However, whether this apoplastic pH (pHapo) transient initiates stomatal closure by interacting with other chloride stress-induced responses or whether the pH transient alone initiates stomatal closure is unknown. To clarify the problem, the transient alkalinization of the leaf apoplast was mimicked in intact maize (Zea mays L.) by infiltrating near-neutral pH buffers into the leaf apoplast. Effects of the pHapo transient could thus be investigated independently from other chloride stress-derived effects. Microscopy-based ratiometric live pHapo imaging was used to monitor pHapoin planta. LC-MS/MS and real-time quantitative reverse transcription-PCR leaf analyses showed that the artificially induced pHapo transient led to an increase in the concentrations of the stomata-regulating plant hormone abscisic acid (ABA) and in transcripts of the key ABA-synthesizing gene ZmVp14 in the leaf. Since stomatal aperture and stomatal conductance decreased according to pHapo, we conclude that the pHapo transient alone initiates stomatal closure. Therefore, the functionality does not depend on interactions with other compounds induced by chloride stress. Overall, our data indicate that the pH of the leaf apoplast links chloride salinity with the control of stomatal aperture via effects exerted on the transcription of ABA.
Collapse
Affiliation(s)
- Christoph-Martin Geilfus
- Division of Controlled Environment Horticulture, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Xudong Zhang
- Institute of Crop Science, Quality of Plant Products, University Hohenheim, Schloss, Westhof-West, Stuttgart, Germany
| | - Axel Mithöfer
- Max Planck Institute for Chemical Ecology, Research Group Plant Defense Physiology, Hans-Knöll-Straße, Jena, Germany
| | - Lisa Burgel
- Institute of Crop Science, Quality of Plant Products, University Hohenheim, Schloss, Westhof-West, Stuttgart, Germany
| | - Gyöngyi Bárdos
- Institute of Crop Science, Quality of Plant Products, University Hohenheim, Schloss, Westhof-West, Stuttgart, Germany
| | - Christian Zörb
- Institute of Crop Science, Quality of Plant Products, University Hohenheim, Schloss, Westhof-West, Stuttgart, Germany
| |
Collapse
|
32
|
Huang X, Zhang H. Corrected score methods for estimating Bayesian networks with error-prone nodes. Stat Med 2021; 40:2692-2712. [PMID: 33665887 DOI: 10.1002/sim.8925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/29/2020] [Accepted: 02/06/2021] [Indexed: 01/16/2023]
Abstract
Motivated by inferring cellular signaling networks using noisy flow cytometry data, we develop procedures to draw inference for Bayesian networks based on error-prone data. Two methods for inferring causal relationships between nodes in a network are proposed based on penalized estimation methods that account for measurement error and encourage sparsity. We discuss consistency of the proposed network estimators and develop an approach for selecting the tuning parameter in the penalized estimation methods. Empirical studies are carried out to compare the proposed methods with a naive method that ignores measurement error. Finally, we apply these methods to infer signaling networks using single cell flow cytometry data.
Collapse
Affiliation(s)
- Xianzheng Huang
- Department of Statistics, University of South Carolina, Columbia, South Carolina, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tennessee, USA
| |
Collapse
|
33
|
Hershey DM. Integrated control of surface adaptation by the bacterial flagellum. Curr Opin Microbiol 2021; 61:1-7. [PMID: 33640633 DOI: 10.1016/j.mib.2021.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 02/05/2023]
Abstract
Many bacteria can alternate between motile and sessile lifestyles, and wide-ranging sets of environmental stimuli regulate the transition from a free-swimming to a surface-attached state. A transenvelope machine called the flagellum, known primarily for its role in promoting cellular motility, stimulates the motile-sessile transition by detecting contact with solid substrates. Recent work has revealed a striking level of sophistication within the regulatory circuits that link flagellar function to surface colonization. I describe the current paradigm whereby the flagellum promotes the sessile state by increasing production of the second-messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP). I then highlight studies that have identified multiple routes by which the flagellum activates c-di-GMP production, calling the concept of a linear surface recognition pathway into the question. I conclude by proposing a role for the flagellum as a signaling hub that integrates environmental stimuli to coordinate a surface colonization program that occurs across a range of spatial and temporal scales.
Collapse
Affiliation(s)
- David M Hershey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
34
|
Abstract
Molecular dynamics simulations of membrane proteins have grown dramatically in the last 20 years. Running these simulations first requires embedding the protein's three-dimensional structure in a lipid bilayer of a suitable composition, one that resembles its native environment. This step is far from trivial, especially for modeling heterogeneous mixtures of lipids. CHARMM-GUI, a webserver for simulation system preparation greatly simplifies this step, allowing for the construction of complex heterogeneous and/or asymmetric membranes. Here, we demonstrate how to use CHARMM-GUI to build the membrane for the outer-membrane protein BamA.
Collapse
|
35
|
Pathak P, Rimac H, Grishina M, Verma A, Potemkin V. Hybrid Quinazoline 1,3,5-Triazines as Epidermal Growth Factor Receptor (EGFR) Inhibitors with Anticancer Activity: Design, Synthesis, and Computational Study. ChemMedChem 2020; 16:822-838. [PMID: 33155373 DOI: 10.1002/cmdc.202000646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/08/2020] [Indexed: 11/07/2022]
Abstract
We report a series of hybrid quinazoline-1,3,5-triazine derivatives as EGFR inhibitors, which were synthesised and tested by using a variety of in vitro, in silico, and in vivo techniques. The derivatives were found to be active against different cancer cell lines and nontoxic against normal ones, with compounds 7 c, 7 d, 7 e, and 7 j being the most potent ones. The derivatives were also evaluated for angiogenesis inhibition potency in chicken eggs, and molecular docking and dynamics simulation studies were carried out to elucidate the fundamental substituent groups essential for their bioactivity. Additionally, a SAR study of the derivatives was performed for future compound optimisation. These studies suggested that the derivatives have a high affinity towards EGFR with favourable pharmacological properties. The most active compound (7 e) was further evaluated for in vivo anticancer activity against DMBA-induced tumours in female Sprague-Dawley rats as well as its effects on plasma antioxidant status, biotransformation enzymes, and lipid profile. The study suggested that 7 e has lead properties against breast cancer and can serve as a starting compound for further development of anti-EGFR compounds.
Collapse
MESH Headings
- 9,10-Dimethyl-1,2-benzanthracene
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Dose-Response Relationship, Drug
- Drug Design
- Drug Screening Assays, Antitumor
- ErbB Receptors/antagonists & inhibitors
- ErbB Receptors/metabolism
- Female
- Humans
- Mammary Neoplasms, Experimental/chemically induced
- Mammary Neoplasms, Experimental/drug therapy
- Mammary Neoplasms, Experimental/pathology
- Models, Molecular
- Molecular Structure
- Protein Kinase Inhibitors/chemical synthesis
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Quinazolines/chemistry
- Quinazolines/pharmacology
- Rats
- Rats, Sprague-Dawley
- Structure-Activity Relationship
- Triazines/chemistry
- Triazines/pharmacology
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| | - Hrvoje Rimac
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovacica 1, Zagreb, 10000, Croatia
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences Naini, Prayagraj, Uttar Pradesh, 211007, India
| | - Vladimir Potemkin
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| |
Collapse
|
36
|
Henriques JF, Serra D, Dinis TCP, Almeida LM. The Anti-Neuroinflammatory Role of Anthocyanins and Their Metabolites for the Prevention and Treatment of Brain Disorders. Int J Mol Sci 2020; 21:E8653. [PMID: 33212797 PMCID: PMC7696928 DOI: 10.3390/ijms21228653] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022] Open
Abstract
Anthocyanins are naturally occurring polyphenols commonly found in fruits and vegetables. Numerous studies have described that anthocyanin-rich foods may play a crucial role in the prevention and treatment of different pathological conditions, which have encouraged their consumption around the world. Anthocyanins exhibit a significant neuroprotective role, mainly due to their well-recognized antioxidant and anti-inflammatory properties. Neuroinflammation is an intricate process relevant in both homeostatic and pathological circumstances. Since the progression of several neurological disorders relies on neuroinflammatory process, targeting brain inflammation has been considered a promising strategy in those conditions. Recent data have shown the anti-neuroinflammatory abilities of many anthocyanins and of their metabolites in the onset and development of several neurological disorders. In this review, it will be discussed the importance and the applicability of these polyphenolic compounds as neuroprotective agents and it will be also scrutinized the molecular mechanisms underlying the modulation of neuroinflammation by these natural compounds in the context of several brain diseases.
Collapse
Affiliation(s)
- Joana F. Henriques
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.F.H.); (T.C.P.D.); (L.M.A.)
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Diana Serra
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.F.H.); (T.C.P.D.); (L.M.A.)
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Teresa C. P. Dinis
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.F.H.); (T.C.P.D.); (L.M.A.)
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Leonor M. Almeida
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.F.H.); (T.C.P.D.); (L.M.A.)
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| |
Collapse
|
37
|
Dual-memory retrieval efficiency after practice: effects of strategy manipulations. PSYCHOLOGICAL RESEARCH 2020; 84:2210-2236. [PMID: 31218397 DOI: 10.1007/s00426-019-01217-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 06/12/2019] [Indexed: 10/26/2022]
Abstract
The study investigated practice effects, instruction manipulations, and the associated cognitive architecture of dual-memory retrieval from a single cue. In two experiments, we tested predictions about the presence of learned parallelism in dual-memory retrieval within the framework of the set-cue bottleneck model. Both experiments included three experimental laboratory sessions and involved computerized assessments of dual-memory retrieval performance with strategy instruction manipulations. In Experiment 1, subjects were assigned to three distinct dual-task practice instruction groups: (1) a neutral instruction group without a specific direction on how to solve the task (i.e., neutral instruction), (2) an instruction to synchronize the responses (i.e., synchronize instruction), and (3) an instruction to use a sequential response style (i.e., immediate instruction). Results indicate that strategy instructions are able to effectively influence dual retrieval during practice. Mainly, the instruction to synchronize responses led to the presence of learned retrieval parallelism. Experiment 2 provided an assessment of the cognitive processing architecture of dual-memory retrieval. The results provide support for the presence of a structural bottleneck that cannot be eliminated by extensive practice and instruction manipulations. Further results are discussed with respect to the set-cue bottleneck model.
Collapse
|
38
|
Islam T, Majumder M, Kalita B, Bhattacharjee A, Mukhopadhyay R, Mukherjee AK. Transcriptomic, proteomic, and biochemical analyses reveal a novel neuritogenesis mechanism of
Naja naja
venom α‐elapitoxin post binding to TrkA receptor of rat pheochromocytoma cells. J Neurochem 2020; 155:612-637. [DOI: 10.1111/jnc.15153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Taufikul Islam
- Microbial Biotechnology and Protein Research Laboratory Department of Molecular Biology and Biotechnology School of Sciences Tezpur University Tezpur Assam India
| | - Munmi Majumder
- Cellular, Molecular, and Environmental Biotechnology Laboratory Department of Molecular Biology and Biotechnology School of Sciences Tezpur University Tezpur Assam India
| | - Bhargab Kalita
- Microbial Biotechnology and Protein Research Laboratory Department of Molecular Biology and Biotechnology School of Sciences Tezpur University Tezpur Assam India
| | - Atanu Bhattacharjee
- Department of Biotechnology and Bioinformatics North Eastern Hill University Shillong Meghalaya India
| | - Rupak Mukhopadhyay
- Cellular, Molecular, and Environmental Biotechnology Laboratory Department of Molecular Biology and Biotechnology School of Sciences Tezpur University Tezpur Assam India
| | - Ashis K. Mukherjee
- Microbial Biotechnology and Protein Research Laboratory Department of Molecular Biology and Biotechnology School of Sciences Tezpur University Tezpur Assam India
| |
Collapse
|
39
|
Zhou X, Mehta S, Zhang J. Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks. Trends Biochem Sci 2020; 45:889-905. [PMID: 32660810 PMCID: PMC7502535 DOI: 10.1016/j.tibs.2020.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Cell signaling networks are intricately regulated in time and space to determine the responses and fates of cells to different cues. Genetically encodable fluorescent and bioluminescent biosensors enable the direct visualization of these spatiotemporal signaling dynamics within the native biological context, and have therefore become powerful molecular tools whose unique benefits are being used to address challenging biological questions. We first review the basis of biosensor design and remark on recent technologies that are accelerating biosensor development. We then discuss a few of the latest advances in the development and application of genetically encodable fluorescent and bioluminescent biosensors that have led to scientific or technological breakthroughs.
Collapse
Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
40
|
Measuring signal transduction and transcription molecules for clinical use. ASIAN BIOMED 2020; 14:175-176. [PMID: 37551264 PMCID: PMC10373411 DOI: 10.1515/abm-2020-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
|
41
|
Jasmine S, Thangavelu A, Krishnamoorthy R, Alshuniaber MA, Alshatwi AA. Cytokine Expression Pattern and Protein-Protein interaction network analysis of Leucocyte Rich Platelet Rich Fibrin and Injectable Form of Platelet Rich Fibrin. Oral Maxillofac Surg 2020; 25:223-229. [PMID: 32915342 DOI: 10.1007/s10006-020-00899-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
PURPOSE Platelet-rich fibrin (PRF) such as leucocyte-rich PRF (L-PRF) and injectable form of PRF (i-PRF) are widely used in various surgical applications. L-PRF- and i-PRF-derived cytokine variations and functional pathways are still unexplored. The aim of the study was to evaluate the expression pattern of Th1-, Th2-, and Th17-related cytokines by L-PRF and i-PRF under in vitro. METHODS Cytokine levels were evaluated using multi-analyte ELISArray kit. Using elevated level of cytokines, the protein-protein interaction and pathway were predicted by computational method. RESULTS The expressed cytokine levels were higher in L-PRF than in i-PRF. Specifically in L-PRF, IL8, IL2, IL6, and IL1A were expressed abundantly, whereas IL4, IL10, and IL6 were significantly high in i-PRF. Furthermore, protein-protein interaction (PPI) networks (cytokine-cytokine interactions) and pathway analyses were predicted using higher-order cytokines. PPI networks and gene ontology enrichment analysis showed functional variations between L-PRF and i-PRF. Kyoto Encyclopedia of Gene and Genome pathway analysis found that L-PRF mediates NF-k B signaling, Toll-like receptor signaling (TLR), and MAPK signaling via T-cell receptor signaling pathway. i-PRF is significantly involved in JAK-STAT signaling pathway through upregulation of STAT1. CONCLUSION Our study concludes that L-PRF and i-PRF act via different pathways that confirm functional variations between them. Therefore, we speculate that L-PRF may be effective in acute phase of chronic wounds such as in diabetes mellitus and immunocompromised patients whereas i-PRF may have a better outcome in acute wounds.
Collapse
Affiliation(s)
- Sharmila Jasmine
- Department of Oral Maxillofacial Surgery, Rajah Muthiah Dental College and Hospital, Annamalai University, Chidambaram, Tamil Nadu, 608002, India.
| | - Annamalai Thangavelu
- Department of Oral Maxillofacial Surgery, Rajah Muthiah Dental College and Hospital, Annamalai University, Chidambaram, Tamil Nadu, 608002, India
| | - Rajapandiyan Krishnamoorthy
- Nanobiotechnology and Molecular Biology Research Lab, Department of Food Science and Nutrition, College of Food Science, King Saud University, Riyadh, 11541, Kingdom of Saudi Arabia
| | - Mohammed A Alshuniaber
- Nanobiotechnology and Molecular Biology Research Lab, Department of Food Science and Nutrition, College of Food Science, King Saud University, Riyadh, 11541, Kingdom of Saudi Arabia
| | - Ali A Alshatwi
- Nanobiotechnology and Molecular Biology Research Lab, Department of Food Science and Nutrition, College of Food Science, King Saud University, Riyadh, 11541, Kingdom of Saudi Arabia
| |
Collapse
|
42
|
Fortelny N, Bock C. Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data. Genome Biol 2020; 21:190. [PMID: 32746932 PMCID: PMC7397672 DOI: 10.1186/s13059-020-02100-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Deep learning has emerged as a versatile approach for predicting complex biological phenomena. However, its utility for biological discovery has so far been limited, given that generic deep neural networks provide little insight into the biological mechanisms that underlie a successful prediction. Here we demonstrate deep learning on biological networks, where every node has a molecular equivalent, such as a protein or gene, and every edge has a mechanistic interpretation, such as a regulatory interaction along a signaling pathway. RESULTS With knowledge-primed neural networks (KPNNs), we exploit the ability of deep learning algorithms to assign meaningful weights in multi-layered networks, resulting in a widely applicable approach for interpretable deep learning. We present a learning method that enhances the interpretability of trained KPNNs by stabilizing node weights in the presence of redundancy, enhancing the quantitative interpretability of node weights, and controlling for uneven connectivity in biological networks. We validate KPNNs on simulated data with known ground truth and demonstrate their practical use and utility in five biological applications with single-cell RNA-seq data for cancer and immune cells. CONCLUSIONS We introduce KPNNs as a method that combines the predictive power of deep learning with the interpretability of biological networks. While demonstrated here on single-cell sequencing data, this method is broadly relevant to other research areas where prior domain knowledge can be represented as networks.
Collapse
Affiliation(s)
- Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
43
|
Mandal S, Panja P, Debnath K, Jana NR, Jana NR. Small-Molecule-Functionalized Hyperbranched Polyglycerol Dendrimers for Inhibiting Protein Aggregation. Biomacromolecules 2020; 21:3270-3278. [DOI: 10.1021/acs.biomac.0c00713] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Suman Mandal
- School of Material Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prasanta Panja
- School of Material Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Koushik Debnath
- School of Material Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Nihar R. Jana
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Nikhil R. Jana
- School of Material Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| |
Collapse
|
44
|
Rosario D, Boren J, Uhlen M, Proctor G, Aarsland D, Mardinoglu A, Shoaie S. Systems Biology Approaches to Understand the Host-Microbiome Interactions in Neurodegenerative Diseases. Front Neurosci 2020; 14:716. [PMID: 32733199 PMCID: PMC7360858 DOI: 10.3389/fnins.2020.00716] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases (NDDs) comprise a broad range of progressive neurological disorders with multifactorial etiology contributing to disease pathophysiology. Evidence of the microbiome involvement in the gut-brain axis urges the interest in understanding metabolic interactions between the microbiota and host physiology in NDDs. Systems Biology offers a holistic integrative approach to study the interplay between the different biologic systems as part of a whole, and may elucidate the host–microbiome interactions in NDDs. We reviewed direct and indirect pathways through which the microbiota can modulate the bidirectional communication of the gut-brain axis, and explored the evidence of microbial dysbiosis in Alzheimer’s and Parkinson’s diseases. As the gut microbiota being strongly affected by diet, the potential approaches to targeting the human microbiota through diet for the stimulation of neuroprotective microbial-metabolites secretion were described. We explored the potential of Genome-scale metabolic models (GEMs) to infer microbe-microbe and host-microbe interactions and to identify the microbiome contribution to disease development or prevention. Finally, a systemic approach based on GEMs and ‘omics integration, that would allow the design of sustainable personalized anti-inflammatory diets in NDDs prevention, through the modulation of gut microbiota was described.
Collapse
Affiliation(s)
- Dorines Rosario
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Jan Boren
- Department of Molecular and Clinical Medicine, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Gordon Proctor
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
45
|
Miralda I, Vashishta A, Rogers MN, Rouchka EC, Li X, Waigel S, Lamont RJ, Uriarte SM. Whole Transcriptome Analysis Reveals That Filifactor alocis Modulates TNFα-Stimulated MAPK Activation in Human Neutrophils. Front Immunol 2020; 11:497. [PMID: 32373107 PMCID: PMC7179764 DOI: 10.3389/fimmu.2020.00497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/04/2020] [Indexed: 12/27/2022] Open
Abstract
Periodontitis is an irreversible, bacteria-induced, chronic inflammatory disease that compromises the integrity of tooth-supporting tissues and adversely affects systemic health. As the immune system's first line of defense against bacteria, neutrophils use their microbicidal functions in the oral cavity to protect the host against periodontal disease. However, periodontal pathogens have adapted to resist neutrophil microbicidal mechanisms while still propagating inflammation, which provides essential nutrients for the bacteria to proliferate and cause disease. Advances in sequencing technologies have recognized several newly appreciated bacteria associated with periodontal lesions such as the Gram-positive anaerobic rod, Filifactor alocis. With the discovery of these oral bacterial species, there is also a growing need to assess their pathogenic potential and determine their contribution to disease progression. Currently, few studies have addressed the pathogenic mechanisms used by oral bacteria to manipulate the neutrophil functional responses at the level of the transcriptome. Thus, this study aims to characterize the global changes at the gene expression level in human neutrophils during infection with F. alocis. Our results indicate that the challenge of human neutrophils with F. alocis results in the differential expression of genes involved in multiple neutrophil effector functions such as chemotaxis, cytokine and chemokine signaling pathways, and apoptosis. Moreover, F. alocis challenges affected the expression of components from the TNF and MAPK kinase signaling pathways. This resulted in transient, dampened p38 MAPK activation by secondary stimuli TNFα but not by fMLF. Functionally, the F. alocis-mediated inhibition of p38 activation by TNFα resulted in decreased cytokine production but had no effect on the priming of the respiratory burst response or the delay of apoptosis by TNFα. Since the modulatory effect was characteristic of viable F. alocis only, we propose this as one of F. alocis' mechanisms to control neutrophils and their functional responses.
Collapse
Affiliation(s)
- Irina Miralda
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Aruna Vashishta
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States.,Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, United States
| | - Max N Rogers
- Department of Biology, School of Arts and Sciences, University of Louisville, Louisville, KY, United States
| | - Eric C Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY, United States.,KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, United States
| | - Xiaohong Li
- KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, United States.,Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States
| | - Sabine Waigel
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States.,Department of Medicine, University of Louisville Genomics Facility, Louisville, KY, United States
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, United States
| | - Silvia M Uriarte
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, United States.,Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States.,Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, United States
| |
Collapse
|
46
|
Wei X, Zhang Y, Li C, Ai K, Li K, Li H, Yang J. The evolutionarily conserved MAPK/Erk signaling promotes ancestral T-cell immunity in fish via c-Myc-mediated glycolysis. J Biol Chem 2020; 295:3000-3016. [PMID: 31996375 DOI: 10.1074/jbc.ra119.012231] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/23/2020] [Indexed: 01/02/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) cascade is an ancient and evolutionarily conserved signaling pathway involved in numerous physiological processes. Despite great advances in understanding MAPK-mediated regulation of adaptive immune responses in mammals, its contribution to T-cell immunity in early vertebrates remains unclear. Herein, we used Nile tilapia (Oreochromis niloticus) to investigate the regulatory roles of MAPK/extracellular signal-regulated kinase (Erk) signaling in ancestral T-cell immunity of jawed fish. We found that Nile tilapia possesses an evolutionarily conserved MAPK/Erk axis that is activated through a classical three-tier kinase cascade, involving sequential phosphorylation of RAF proto-oncogene serine/threonine-protein kinase (Raf), MAPK/Erk kinase 1/2 (Mek1/2), and Erk1/2. In Nile tilapia, MAPK/Erk signaling participates in adaptive immune responses during bacterial infection. Upon T-cell activation, the MAPK/Erk axis is robustly activated, and MAPK/Erk blockade by specific inhibitors severely impairs T-cell activation. Furthermore, signals from MAPK/Erk were indispensable for primordial T cells to proliferate and exert their effector functions. Mechanistically, activation of the MAPK/Erk axis promoted glycolysis via induction of the transcriptional regulator proto-oncogene c-Myc (c-Myc), to ensure the proper activation and proliferation of fish T cells. Our results reveal the regulatory mechanisms of MAPK/Erk signaling in T-cell immunity in fish and highlight a close link between immune signals and metabolic programs. We propose that regulation of T-cell immunity by MAPK/Erk is a basic and sophisticated strategy that evolved before the emergence of the tetrapod lineage. These findings shed light on the evolution of the adaptive immune system.
Collapse
Affiliation(s)
- Xiumei Wei
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yu Zhang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Cheng Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Kete Ai
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Kang Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Huiying Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialong Yang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai 200241, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| |
Collapse
|
47
|
Jeffery K, Pollack R, Rovelli C. On the Statistical Mechanics of Life: Schrödinger Revisited. ENTROPY 2019. [PMCID: PMC7514554 DOI: 10.3390/e21121211] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We study the statistical underpinnings of life, in particular its increase in order and complexity over evolutionary time. We question some common assumptions about the thermodynamics of life. We recall that contrary to widespread belief, even in a closed system entropy growth can accompany an increase in macroscopic order. We view metabolism in living things as microscopic variables directly driven by the second law of thermodynamics, while viewing the macroscopic variables of structure, complexity and homeostasis as mechanisms that are entropically favored because they open channels for entropy to grow via metabolism. This perspective reverses the conventional relation between structure and metabolism, by emphasizing the role of structure for metabolism rather than the converse. Structure extends in time, preserving information along generations, particularly in the genetic code, but also in human culture. We argue that increasing complexity is an inevitable tendency for systems with these dynamics and explain this with the notion of metastable states, which are enclosed regions of the phase-space that we call “bubbles,” and channels between these, which are discovered by random motion of the system. We consider that more complex systems inhabit larger bubbles (have more available states), and also that larger bubbles are more easily entered and less easily exited than small bubbles. The result is that the system entropically wanders into ever-larger bubbles in the foamy phase space, becoming more complex over time. This formulation makes intuitive why the increase in order/complexity over time is often stepwise and sometimes collapses catastrophically, as in biological extinction.
Collapse
Affiliation(s)
- Kate Jeffery
- Institute of Behavioural Neuroscience, University College, London WC1H 0AP, UK;
| | - Robert Pollack
- Biological Sciences, Columbia University, 749 Mudd, Mailcode 2419, NY 10027, USA;
| | - Carlo Rovelli
- Centre de Physique Théorique, Aix-Marseille Université, Université de Toulon, CNRS, 13009 Marseille, France
- Perimeter Institute, 31 Caroline Street North, Waterloo, ON N2L 2Y5, Canada
- Rotman Institute of Philosophy, 1151 Richmond St. North, London, ON N6A 5B7, Canada
- Correspondence:
| |
Collapse
|
48
|
Alexiou A, Chatzichronis S, Perveen A, Hafeez A, Ashraf GM. Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions. Curr Top Med Chem 2019; 19:413-425. [PMID: 30854971 DOI: 10.2174/1568026619666190311125256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/15/2018] [Accepted: 12/26/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems. OBJECTIVE Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically. METHODS Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations. RESULTS GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools. CONCLUSION In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.
Collapse
Affiliation(s)
| | | | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Ghulam Md. Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
49
|
Das D, Xie L, Wang J, Xu X, Zhang Z, Shi J, Le X, Hong J. Discovery of new quinazoline derivatives as irreversible dual EGFR/HER2 inhibitors and their anticancer activities – Part 1. Bioorg Med Chem Lett 2019; 29:591-596. [DOI: 10.1016/j.bmcl.2018.12.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/17/2018] [Accepted: 12/24/2018] [Indexed: 11/25/2022]
|
50
|
Tareen A, Wingreen NS, Mukhopadhyay R. Modeling evolution of crosstalk in noisy signal transduction networks. Phys Rev E 2018; 97:020402. [PMID: 29548149 DOI: 10.1103/physreve.97.020402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 12/17/2022]
Abstract
Signal transduction networks can form highly interconnected systems within cells due to crosstalk between constituent pathways. To better understand the evolutionary design principles underlying such networks, we study the evolution of crosstalk for two parallel signaling pathways that arise via gene duplication. We use a sequence-based evolutionary algorithm and evolve the network based on two physically motivated fitness functions related to information transmission. We find that one fitness function leads to a high degree of crosstalk while the other leads to pathway specificity. Our results offer insights on the relationship between network architecture and information transmission for noisy biomolecular networks.
Collapse
Affiliation(s)
- Ammar Tareen
- Department of Physics, Clark University, Worcester, Massachusetts 01610, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Washington Road, Princeton, New Jersey 08544, USA
| | - Ranjan Mukhopadhyay
- Department of Physics, Clark University, Worcester, Massachusetts 01610, USA
| |
Collapse
|