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Xia Q, Liu F, Zhou Y, Yang G, Li F, Liang T, Liu J, Li W, Huang Y, Zhu C. CD47-SIRPα signaling-inspired engineered monocytes for preventing the progression of atherosclerotic plaques. Mater Today Bio 2024; 28:101178. [PMID: 39211288 PMCID: PMC11357865 DOI: 10.1016/j.mtbio.2024.101178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/14/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
The accumulation of foam cells in the subendothelial space of the vascular wall to form plaques is the real cause of atherosclerotic lesions. Conventional interventions, such as statins and anti-cytokine or anti-inflammatory therapies, suffer problems in terms of their short therapeutic outcomes and potential disruption of the immune system. The development of more efficient therapeutics to restrict the initial progression of plaques appears to be crucial for treating and preventing atherosclerosis. Decreasing foam cell formation by reversing the excessive phagocytosis of modified low-density lipoprotein (LDL) in macrophages is highly desirable. Here, we developed a strategy based on engineered monocytes to dynamically regulate lipid uptake by macrophages inspired by a CD47-SIRPα signaling-induced defect in the phagocytosis of lesional macrophages at the advanced stage of AS. Briefly, a complex called CD47p-GQDs-miR223, which is designed to interact with SIRPα, was synthesized to remodel monocytes by decreasing the uptake of oxidized LDL through the activation of CD47-SIRPα signaling. After injection, these monocytes compete for recruitment to atherosclerotic plaques, release gene drugs and mediate anti-inflammatory phenotypic remodeling of the aboriginal macrophages, effectively inhibiting the development of foam cells. Our strategy provides a new therapeutic for preventing the progression of atherosclerosis.
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Affiliation(s)
- Qing Xia
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Feila Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yue Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Guanyuan Yang
- Department of Anatomy, State Key Laboratory of Trauma, Burn and Combined Injury, National and Regional Engineering Laboratory of Tissue Engineering, Third Military Medical University, Chongqing, 400038, China
| | - Fangzhou Li
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Tingting Liang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jun Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Wanling Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yaqing Huang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Chuhong Zhu
- Department of Anatomy, State Key Laboratory of Trauma, Burn and Combined Injury, National and Regional Engineering Laboratory of Tissue Engineering, Third Military Medical University, Chongqing, 400038, China
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Choi JH, Kim S, Kang OY, Choi SY, Hyun JY, Lee HS, Shin I. Selective fluorescent labeling of cellular proteins and its biological applications. Chem Soc Rev 2024; 53:9446-9489. [PMID: 39109465 DOI: 10.1039/d4cs00094c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Proteins, which are ubiquitous in cells and critical to almost all cellular functions, are indispensable for life. Fluorescence imaging of proteins is key to understanding their functions within their native milieu, as it provides insights into protein localization, dynamics, and trafficking in living systems. Consequently, the selective labeling of target proteins with fluorophores has emerged as a highly active research area, encompassing bioorganic chemistry, chemical biology, and cell biology. Various methods for selectively labeling proteins with fluorophores in cells and tissues have been established and are continually being developed to visualize and characterize proteins. This review highlights research findings reported since 2018, with a focus on the selective labeling of cellular proteins with small organic fluorophores and their biological applications in studying protein-associated biological events. We also discuss the strengths and weaknesses of each labeling approach for their utility in living systems.
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Affiliation(s)
- Joo Hee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Sooin Kim
- Department of Chemistry, Sogang University, 04107 Seoul, Republic of Korea.
| | - On-Yu Kang
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Seong Yun Choi
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 04107 Seoul, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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Jones K, Keddy C, Jenkins C, Nicholson K, Shinde U, Davare MA. Novel insight into mechanisms of ROS1 catalytic activation via loss of the extracellular domain. Sci Rep 2024; 14:22191. [PMID: 39333184 PMCID: PMC11437283 DOI: 10.1038/s41598-024-71687-7] [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: 07/10/2023] [Accepted: 08/30/2024] [Indexed: 09/29/2024] Open
Abstract
The ROS1 receptor tyrosine kinase (RTK) possesses the largest extracellular amino-terminal domain (ECD) among the human RTK family, yet the mechanisms regulating its activation are not fully understood. While chimeric ROS1 fusion proteins, resulting from chromosomal rearrangements, are well-known oncogenic drivers, their activation mechanisms also remain underexplored. To elucidate the role of the ROS1 ECD in catalytic regulation, we engineered a series of amino-terminal deletion mutants. Our functional studies compared the full-length ROS1 receptor, the CD74-ROS1 oncogenic fusion, and ECD-deleted ROS1 constructs, identifying the ECD regions that inhibit ROS1 tyrosine kinase activity. Notably, we found that deletion of the ROS1 ECD alone significantly increases constitutive catalytic activation and neoplastic transformation in the absence of an amino-terminal fusion partner, challenging the presumed necessity for a dimerization domain in the activation mechanism of kinase fusions in cancer. Our data suggest that inter-genic deletions resulting in the loss of the ECD may be underappreciated oncogenic drivers in cancer. Furthermore, our studies demonstrate that RNASE7 is not a ligand for the ROS1 receptor as previously reported, confirming that ROS1 remains an orphan receptor. Thus, the discovery of a ROS1 ligand remains an important future priority. These findings highlight the potential for disease-associated somatic aberrations or splice variants that modify the ROS1 ECD to promote constitutive receptor activation, warranting further investigation.
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Affiliation(s)
- Kristen Jones
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Clare Keddy
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Chelsea Jenkins
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Katelyn Nicholson
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA
| | - Ujwal Shinde
- Department of Chemical Physiology and Biochemistry, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Monika A Davare
- Department of Pediatrics, School of Medicine, Papé Pediatric Research Institute, OHSU, Portland, OR, 97239, USA.
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Lee CH, Li H, Hyun JY, Shin I. Strategy for Construction of Homogeneous Glycoproteins in Mammalian Cells. Bioconjug Chem 2024. [PMID: 39319574 DOI: 10.1021/acs.bioconjchem.4c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
A general strategy that combines genetic code expansion with bio-orthogonal ligation techniques was developed and utilized to prepare homogeneously glycosylated receptors on the surface of mammalian cells. Using this approach, conjugates of the cell-surface oxytocin receptor (OTR) with oligosaccharides were efficiently generated in the cells. Cell studies revealed that glycans linked to the OTR are not essential for agonist-induced calcium flux and its internalization into cells via an OTR-mediated endocytosis.
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Affiliation(s)
- Chang-Hee Lee
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
- Pharmaceutical Chemistry, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea
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Zulueta Diaz YDLM, Arnspang EC. Super-resolution microscopy to study membrane nanodomains and transport mechanisms in the plasma membrane. Front Mol Biosci 2024; 11:1455153. [PMID: 39290992 PMCID: PMC11405310 DOI: 10.3389/fmolb.2024.1455153] [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: 06/26/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.
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Affiliation(s)
| | - Eva C Arnspang
- Department of Green Technology, SDU Biotechnology, University of Southern Denmark, Odense, Denmark
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Wang LY, He LH, Xu LJ, Li SB. Short-chain fatty acids: bridges between diet, gut microbiota, and health. J Gastroenterol Hepatol 2024; 39:1728-1736. [PMID: 38780349 DOI: 10.1111/jgh.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
In recent years, gut microbiota has become a hot topic in the fields of medicine and life sciences. Short-chain fatty acids (SCFAs), the main metabolites of gut microbiota produced by microbial fermentation of dietary fiber, play a vital role in healthy and ill hosts. SCFAs regulate the process of metabolism, immune, and inflammation and have therapeutic effects on gastrointestinal and neurological disorders, as well as antitumor properties. This review summarized the production, distribution, and molecular mechanism of SCFAs, as well as their mechanisms of action in healthy and ill hosts. In addition, we also emphasized the negative effects of SCFAs, aiming to provide the public with a more comprehensive understanding of SCFAs.
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Affiliation(s)
- Ling-Yun Wang
- Department of Infectious Diseases, Zhoushan Hospital, Zhejiang University, Zhoushan, China
- College of Medicine, Zhejiang University, Hangzhou, China
| | - Li-Hong He
- College of Medicine, Zhejiang University, Hangzhou, China
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li-Jun Xu
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shi-Bo Li
- Department of Infectious Diseases, Zhoushan Hospital, Zhejiang University, Zhoushan, China
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Wen L, Hu W, Hou S, Luo C, Jin Y, Zeng Z, Zhang Z, Meng Y. GRB7 Plays a Vital Role in Promoting the Progression and Mediating Immune Evasion of Ovarian Cancer. Pharmaceuticals (Basel) 2024; 17:1043. [PMID: 39204147 PMCID: PMC11357674 DOI: 10.3390/ph17081043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/31/2024] [Accepted: 07/30/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND Despite breakthroughs in treatment, ovarian cancer (OC) remains one of the most lethal gynecological malignancies, with an increasing age-standardized mortality rate. This underscores an urgent need for novel biomarkers and therapeutic targets. Although growth factor receptor-bound protein 7 (GRB7) is implicated in cell signaling and tumorigenesis, its expression pattern and clinical implications in OC remain poorly characterized. METHODS To systematically investigate GRB7's expression in OC, our study utilized extensive datasets from TCGA, GTEx, CCLE, and GEO. The prognostic significance of GRB7 was evaluated by means of Kaplan-Meier and Cox regression analyses. Using a correlation analysis and gene set enrichment analysis, relationships between GRB7's expression and gene networks, immune cell infiltration and immunotherapy response were investigated. In vitro experiments were conducted to confirm GRB7's function in the biology of OC. RESULTS Compared to normal tissues, OC tissues exhibited a substantial upregulation of GRB7. Reduced overall survival, disease-specific survival, and disease-free interval were all connected with high GRB7 mRNA levels. The network study demonstrated that GRB7 is involved in pathways relevant to the course of OC and has a positive connection with several key driver genes. Notably, GRB7's expression was linked to the infiltration of M2 macrophage and altered response to immunotherapy. Data from single-cell RNA sequencing data across multiple cancer types indicated GRB7's predominant expression in malignant cells. Moreover, OC cells with GRB7 deletion showed decreased proliferation and migration, as well as increased susceptibility to T cell-mediated cytotoxicity. CONCLUSION With respect to OC, our results validated GRB7 as a viable prognostic biomarker and a promising therapeutic target, providing information about its function in tumorigenesis and immune modulation. GRB7's preferential expression in malignant cells highlights its significance in the biology of cancer and bolsters the possibility that it could be useful in enhancing the effectiveness of immunotherapy.
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Affiliation(s)
- Liang Wen
- Chinese People’s Liberation Army (PLA) Medical School, Beijing 100853, China;
| | - Wei Hu
- Department of Emergency, The Fifth Medical Center of Chinese PLA Hospital, Beijing 100039, China;
| | - Sen Hou
- Department of Gastrointestinal Surgery, Peking University People’s Hospital, Beijing 100032, China;
| | - Ce Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100091, China; (C.L.); (Y.J.); (Z.Z.)
| | - Yiteng Jin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100091, China; (C.L.); (Y.J.); (Z.Z.)
| | - Zexian Zeng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100091, China; (C.L.); (Y.J.); (Z.Z.)
| | - Zhe Zhang
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100700, China
| | - Yuanguang Meng
- Chinese People’s Liberation Army (PLA) Medical School, Beijing 100853, China;
- Department of Obstetrics and Gynecology, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100700, China
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8
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Bjørklund G, Oliinyk P, Khavrona O, Lozynska I, Lysiuk R, Darmohray R, Antonyak H, Dub N, Zayachuk V, Antoniv O, Rybak O, Peana M. The Effects of Fisetin and Curcumin on Oxidative Damage Caused by Transition Metals in Neurodegenerative Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04321-2. [PMID: 38970766 DOI: 10.1007/s12035-024-04321-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/19/2024] [Indexed: 07/08/2024]
Abstract
Neurodegenerative diseases pose a significant health challenge for the elderly. The escalating presence of toxic metals and chemicals in the environment is a potential contributor to central nervous system dysfunction and the onset of neurodegenerative conditions. Transition metals play a crucial role in various pathophysiological mechanisms associated with prevalent neurodegenerative diseases such as Alzheimer's and Parkinson's. Given the ubiquitous exposure to metals from diverse sources in everyday life, the workplace, and the environment, most of the population faces regular contact with different forms of these metals. Disturbances in the levels and homeostasis of certain transition metals are closely linked to the manifestation of neurodegenerative disorders. Oxidative damage further exacerbates the progression of neurological consequences. Presently, there exists no curative therapy for individuals afflicted by neurodegenerative diseases, with treatment approaches primarily focusing on alleviating pathological symptoms. Within the realm of biologically active compounds derived from plants, flavonoids and curcuminoids stand out for their extensively documented antioxidant, antiplatelet, and neuroprotective properties. The utilization of these compounds holds the potential to formulate highly effective therapeutic strategies for managing neurodegenerative diseases. This review provides a comprehensive overview of the impact of abnormal metal levels, particularly copper, iron, and zinc, on the initiation and progression of neurodegenerative diseases. Additionally, it aims to elucidate the potential of fisetin and curcumin to inhibit or decelerate the neurodegenerative process.
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Affiliation(s)
- Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Toften 24, 8610, Mo I Rana, Norway.
| | - Petro Oliinyk
- Department of Disaster Medicine and Military Medicine, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Oksana Khavrona
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Biological Chemistry, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Iryna Lozynska
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Biological Chemistry, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Roman Lysiuk
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Pharmacognosy and Botany, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Roman Darmohray
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Pharmacognosy and Botany, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Halyna Antonyak
- Department of Ecology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Natalia Dub
- Andrei Krupynskyi Lviv Medical Academy, Lviv, 79000, Ukraine
| | - Vasyl Zayachuk
- Department of Botany, Ukrainian National Forestry University, Wood Science and Non-Wood Forest Products, Lviv, 79057, Ukraine
| | - Olha Antoniv
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Pharmacology, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Oksana Rybak
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Pharmacognosy and Botany, Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100, Sassari, Italy.
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Copperman J, Mclean IC, Gross SM, Singh J, Chang YH, Zuckerman DM, Heiser LM. Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576248. [PMID: 38293173 PMCID: PMC10827140 DOI: 10.1101/2024.01.18.576248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Extracellular signals induce changes to molecular programs that modulate multiple cellular phenotypes, including proliferation, motility, and differentiation status. The connection between dynamically adapting phenotypic states and the molecular programs that define them is not well understood. Here we develop data-driven models of single-cell phenotypic responses to extracellular stimuli by linking gene transcription levels to "morphodynamics" - changes in cell morphology and motility observable in time-lapse image data. We adopt a dynamics-first view of cell state by grouping single-cell trajectories into states with shared morphodynamic responses. The single-cell trajectories enable development of a first-of-its-kind computational approach to map live-cell dynamics to snapshot gene transcript levels, which we term MMIST, Molecular and Morphodynamics-Integrated Single-cell Trajectories. The key conceptual advance of MMIST is that cell behavior can be quantified based on dynamically defined states and that extracellular signals alter the overall distribution of cell states by altering rates of switching between states. We find a cell state landscape that is bound by epithelial and mesenchymal endpoints, with distinct sequences of epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET) intermediates. The analysis yields predictions for gene expression changes consistent with curated EMT gene sets and provides a prediction of thousands of RNA transcripts through extracellular signal-induced EMT and MET with near-continuous time resolution. The MMIST framework leverages true single-cell dynamical behavior to generate molecular-level omics inferences and is broadly applicable to other biological domains, time-lapse imaging approaches and molecular snapshot data.
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Affiliation(s)
- Jeremy Copperman
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Ian C. Mclean
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
| | | | - Jalim Singh
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Laura M. Heiser
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland OR 97239, U.S.A
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10
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Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN. Altered glia-neuron communication in Alzheimer's Disease affects WNT, p53, and NFkB Signaling determined by snRNA-seq. Cell Commun Signal 2024; 22:317. [PMID: 38849813 PMCID: PMC11157763 DOI: 10.1186/s12964-024-01686-8] [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: 12/06/2023] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Alzheimer's disease is the most common cause of dementia and is characterized by amyloid-β plaques, tau neurofibrillary tangles, and neuronal loss. Although neuronal loss is a primary hallmark of Alzheimer's disease, it is known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk. Many signaling pathways have been proposed to be dysregulated in Alzheimer's disease, including WNT, TGFβ, p53, mTOR, NFkB, and Pi3k/Akt signaling. Here, we predict altered cell-cell communication between glia and neurons. METHODS Using public snRNA-sequencing data generated from postmortem human prefrontal cortex, we predicted altered cell-cell communication between glia (astrocytes, microglia, oligodendrocytes, and oligodendrocyte progenitor cells) and neurons (excitatory and inhibitory). We confirmed interactions in a second and third independent orthogonal dataset. We determined cell-type-specificity using Jaccard Similarity Index and investigated the downstream effects of altered interactions in inhibitory neurons through gene expression and transcription factor activity analyses of signaling mediators. Finally, we determined changes in pathway activity in inhibitory neurons. RESULTS Cell-cell communication between glia and neurons is altered in Alzheimer's disease in a cell-type-specific manner. As expected, ligands are more cell-type-specific than receptors and targets. We identified ligand-receptor pairs in three independent datasets and found involvement of the Alzheimer's disease risk genes APP and APOE across datasets. Most of the signaling mediators of these interactions were not significantly differentially expressed, however, the mediators that are also transcription factors had differential activity between AD and control. Namely, MYC and TP53, which are associated with WNT and p53 signaling, respectively, had decreased TF activity in Alzheimer's disease, along with decreased WNT and p53 pathway activity in inhibitory neurons. Additionally, inhibitory neurons had both increased NFkB signaling pathway activity and increased TF activity of NFIL3, an NFkB signaling-associated transcription factor. CONCLUSIONS Cell-cell communication between glia and neurons in Alzheimer's disease is altered in a cell-type-specific manner involving Alzheimer's disease risk genes. Signaling mediators had altered transcription factor activity suggesting altered glia-neuron interactions may dysregulate signaling pathways including WNT, p53, and NFkB in inhibitory neurons.
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Affiliation(s)
- Tabea M Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Timothy C Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda D Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Vishal H Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Brittany N Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America.
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11
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Giudice G, Chen H, Koutsandreas T, Petsalaki E. phuEGO: A Network-Based Method to Reconstruct Active Signaling Pathways From Phosphoproteomics Datasets. Mol Cell Proteomics 2024; 23:100771. [PMID: 38642805 PMCID: PMC11134849 DOI: 10.1016/j.mcpro.2024.100771] [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: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024] Open
Abstract
Signaling networks are critical for virtually all cell functions. Our current knowledge of cell signaling has been summarized in signaling pathway databases, which, while useful, are highly biased toward well-studied processes, and do not capture context specific network wiring or pathway cross-talk. Mass spectrometry-based phosphoproteomics data can provide a more unbiased view of active cell signaling processes in a given context, however, it suffers from low signal-to-noise ratio and poor reproducibility across experiments. While progress in methods to extract active signaling signatures from such data has been made, there are still limitations with respect to balancing bias and interpretability. Here we present phuEGO, which combines up-to-three-layer network propagation with ego network decomposition to provide small networks comprising active functional signaling modules. PhuEGO boosts the signal-to-noise ratio from global phosphoproteomics datasets, enriches the resulting networks for functional phosphosites and allows the improved comparison and integration across datasets. We applied phuEGO to five phosphoproteomics data sets from cell lines collected upon infection with SARS CoV2. PhuEGO was better able to identify common active functions across datasets and to point to a subnetwork enriched for known COVID-19 targets. Overall, phuEGO provides a flexible tool to the community for the improved functional interpretation of global phosphoproteomics datasets.
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Affiliation(s)
- Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Haoqi Chen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Thodoris Koutsandreas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, United Kingdom.
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Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN. Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.29.569304. [PMID: 38076822 PMCID: PMC10705421 DOI: 10.1101/2023.11.29.569304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Background Alzheimer's disease is the most common cause of dementia and is characterized by amyloid-β plaques, tau neurofibrillary tangles, and neuronal loss. Although neuronal loss is a primary hallmark of Alzheimer's disease, it is known that non-neuronal cell populations are ultimately responsible for maintaining brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk. Many signaling pathways have been proposed to be dysregulated in Alzheimer's disease, including WNT, TGFβ, p53, mTOR, NFkB, and Pi3k/Akt signaling. Here, we predict altered cell-cell communication between glia and neurons. Methods Using public snRNA-sequencing data generated from postmortem human prefrontal cortex, we predicted altered cell-cell communication between glia (astrocytes, microglia, oligodendrocytes, and oligodendrocyte progenitor cells) and neurons (excitatory and inhibitory). We confirmed interactions in a second and third independent orthogonal dataset. We determined cell-type-specificity using Jaccard Similarity Index and investigated the downstream effects of altered interactions in inhibitory neurons through gene expression and transcription factor activity analyses of signaling mediators. Finally, we determined changes in pathway activity in inhibitory neurons. Results Cell-cell communication between glia and neurons is altered in Alzheimer's disease in a cell-type-specific manner. As expected, ligands are more cell-type-specific than receptors and targets. We identified ligand-receptor pairs in three independent datasets and found involvement of the Alzheimer's disease risk genes APP and APOE across datasets. Most of the signaling mediators of these interactions were not differentially expressed, however, the mediators that are also transcription factors had differential activity between AD and control. Namely, MYC and TP53, which are associated with WNT and p53 signaling, respectively, had decreased TF activity in Alzheimer's disease, along with decreased WNT and p53 pathway activity in inhibitory neurons. Additionally, inhibitory neurons had both increased NFkB signaling pathway activity and increased TF activity of NFIL3, an NFkB signaling-associated transcription factor. Conclusions Cell-cell communication between glia and neurons in Alzheimer's disease is altered in a cell-type-specific manner involving Alzheimer's disease risk genes. Signaling mediators had altered transcription factor activity suggesting altered glia-neuron interactions may dysregulate signaling pathways including WNT, p53, and NFkB in inhibitory neurons.
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Affiliation(s)
- Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Vishal H. Oza
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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13
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Nürnberg B, Beer-Hammer S, Reisinger E, Leiss V. Non-canonical G protein signaling. Pharmacol Ther 2024; 255:108589. [PMID: 38295906 DOI: 10.1016/j.pharmthera.2024.108589] [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: 07/03/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
The original paradigm of classical - also referred to as canonical - cellular signal transduction of heterotrimeric G proteins (G protein) is defined by a hierarchical, orthograde interaction of three players: the agonist-activated G protein-coupled receptor (GPCR), which activates the transducing G protein, that in turn regulates its intracellular effectors. This receptor-transducer-effector concept was extended by the identification of regulators and adapters such as the regulators of G protein signaling (RGS), receptor kinases like βARK, or GPCR-interacting arrestin adapters that are integrated into this canonical signaling process at different levels to enable fine-tuning. Finally, the identification of atypical signaling mechanisms of classical regulators, together with the discovery of novel modulators, added a new and fascinating dimension to the cellular G protein signal transduction. This heterogeneous group of accessory G protein modulators was coined "activators of G protein signaling" (AGS) proteins and plays distinct roles in canonical and non-canonical G protein signaling pathways. AGS proteins contribute to the control of essential cellular functions such as cell development and division, intracellular transport processes, secretion, autophagy or cell movements. As such, they are involved in numerous biological processes that are crucial for diseases, like diabetes mellitus, cancer, and stroke, which represent major health burdens. Although the identification of a large number of non-canonical G protein signaling pathways has broadened the spectrum of this cellular communication system, their underlying mechanisms, functions, and biological effects are poorly understood. In this review, we highlight and discuss atypical G protein-dependent signaling mechanisms with a focus on inhibitory G proteins (Gi) involved in canonical and non-canonical signal transduction, review recent developments and open questions, address the potential of new approaches for targeted pharmacological interventions.
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Affiliation(s)
- Bernd Nürnberg
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomics, and ICePhA Mouse Clinic, University of Tübingen, Wilhelmstraße 56, D-72074 Tübingen, Germany.
| | - Sandra Beer-Hammer
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomics, and ICePhA Mouse Clinic, University of Tübingen, Wilhelmstraße 56, D-72074 Tübingen, Germany
| | - Ellen Reisinger
- Gene Therapy for Hearing Impairment Group, Department of Otolaryngology - Head & Neck Surgery, University of Tübingen Medical Center, Elfriede-Aulhorn-Straße 5, D-72076 Tübingen, Germany
| | - Veronika Leiss
- Department of Pharmacology, Experimental Therapy and Toxicology, Institute of Experimental and Clinical Pharmacology and Pharmacogenomics, and ICePhA Mouse Clinic, University of Tübingen, Wilhelmstraße 56, D-72074 Tübingen, Germany
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14
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Akompong SK, Li Y, Gong W, Ye L, Liu J. Recently reported cell migration inhibitors: Opportunities and challenges for antimetastatic agents. Drug Discov Today 2024; 29:103906. [PMID: 38309689 DOI: 10.1016/j.drudis.2024.103906] [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: 09/25/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
Antimetastatic agents are highly desirable for cancer treatment because of the severe medical challenges and high mortality resulting from tumor metastasis. Having demonstrated antimetastatic effects in numerous in vitro and in vivo studies, migration inhibitors present significant opportunities for developing a new class of anticancer drugs. To provide a useful overview on the latest research in migration inhibitors, this article first discusses their therapeutic significance, targetable proteins, and developmental avenues. Subsequently it reviews over 20 representative migration inhibitors reported in recent journals in terms of their inhibitory mechanism, potency, and potential clinical utility. The relevance of the target proteins to cellular migratory function is focused on as it is crucial for assessing the overall efficacy of the inhibitors.
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Affiliation(s)
- Samuel K Akompong
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Yang Li
- Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wenxue Gong
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Long Ye
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Jinping Liu
- Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
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15
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Sakurada K, Ishikawa T. Synthesis of causal and surrogate models by non-equilibrium thermodynamics in biological systems. Sci Rep 2024; 14:1001. [PMID: 38200211 PMCID: PMC10781949 DOI: 10.1038/s41598-024-51426-8] [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: 10/17/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
We developed a model to represent the time evolution phenomena of life through physics constraints. To do this, we took into account that living organisms are open systems that exchange messages through intracellular communication, intercellular communication and sensory systems, and introduced the concept of a message force field. As a result, we showed that the maximum entropy generation principle is valid in time evolution. Then, in order to explain life phenomena based on this principle, we modelled the living system as a nonlinear oscillator coupled by a message and derived the governing equations. The governing equations consist of two laws: one states that the systems are synchronized when the variation of the natural frequencies between them is small or the coupling strength through the message is sufficiently large, and the other states that the synchronization is broken by the proliferation of biological systems. Next, to simulate the phenomena using data obtained from observations of the temporal evolution of life, we developed an inference model that combines physics constraints and a discrete surrogate model using category theory, and simulated the phenomenon of early embryogenesis using this inference model. The results show that symmetry creation and breaking based on message force fields can be widely used to model life phenomena.
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Affiliation(s)
- Kazuhiro Sakurada
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan.
- Open Systems Information Science Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, Japan.
| | - Tetsuo Ishikawa
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Medical Data Mathematical Reasoning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
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16
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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17
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Lee CH, Park S, Kim S, Hyun JY, Lee HS, Shin I. Engineering of cell-surface receptors for analysis of receptor internalization and detection of receptor-specific glycosylation. Chem Sci 2024; 15:555-565. [PMID: 38179521 PMCID: PMC10762726 DOI: 10.1039/d3sc05054h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) is a cell-surface glycoprotein that is involved mainly in cell proliferation. Overexpression of this receptor is intimately related to the development of a broad spectrum of tumors. In addition, glycans linked to the EGFR are known to affect its EGF-induced activation. Because of the pathophysiological significance of the EGFR, we prepared a fluorescently labeled EGFR (EGFR128-AZDye 488) on the cell surface by employing the genetic code expansion technique and bioorthogonal chemistry. EGFR128-AZDye 488 was initially utilized to investigate time-dependent endocytosis of the EGFR in live cells. The results showed that an EGFR inhibitor and antibody suppress endocytosis of the EGFR promoted by the EGF, and that lectins recognizing glycans of the EGFR do not enhance EGFR internalization into cells. Observations made in studies of the effects of appended glycans on the entry of the EGFR into cells indicate that a de-sialylated or de-fucosylated EGFR is internalized into cells more efficiently than a wild-type EGFR. Furthermore, by using the FRET-based imaging method of cells which contain an EGFR linked to AZDye 488 (a FRET donor) and cellular glycans labeled with rhodamine (a FRET acceptor), sialic acid residues attached to the EGFR were specifically detected on the live cell surface. Taken together, the results suggest that a fluorescently labeled EGFR will be a valuable tool in studies aimed at gaining an understanding of cellular functions of the EGFR.
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Affiliation(s)
- Chang-Hee Lee
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
| | - Sookil Park
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
| | - Sanggil Kim
- Department of Chemistry, Sogang University Seoul 04107 Republic of Korea
| | - Ji Young Hyun
- Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology Daejeon 34114 Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University Seoul 04107 Republic of Korea
| | - Injae Shin
- Department of Chemistry, Yonsei University Seoul 03722 Republic of Korea
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18
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Novikova SE, Tolstova TV, Soloveva NA, Farafonova TE, Tikhonova OV, Kurbatov LK, Rusanov AL, Zgoda VG. System analysis of surface CD markers during the process of granulocytic differentiation. BIOMEDITSINSKAIA KHIMIIA 2023; 69:383-393. [PMID: 38153053 DOI: 10.18097/pbmc20236906383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Plasma membrane proteins with extracellular-exposed domains are responsible for transduction of extracellular signals into intracellular responses, and their accessibility to therapeutic molecules makes them attractive targets for drug development. In this work, using omics technologies and immunochemical methods, we have studied changes in the content of markers of clusters of differentiation (CD markers) of neutrophils (CD33, CD97, CD54, CD38, CD18, CD11b, CD44, and CD71) at the level of transcripts and proteins in NB4, HL-60 and K562 cell lines, induced by the treatment with all-trans-retinoic acid (ATRA). Transcriptomic analysis revealed the induction of CD38, CD54, CD11b, and CD18 markers as early as 3 h after the addition of the inducer in the ATRA-responsive cell lines HL-60 and NB4. After 24 h, a line-specific expression pattern of CD markers could be observed in all cell lines. Studies of changes in the content of CD antigens by means of flow cytometry and targeted mass spectrometry (MS) gave similar results. The proteomic profile of the surface markers (CD38, CD54, CD11b, and CD18), characteristic of the NB4 and HL-60 lines, reflects different molecular pathways for the implementation of ATRA-induced differentiation of leukemic cells into mature neutrophils.
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Affiliation(s)
- S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - T V Tolstova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - N A Soloveva
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - L K Kurbatov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A L Rusanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
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19
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Page KR, Nguyen VN, Pleiner T, Tomaleri GP, Wang ML, Guna A, Wang TY, Chou TF, Voorhees RM. Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569054. [PMID: 38076791 PMCID: PMC10705394 DOI: 10.1101/2023.11.28.569054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we systematically studied the biogenesis of a panel of membrane proteins, including several G-protein coupled receptors (GPCRs). We observed a central role for the insertase, the ER membrane protein complex (EMC), and developed a dual-guide approach to identify genetic modifiers of the EMC. We found that the back of sec61 (BOS) complex, a component of the 'multipass translocon', was a physical and genetic interactor of the EMC. Functional and structural analysis of the EMC•BOS holocomplex showed that characteristics of a GPCR's soluble domain determine its biogenesis pathway. In contrast to prevailing models, no single insertase handles all substrates. We instead propose a unifying model for coordination between the EMC, multipass translocon, and Sec61 for biogenesis of diverse membrane proteins in human cells.
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20
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Su Z, Wu Y. How does the same ligand activate signaling of different receptors in TNFR superfamily: a computational study. J Cell Commun Signal 2023; 17:657-671. [PMID: 36167956 PMCID: PMC10409953 DOI: 10.1007/s12079-022-00701-2] [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: 06/02/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
TNFα is a highly pleiotropic cytokine inducing inflammatory signaling pathways. It is initially presented on plasma membrane of cells (mTNFα), and also exists in a soluble variant (sTNFα) after cleavage. The ligand is shared by two structurally similar receptors, TNFR1 and TNFR2. Interestingly, while sTNFα preferentially stimulates TNFR1, TNFR2 signaling can only be activated by mTNFα. How can two similar receptors respond to the same ligand in such a different way? We employed computational simulations in multiple scales to address this question. We found that both mTNFα and sTNFα can trigger the clustering of TNFR1. The size of clusters induced by sTNFα is constantly larger than the clusters induced by mTNFα. The systems of TNFR2, on the other hand, show very different behaviors. Only when the interactions between TNFR2 are very weak, mTNFα can trigger the receptors to form very large clusters. Given the same weak binding affinity, only small oligomers were obtained in the system of sTNFα. Considering that TNF-mediated signaling is modulated by the ligand-induced clustering of receptors on cell surface, our study provided the mechanistic foundation to the phenomenon that different isoforms of the ligand can lead to highly distinctive signaling patterns for its receptors.
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Affiliation(s)
- Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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21
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Wang X, Wang T, Lam E, Alvarez D, Sun Y. Ocular Vascular Diseases: From Retinal Immune Privilege to Inflammation. Int J Mol Sci 2023; 24:12090. [PMID: 37569464 PMCID: PMC10418793 DOI: 10.3390/ijms241512090] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The eye is an immune privileged tissue that insulates the visual system from local and systemic immune provocation to preserve homeostatic functions of highly specialized retinal neural cells. If immune privilege is breached, immune stimuli will invade the eye and subsequently trigger acute inflammatory responses. Local resident microglia become active and release numerous immunological factors to protect the integrity of retinal neural cells. Although acute inflammatory responses are necessary to control and eradicate insults to the eye, chronic inflammation can cause retinal tissue damage and cell dysfunction, leading to ocular disease and vision loss. In this review, we summarized features of immune privilege in the retina and the key inflammatory responses, factors, and intracellular pathways activated when retinal immune privilege fails, as well as a highlight of the recent clinical and research advances in ocular immunity and ocular vascular diseases including retinopathy of prematurity, age-related macular degeneration, and diabetic retinopathy.
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Affiliation(s)
- Xudong Wang
- Department of Ophthalmology, Harvard Medical School, Boston Children’s Hospital, Boston, MA 02115, USA; (X.W.)
| | - Tianxi Wang
- Department of Ophthalmology, Harvard Medical School, Boston Children’s Hospital, Boston, MA 02115, USA; (X.W.)
| | - Enton Lam
- Department of Ophthalmology, Harvard Medical School, Boston Children’s Hospital, Boston, MA 02115, USA; (X.W.)
| | - David Alvarez
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Ye Sun
- Department of Ophthalmology, Harvard Medical School, Boston Children’s Hospital, Boston, MA 02115, USA; (X.W.)
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22
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Luo X, Zhang H, Cao X, Yang D, Yan Y, Lu J, Wang X, Wang H. Endurance Exercise-Induced Fgf21 Promotes Skeletal Muscle Fiber Conversion through TGF-β1 and p38 MAPK Signaling Pathway. Int J Mol Sci 2023; 24:11401. [PMID: 37511159 PMCID: PMC10379449 DOI: 10.3390/ijms241411401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Fgf21 has been identified as playing a regulatory role in muscle growth and function. Although the mechanisms through which endurance training regulates skeletal muscle have been widely studied, the contribution of Fgf21 remains poorly understood. Here, muscle size and function were measured, and markers of fiber type were evaluated using immunohistochemistry, immunoblots, or qPCR in endurance-exercise-trained wild-type and Fgf21 KO mice. We also investigated Fgf21-induced fiber conversion in C2C12 cells, which were incubated with lentivirus and/or pathway inhibitors. We found that endurance exercise training enhanced the Fgf21 levels of liver and GAS muscle and exercise capacity and decreased the distribution of skeletal muscle fiber size, and fast-twitch fibers were observed converting to slow-twitch fibers in the GAS muscle of mice. Fgf21 promoted the markers of fiber-type transition and eMyHC-positive myotubes by inhibiting the TGF-β1 signaling axis and activating the p38 MAPK signaling pathway without apparent crosstalk. Our findings suggest that the transformation and function of skeletal muscle fiber types in response to endurance training could be mediated by Fgf21 and its downstream signaling pathways. Our results illuminate the mechanisms of Fgf21 in endurance-exercise-induced fiber-type conversion and suggest a potential use of Fgf21 in improving muscle health and combating fatigue.
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Affiliation(s)
- Xiaomao Luo
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Huiling Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Xiaorui Cao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Ding Yang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yi Yan
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Jiayin Lu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Xiaonan Wang
- Renal Division, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
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23
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He L, Xu Z, Niu X, Li R, Wang F, You Y, Gao J, Zhao L, Shah KM, Fan J, Liu M, Luo J. GPRC5B protects osteoarthritis by regulation of autophagy signaling. Acta Pharm Sin B 2023; 13:2976-2989. [PMID: 37521864 PMCID: PMC10372909 DOI: 10.1016/j.apsb.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/17/2023] [Accepted: 03/14/2023] [Indexed: 08/01/2023] Open
Abstract
Osteoarthritis (OA) is one of the most common chronic diseases in the world. However, current treatment modalities mainly relieve pain and inhibit cartilage degradation, but do not promote cartilage regeneration. In this study, we show that G protein-coupled receptor class C group 5 member B (GPRC5B), an orphan G-protein-couple receptor, not only inhibits cartilage degradation, but also increases cartilage regeneration and thereby is protective against OA. We observed that Gprc5b deficient chondrocytes had an upregulation of cartilage catabolic gene expression, along with downregulation of anabolic genes in vitro. Furthermore, mice deficient in Gprc5b displayed a more severe OA phenotype in the destabilization of the medial meniscus (DMM) induced OA mouse model, with upregulation of cartilage catabolic factors and downregulation of anabolic factors, consistent with our in vitro findings. Overexpression of Gprc5b by lentiviral vectors alleviated the cartilage degeneration in DMM-induced OA mouse model by inhibiting cartilage degradation and promoting regeneration. We also assessed the molecular mechanisms downstream of Gprc5b that may mediate these observed effects and identify the role of protein kinase B (AKT)-mammalian target of rapamycin (mTOR)-autophagy signaling pathway. Thus, we demonstrate an integral role of GPRC5B in OA pathogenesis, and activation of GPRC5B has the potential in preventing the progression of OA.
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Affiliation(s)
- Liang He
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Ziwei Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xin Niu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Rong Li
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Fanhua Wang
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Yu You
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jingduo Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lei Zhao
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Karan M. Shah
- Department of Oncology and Metabolism, the Medical School, the University of Sheffield, Sheffield S10 2TN, UK
| | - Jian Fan
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jian Luo
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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25
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Lazarov T, Juarez-Carreño S, Cox N, Geissmann F. Physiology and diseases of tissue-resident macrophages. Nature 2023; 618:698-707. [PMID: 37344646 PMCID: PMC10649266 DOI: 10.1038/s41586-023-06002-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 03/23/2023] [Indexed: 06/23/2023]
Abstract
Embryo-derived tissue-resident macrophages are the first representatives of the haematopoietic lineage to emerge in metazoans. In mammals, resident macrophages originate from early yolk sac progenitors and are specified into tissue-specific subsets during organogenesis-establishing stable spatial and functional relationships with specialized tissue cells-and persist in adults. Resident macrophages are an integral part of tissues together with specialized cells: for instance, microglia reside with neurons in brain, osteoclasts reside with osteoblasts in bone, and fat-associated macrophages reside with white adipocytes in adipose tissue. This ancillary cell type, which is developmentally and functionally distinct from haematopoietic stem cell and monocyte-derived macrophages, senses and integrates local and systemic information to provide specialized tissue cells with the growth factors, nutrient recycling and waste removal that are critical for tissue growth, homeostasis and repair. Resident macrophages contribute to organogenesis, promote tissue regeneration following damage and contribute to tissue metabolism and defence against infectious disease. A correlate is that genetic or environment-driven resident macrophage dysfunction is a cause of degenerative, metabolic and possibly inflammatory and tumoural diseases. In this Review, we aim to provide a conceptual outline of our current understanding of macrophage physiology and its importance in human diseases, which may inform and serve the design of future studies.
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Affiliation(s)
- Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Sergio Juarez-Carreño
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nehemiah Cox
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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26
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Sarkar T, Chen Y, Wang Y, Chen Y, Chen F, Reaux CR, Moore LE, Raghavan V, Xu W. Introducing mirror-image discrimination capability to the TSR-based method for capturing stereo geometry and understanding hierarchical structure relationships of protein receptor family. Comput Biol Chem 2023; 103:107824. [PMID: 36753783 PMCID: PMC9992349 DOI: 10.1016/j.compbiolchem.2023.107824] [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: 09/09/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
We have developed a Triangular Spatial Relationship (TSR)-based computational method for protein structure comparison and motif discovery that is both sequence and structure alignment-free. A protein 3D structure is modeled by all possible triangles that are constructed with every three Cα atoms of amino acids as vertices. Every triangle is represented using an integer (a key). The keys are calculated by a rule-based formula which is a function of a representative length, a representative angle, and the vertex labels associated with amino acids. A 3D structure is thereby represented by a vector of integers (TSR keys). Global or local structure comparisons are achieved by computing all keys or a set of keys, respectively. Many enzymatic reactions and notable marketed drugs are highly stereospecific. Thus, in this paper, we propose a modified key calculation formula by including a mechanism for discriminating mirror-image keys to capture stereo geometry. We assign a positive or a negative sign to the integers representing mirror-image keys. Applying the new key calculation function provides the ability to further discriminate mirror-image keys that were previously considered identical. As the result, applying the mirror-image discrimination capability (i) significantly increases the number of distinct keys; (ii) decreases the number of common keys; (iii) decreases structural similarity; (iv) increases the opportunity to identify specific keys for each type of the receptors. The specific keys identified in this study for the cases of without (not applying) and with (applying) mirror-image discrimination can be considered as the structure signatures that exclusively belong to a certain type of receptors. Applying mirror-image discrimination introduces stereospecificity to keys for allowing more precise modeling of ligand - target interactions. The development of mirror-image TSR keys of Cα atom, in conjunction with the integration of Cα TSR keys with all-atom TSR keys for amino acids and drugs, will lead to a new and promising computational method for aiding drug design and discovery.
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Affiliation(s)
- Titli Sarkar
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yuwu Chen
- San Diego Supercomputer Center, University of California San Diego, Gilman Drive, La Jolla, CA 92093, USA
| | - Yu Wang
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Yixin Chen
- Department of Computer and Information Science, The University of Mississippi, MS 38677, USA
| | - Feng Chen
- High Performance Computing, Frey Computing Services Center, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Camille R Reaux
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Laura E Moore
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Vijay Raghavan
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
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27
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Alva-Gallegos R, Carazo A, Mladěnka P. Toxicity overview of endocrine disrupting chemicals interacting in vitro with the oestrogen receptor. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 99:104089. [PMID: 36841273 DOI: 10.1016/j.etap.2023.104089] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The oestrogen receptor (ER) from the nuclear receptor family is involved in different physiological processes, which can be affected by multiple xenobiotics. Some of these compounds, such as bisphenols, pesticides, and phthalates, are widespread as consequence of human activities and are commonly present also in human organism. Xenobiotics able to interact with ER and trigger a hormone-like response, are known as endocrine disruptors. In this review, we aim to summarize the available knowledge on products derived from human industrial activity and other xenobiotics reported to interact with ER. ER-disrupting chemicals behave differently towards oestrogen-dependent cell lines than endogenous oestradiol. In low concentrations, they stimulate proliferation, whereas at higher concentrations, are toxic to cells. In addition, most of the knowledge on the topic is based on individual compound testing, and only a few studies assess xenobiotic combinations, which better resemble real circumstances. Confirmation from in vivo models is lacking also.
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Affiliation(s)
- Raul Alva-Gallegos
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Alejandro Carazo
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic.
| | - Přemysl Mladěnka
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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28
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Pawlicki P, Koziorowska A, Koziorowski M, Pawlicka B, Duliban M, Wieczorek J, Płachno BJ, Pardyak L, Korzekwa AJ, Kotula-Balak M. Senescence and autophagy relation with the expressional status of non-canonical estrogen receptors in testes and adrenals of roe deer (Capreolus capreolus) during the pre-rut period. Theriogenology 2023; 198:141-152. [PMID: 36586352 DOI: 10.1016/j.theriogenology.2022.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The roe deer bucks represent a spontaneous model to study the synchronized testicular involution and recrudescence cycles. However, cellular processes and hormonal control of steroidogenic glands are scarcely known. For the present study testes and adrenal glands obtained from roe deer during the pre-rut season were used. We aimed to determine (i) senescence and autophagy involvement in testis atrophy (immunohistochemical analysis for tumor suppressor protein encoded by the cyclin-dependent kinase inhibitor 2A; p16 and microtubule-associated protein 1A/1B-light chain 3; LC3, respectively), (ii) the size of the adrenal cortex and medulla (morphometric analysis), (iii) G-protein coupled estrogen receptor (GPER) and estrogen-related receptors (ERRs; type α, β, and Y) distribution and expression (qRT-PCR and immunohistochemical analyses) and (iv) serum testosterone and estradiol levels (immunoassay ELISA). This study revealed pre-rut characteristics of testis structure with the presence of both senescence and autophagy-positive cells and higher involvement of senescence, especially in spermatogenic cells (P < 0.05). In the adrenal cortex, groups of cells exhibiting shrinkage were observed. The presence of ERRs in cells of the seminiferous epithelium and interstitial Leydig cells and GPER presence distinctly in Leydig cells was revealed. In adrenals, these receptors were localized in groups of normal-looking cells and those with shrinkage. Morphometric analysis showed differences in cortex width which was smaller (P < 0.05) than that of the medulla. A weak immunohistochemical signal was observed for ERRβ when compared to ERRα and ERRγ. The mRNA expression level of ERRα and ERRγ was lower (P < 0.001 and P < 0.05, respectively) while ERRβ was higher (P < 0.001) in adrenals when compared to testes. mRNA GPER expression was similar in both glands. In the pre-rut season, the testosterone level was 4.89 ng/ml while the estradiol level was 0.234 ng/ml. We postulate that: (i) senescence and autophagy may be involved in both reinitiation of testis function and/or induction of abnormal processes, (ii) hormonal modulation of testis inactivity may affect adrenal cortex causing cell shrinkage, (iii) ERRs and GPER localization in spermatogenic cells and interstitial cells, as well as cortex cells, may maintain and control the morpho-functional status of both glands, and (iv) androgens and estrogens (via ERRs and GPER) drive cellular processes in the testis and adrenal pre-rut physiology.
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Affiliation(s)
- Piotr Pawlicki
- Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
| | - Anna Koziorowska
- College of Natural Sciences, Institute of Material Engineering, University of Rzeszow, Pigonia 1, 35-310, Rzeszow, Poland; College of Natural Sciences, Institute of Biology and Biotechnology, University of Rzeszów, Pigonia 1, 35-310, Rzeszów, Poland
| | - Marek Koziorowski
- College of Natural Sciences, Institute of Material Engineering, University of Rzeszow, Pigonia 1, 35-310, Rzeszow, Poland; Department of Animal Physiology and Reproduction, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310, Rzeszów, Poland
| | - Bernadetta Pawlicka
- Department of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Gronostajowa 9, 30-387, Jagiellonian University in Krakow, Krakow, Poland
| | - Michal Duliban
- Department of Endocrinology, Institute of Zoology and Biomedical Research, Gronostajowa 9, 30-387, Jagiellonian University in Krakow, Krakow, Poland
| | - Jarosław Wieczorek
- Department of Clinical Diagnostics and Internal Animal Diseases, University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059, Krakow, Poland
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University in Krakow, Gronostajowa 9, 30-387, Krakow, Poland
| | - Laura Pardyak
- Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
| | - Anna J Korzekwa
- Department of Biodiversity Protection, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Malgorzata Kotula-Balak
- Department of Animal Anatomy and Preclinical Sciences, University Centre of Veterinary Medicine JU-UA, University of Agriculture in Kraków, 30-059, Krakow, Poland.
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29
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Zanin N, Viaris de Lesegno C, Podkalicka J, Meyer T, Gonzalez Troncoso P, Bun P, Danglot L, Chmiest D, Urbé S, Piehler J, Blouin CM, Lamaze C. STAM and Hrs interact sequentially with IFN-α Receptor to control spatiotemporal JAK-STAT endosomal activation. Nat Cell Biol 2023; 25:425-438. [PMID: 36797476 DOI: 10.1038/s41556-022-01085-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/21/2022] [Indexed: 02/18/2023]
Abstract
Activation of the JAK-STAT pathway by type I interferons (IFNs) requires clathrin-dependent endocytosis of the IFN-α and -β receptor (IFNAR), indicating a role for endosomal sorting in this process. The molecular machinery that brings the selective activation of IFN-α/β-induced JAK-STAT signalling on endosomes remains unknown. Here we show that the constitutive association of STAM with IFNAR1 and TYK2 kinase at the plasma membrane prevents TYK2 activation by type I IFNs. IFN-α-stimulated IFNAR endocytosis delivers the STAM-IFNAR complex to early endosomes where it interacts with Hrs, thereby relieving TYK2 inhibition by STAM and triggering signalling of IFNAR at the endosome. In contrast, when stimulated by IFN-β, IFNAR signalling occurs independently of Hrs as IFNAR is sorted to a distinct endosomal subdomain. Our results identify the molecular machinery that controls the spatiotemporal activation of IFNAR by IFN-α and establish the central role of endosomal sorting in the differential regulation of JAK-STAT signalling by IFN-α and IFN-β.
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Affiliation(s)
- Natacha Zanin
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France.,Namur Research Institute for Life Sciences (NARILIS), URBC, University of Namur, Namur, Belgium
| | - Christine Viaris de Lesegno
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Joanna Podkalicka
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France.,Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, Paris, France.,Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Thomas Meyer
- Department of Biology and Center for Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany
| | - Pamela Gonzalez Troncoso
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Philippe Bun
- Membrane Traffic in Healthy and Diseased Brain, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France.,NeurImag Imaging Facility, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France
| | - Lydia Danglot
- Membrane Traffic in Healthy and Diseased Brain, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France.,NeurImag Imaging Facility, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, Paris, France
| | - Daniela Chmiest
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Centre National de la Recherche Scientifique (CNRS), Paris, France.,Department of Biochemistry, CIIL Biomedical Research Center, University of Lausanne, Epalinges, Switzerland
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, University of Osnabruck, Osnabruck, Germany
| | - Cédric M Blouin
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Centre National de la Recherche Scientifique (CNRS), Paris, France.
| | - Christophe Lamaze
- Membrane Mechanics and Dynamics of Intracellular Signaling Laboratory, Institut Curie-Centre de Recherche, PSL Research University, Paris, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Centre National de la Recherche Scientifique (CNRS), Paris, France.
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30
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Ali S, Rehman MU, Yatoo AM, Arafah A, Khan A, Rashid S, Majid S, Ali A, Ali MN. TGF-β signaling pathway: Therapeutic targeting and potential for anti-cancer immunity. Eur J Pharmacol 2023; 947:175678. [PMID: 36990262 DOI: 10.1016/j.ejphar.2023.175678] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Transforming growth factor-β (TGFβ) is a pleiotropic secretory cytokine exhibiting both cancer-inhibitory and promoting properties. It transmits its signals via Suppressor of Mother against Decapentaplegic (SMAD) and non-SMAD pathways and regulates cell proliferation, differentiation, invasion, migration, and apoptosis. In non-cancer and early-stage cancer cells, TGFβ signaling suppresses cancer progression via inducing apoptosis, cell cycle arrest, or anti-proliferation, and promoting cell differentiation. On the other hand, TGFβ may also act as an oncogene in advanced stages of tumors, wherein it develops immune-suppressive tumor microenvironments and induces the proliferation of cancer cells, invasion, angiogenesis, tumorigenesis, and metastasis. Higher TGFβ expression leads to the instigation and development of cancer. Therefore, suppressing TGFβ signals may present a potential treatment option for inhibiting tumorigenesis and metastasis. Different inhibitory molecules, including ligand traps, anti-sense oligo-nucleotides, small molecule receptor-kinase inhibitors, small molecule inhibitors, and vaccines, have been developed and clinically trialed for blocking the TGFβ signaling pathway. These molecules are not pro-oncogenic response-specific but block all signaling effects induced by TGFβ. Nonetheless, targeting the activation of TGFβ signaling with maximized specificity and minimized toxicity can enhance the efficacy of therapeutic approaches against this signaling pathway. The molecules that are used to target TGFβ are non-cytotoxic to cancer cells but designed to curtail the over-activation of invasion and metastasis driving TGFβ signaling in stromal and cancer cells. Here, we discussed the critical role of TGFβ in tumorigenesis, and metastasis, as well as the outcome and the promising achievement of TGFβ inhibitory molecules in the treatment of cancer.
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Mariottini D, Idili A, Ercolani G, Ricci F. Thermo-Programmed Synthetic DNA-Based Receptors. ACS NANO 2023; 17:1998-2006. [PMID: 36689298 PMCID: PMC9933611 DOI: 10.1021/acsnano.2c07039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Herein, we present a generalizable and versatile strategy to engineer synthetic DNA ligand-binding devices that can be programmed to load and release a specific ligand at a defined temperature. We do so by re-engineering two model DNA-based receptors: a triplex-forming bivalent DNA-based receptor that recognizes a specific DNA sequence and an ATP-binding aptamer. The temperature at which these receptors load/release their ligands can be finely modulated by controlling the entropy associated with the linker connecting the two ligand-binding domains. The availability of a set of receptors with tunable and reversible temperature dependence allows achieving complex load/release behavior such as sustained ligand release over a wide temperature range. Similar programmable thermo-responsive synthetic ligand-binding devices can be of utility in applications such as drug delivery and production of smart materials.
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Affiliation(s)
- Davide Mariottini
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Andrea Idili
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Gianfranco Ercolani
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Chemistry
Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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32
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Proteome-Wide Detection and Annotation of Receptor Tyrosine Kinases (RTKs): RTK-PRED and the TyReK Database. Biomolecules 2023; 13:biom13020270. [PMID: 36830638 PMCID: PMC9953206 DOI: 10.3390/biom13020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/16/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) form a highly important group of protein receptors of the eukaryotic cell membrane. They control many vital cellular functions and are involved in the regulation of complex signaling networks. Mutations in RTKs have been associated with different types of cancers and other diseases. Although they are very important for proper cell function, they have been experimentally studied in a limited range of eukaryotic species. Currently, there is no available database for RTKs providing information about their function, expression, and interactions. Therefore, the identification of RTKs in multiple organisms, the documentation of their characteristics, and the collection of related information would be very useful. In this paper, we present a novel RTK detection pipeline (RTK-PRED) and the Receptor Tyrosine Kinases Database (TyReK-DB). RTK-PRED combines profile HMMs with transmembrane topology prediction to identify and classify potential RTKs. Proteins of all eukaryotic reference proteomes of the UniProt database were used as input in RTK-PRED leading to a filtered dataset of 20,478 RTKs. Based on the information collected for these RTKs from multiple databases, the relational TyReK database was created.
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33
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Lin Z, Lin X, Sun Y, Lei S, Cai G, Li Z. Melanoma molecular subtyping and scoring model construction based on ligand-receptor pairs. Front Genet 2023; 14:1098202. [PMID: 36777724 PMCID: PMC9909287 DOI: 10.3389/fgene.2023.1098202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Melanoma is a malignancy of melanocytes, responsible for a high percentage of skin cancer mortality. Ligand-Receptor pairs, a type of cellular communication, are essential for tumor genesis, growth, metastasis, and prognosis. Yet, the role of Ligand-Receptor pairs in melanoma has not been fully elucidated. Our research focused on the function of Ligand-Receptor pairs in melanoma prognosis. We screened 131 melanoma prognosis corresponded ligand-receptor pairs by analyzing the TCGA data of melanoma and the 2293 LR pairs retrieved from the connectomeDB2020 database. And further developed subtypes of melanoma according to the expression of these ligand-receptor pairs by Consensus Clustering. Then we using lasso cox regression and stepwise multivariate regression analysis established a ligand-receptor pairs-based scoring model for the evaluation of melanoma prognosis. Our study demonstrated that the ligand-receptor pairs are vital to the molecular heterogeneity of melanoma, and characterized three different melanoma ligand-receptor pairs subtypes. Among them, the C3 subtype showed a better prognosis, while the C1 subtype exhibited a low prognosis state. And our analysis then found out that this could be related to the differed activation and inhabitation of the cell cycle and immune-related pathways. Using lasso cox regression and stepwise multivariate regression analysis, we further identified 9 key ligand-receptor pairs and established a scoring model that effectively correlated with the prognosis, immune pathways, and therapy of melanoma, showing that the LR.score model was a trustworthy and independent biomarker for melanoma prognosis evaluation. In sum, we found that ligand-receptor pairs are significantly associated with the prognosis and therapy of melanoma. And our ligand-receptor-based scoring model showed potential for the evaluation of melanoma prognosis and immune therapy outcome prediction, which is crucial to the survival for the patients.
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Affiliation(s)
- Zexu Lin
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,Department of Plastic and Cosmetic Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Xin Lin
- Department of Plastic and Cosmetic Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Yuming Sun
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Shaorong Lei
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Gengming Cai
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Zhexuan Li
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, China,*Correspondence: Zhexuan Li,
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Kaur G, Verma SK, Singh D, Singh NK. Role of G-Proteins and GPCRs in Cardiovascular Pathologies. Bioengineering (Basel) 2023; 10:bioengineering10010076. [PMID: 36671648 PMCID: PMC9854459 DOI: 10.3390/bioengineering10010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Cell signaling is a fundamental process that enables cells to survive under various ecological and environmental contexts and imparts tolerance towards stressful conditions. The basic machinery for cell signaling includes a receptor molecule that senses and receives the signal. The primary form of the signal might be a hormone, light, an antigen, an odorant, a neurotransmitter, etc. Similarly, heterotrimeric G-proteins principally provide communication from the plasma membrane G-protein-coupled receptors (GPCRs) to the inner compartments of the cells to control various biochemical activities. G-protein-coupled signaling regulates different physiological functions in the targeted cell types. This review article discusses G-proteins' signaling and regulation functions and their physiological relevance. In addition, we also elaborate on the role of G-proteins in several cardiovascular diseases, such as myocardial ischemia, hypertension, atherosclerosis, restenosis, stroke, and peripheral artery disease.
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Affiliation(s)
- Geetika Kaur
- Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI 48202, USA
| | - Shailendra Kumar Verma
- Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI 48202, USA
| | - Deepak Singh
- Lloyd Institute of Engineering and Technology, Greater Noida 201306, India
| | - Nikhlesh K. Singh
- Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Ophthalmology, Visual and Anatomical Sciences, School of Medicine, Wayne State University, Detroit, MI 48202, USA
- Correspondence:
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35
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Lo CH, Zeng J. Application of polymersomes in membrane protein study and drug discovery: Progress, strategies, and perspectives. Bioeng Transl Med 2023; 8:e10350. [PMID: 36684106 PMCID: PMC9842050 DOI: 10.1002/btm2.10350] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023] Open
Abstract
Membrane proteins (MPs) play key roles in cellular signaling pathways and are responsible for intercellular and intracellular interactions. Dysfunctional MPs are directly related to the pathogenesis of various diseases, and they have been exploited as one of the most sought-after targets in the pharmaceutical industry. However, working with MPs is difficult given that their amphiphilic nature requires protection from biological membrane or membrane mimetics. Polymersomes are bilayered nano-vesicles made of self-assembled block copolymers that have been widely used as cell membrane mimetics for MP reconstitution and in engineering of artificial cells. This review highlights the prevailing trend in the application of polymersomes in MP study and drug discovery. We begin with a review on the techniques for synthesis and characterization of polymersomes as well as methods of MP insertion to form proteopolymersomes. Next, we review the structural and functional analysis of the different types of MPs reconstituted in polymersomes, including membrane transport proteins, MP complexes, and membrane receptors. We then summarize the factors affecting reconstitution efficiency and the quality of reconstituted MPs for structural and functional studies. Additionally, we discuss the potential in using proteopolymersomes as platforms for high-throughput screening (HTS) in drug discovery to identify modulators of MPs. We conclude by providing future perspectives and recommendations on advancing the study of MPs and drug development using proteopolymersomes.
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Affiliation(s)
- Chih Hung Lo
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jialiu Zeng
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Department of Biomedical EngineeringBoston UniversityBostonMassachusettsUSA
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
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36
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Wang D, Zhu L, Zhen X, Yang D, Li C, Chen Y, Wang H, Qu Y, Liu X, Yin Y, Gu H, Xu L, Wan C, Wang Y, Ouyang S, Shen X. A secreted effector with a dual role as a toxin and as a transcriptional factor. Nat Commun 2022; 13:7779. [PMID: 36522324 PMCID: PMC9755527 DOI: 10.1038/s41467-022-35522-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria have evolved multiple secretion systems for delivering effector proteins into the cytosol of neighboring cells, but the roles of many of these effectors remain unknown. Here, we show that Yersinia pseudotuberculosis secretes an effector, CccR, that can act both as a toxin and as a transcriptional factor. The effector is secreted by a type VI secretion system (T6SS) and can enter nearby cells of the same species and other species (such as Escherichia coli) via cell-cell contact and in a contact-independent manner. CccR contains an N-terminal FIC domain and a C-terminal DNA-binding domain. In Y. pseudotuberculosis cells, CccR inhibits its own expression by binding through its DNA-binding domain to the cccR promoter, and affects the expression of other genes through unclear mechanisms. In E. coli cells, the FIC domain of CccR AMPylates the cell division protein FtsZ, inducing cell filamentation and growth arrest. Thus, our results indicate that CccR has a dual role, modulating gene expression in neighboring cells of the same species, and inhibiting the growth of competitors.
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Affiliation(s)
- Dandan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lingfang Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiangkai Zhen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Daoyan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Changfu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yating Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huannan Wang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yichen Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaozhen Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanling Yin
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, China
| | - Huawei Gu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuanxing Wan
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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37
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Merino-Casallo F, Gomez-Benito MJ, Hervas-Raluy S, Garcia-Aznar JM. Unravelling cell migration: defining movement from the cell surface. Cell Adh Migr 2022; 16:25-64. [PMID: 35499121 PMCID: PMC9067518 DOI: 10.1080/19336918.2022.2055520] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
Cell motility is essential for life and development. Unfortunately, cell migration is also linked to several pathological processes, such as cancer metastasis. Cells' ability to migrate relies on many actors. Cells change their migratory strategy based on their phenotype and the properties of the surrounding microenvironment. Cell migration is, therefore, an extremely complex phenomenon. Researchers have investigated cell motility for more than a century. Recent discoveries have uncovered some of the mysteries associated with the mechanisms involved in cell migration, such as intracellular signaling and cell mechanics. These findings involve different players, including transmembrane receptors, adhesive complexes, cytoskeletal components , the nucleus, and the extracellular matrix. This review aims to give a global overview of our current understanding of cell migration.
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Affiliation(s)
- Francisco Merino-Casallo
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza, Spain
- Department of Mechanical Engineering, University of Zaragoza, Zaragoza, Spain
| | - Maria Jose Gomez-Benito
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza, Spain
- Department of Mechanical Engineering, University of Zaragoza, Zaragoza, Spain
| | - Silvia Hervas-Raluy
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza, Spain
- Department of Mechanical Engineering, University of Zaragoza, Zaragoza, Spain
| | - Jose Manuel Garcia-Aznar
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Zaragoza, Spain
- Department of Mechanical Engineering, University of Zaragoza, Zaragoza, Spain
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38
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An SJ, Anneken A, Xi Z, Choi C, Schlessinger J, Toomre D. Regulation of EGF-stimulated activation of the PI-3K/AKT pathway by exocyst-mediated exocytosis. Proc Natl Acad Sci U S A 2022; 119:e2208947119. [PMID: 36417441 PMCID: PMC9860279 DOI: 10.1073/pnas.2208947119] [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] [Indexed: 11/24/2022] Open
Abstract
The phosphoinositide-3 kinase (PI-3K)/AKT cell survival pathway is an important pathway activated by EGFR signaling. Here we show, that in addition to previously described critical components of this pathway, i.e., the docking protein Gab1, the PI-3K/AKT pathway in epithelial cells is regulated by the exocyst complex, which is a vesicle tether that is essential for exocytosis. Using live-cell imaging, we demonstrate that PI(3,4,5)P3 levels fluctuate at the membrane on a minutes time scale and that these fluctuations are associated with local PI(3,4,5)P3 increases at sites where recycling vesicles undergo exocytic fusion. Supporting a role for exocytosis in PI(3,4,5)P3 generation, acute promotion of exocytosis by optogenetically driving exocyst-mediated vesicle tethering up-regulates PI(3,4,5)P3 production and AKT activation. Conversely, acute inhibition of exocytosis using Endosidin2, a small-molecule inhibitor of the exocyst subunit Exo70 (also designated EXOC7), or inhibition of exocyst function by siRNA-mediated knockdown of the exocyst subunit Sec15 (EXOC6), impairs PI(3,4,5)P3 production and AKT activation induced by EGF stimulation of epithelial cells. Moreover, prolonged inhibition of EGF signaling by EGFR tyrosine kinase inhibitors results in spontaneous reactivation of AKT without a concomitant relief of EGFR inhibition. However, this reactivation can be negated by acutely inhibiting the exocyst. These experiments demonstrate that exocyst-mediated exocytosis-by regulating PI(3,4,5)P3 levels at the plasma membrane-subserves activation of the PI-3K/AKT pathway by EGFR in epithelial cells.
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Affiliation(s)
- Seong J. An
- aDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- bDepartment of Pharmacology, Yale University School of Medicine, New Haven, CT06510
- 2To whom correspondence may be addressed. or
| | - Alexander Anneken
- aDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT06510
| | - Zhiqun Xi
- aDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT06510
| | - Changseon Choi
- aDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT06510
| | - Joseph Schlessinger
- bDepartment of Pharmacology, Yale University School of Medicine, New Haven, CT06510
| | - Derek Toomre
- aDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- 2To whom correspondence may be addressed. or
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39
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Zhao Q, Bai J, Chen Y, Liu X, Zhao S, Ling G, Jia S, Zhai F, Xiang R. An optimized herbal combination for the treatment of liver fibrosis: Hub genes, bioactive ingredients, and molecular mechanisms. JOURNAL OF ETHNOPHARMACOLOGY 2022; 297:115567. [PMID: 35870684 DOI: 10.1016/j.jep.2022.115567] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/30/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Liver fibrosis is a chronic liver disease that can lead to cirrhosis, liver failure, and hepatocellular carcinoma, and it is associated with long-term adverse outcomes and mortality. As a primary resource for complementary and alternative medicine, traditional Chinese medicine (TCM) has accumulated a large number of effective formulas for the treatment of liver fibrosis in clinical practice. However, studies on how to systematically optimize TCM formulas are still lacking. AIM OF THE REVIEW To provide a methodological reference for the systematic optimization of TCM formulae against liver fibrosis and explored the underlying molecular mechanisms; To provide an efficient method for searching for lead compounds from natural sources and developing from herbal medicines; To enable clinicians and patients to make more reasonable choices and promote the effective treatment toward those patients with liver fibrosis. MATERIALS AND METHODS TCM formulas related to treating liver fibrosis were collected from the Web of Science, PubMed, the China National Knowledge Infrastructure (CNKI), Wan Fang, and the Chinese Scientific Journals Database (VIP). Furthermore, the TCM compatibility patterns were mined using association analysis. The core TCM combinations were found by designing an optimized formulas algorithm. Finally, the hub target proteins, potential molecular mechanisms, and active compounds were explored through integrative pharmacology and docking-based inverse virtual screening (IVS) approaches. RESULTS We found that the herbs for reinforcing deficiency, activating blood, removing blood stasis, and clearing heat were the basis of TCM formulae patterns. Furthermore, the combination of Salviae Miltiorrhizae (Salvia miltiorrhiza Bunge; Chinese salvia/Danshen), Astragali Radix (Astragalus membranaceus (Fisch.) Bunge; Astragalus/Huangqi), and Radix Bupleuri (Bupleurum chinense DC.; Bupleurum/Chaihu) was identified as core groups. A total of six targets (TNF, STAT3, EGFR, IL2, ICAM1, PTGS2) play a pivotal role in TCM-mediated liver fibrosis inhibition. (-)-Cryptotanshinone, Tanshinaldehyde, Ononin, Thymol, Daidzein, and Formononetin were identified as active compounds in TCM. And mechanistically, TCM could affect the development of liver fibrosis by regulating inflammation, immunity, angiogenesis, antioxidants, and involvement in TNF, MicroRNAs, Jak-STAT, NF-kappa B, and C-type lectin receptors (CLRs) signaling pathways. Molecular docking results showed that key components had good potential to bind to the target genes. CONCLUSION In summary, this study provides a methodological reference for the systematic optimization of TCM formulae and exploration of underlying molecular mechanisms.
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Affiliation(s)
- Qianqian Zhao
- Faculty of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Jinwei Bai
- School of Medical Equipment, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Yiwei Chen
- Faculty of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Xin Liu
- Faculty of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Shangfeng Zhao
- Faculty of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Guixia Ling
- School of Medical Equipment, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Shubing Jia
- Faculty of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Fei Zhai
- School of Medical Equipment, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Rongwu Xiang
- School of Medical Equipment, Shenyang Pharmaceutical University, Shenyang, 110016, China; Liaoning Professional Technology Innovation Center on Medical Big Data and Artificial Intelligence, Shenyang, 110016, China.
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40
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Yehuda GA, Somekh J. A methodology for classifying tissue-specific metabolic and inflammatory receptor functions applied to subcutaneous and visceral adipose. PLoS One 2022; 17:e0276699. [PMID: 36282842 PMCID: PMC9595531 DOI: 10.1371/journal.pone.0276699] [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: 03/11/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
To achieve homeostasis, the human biological system relies on the interaction between organs through the binding of ligands secreted from source organs to receptors located on destination organs. Currently, the changing roles that receptors perform in tissues are only partially understood. Recently, a methodology based on receptor co-expression patterns to classify their tissue-specific metabolic functions was suggested. Here we present an advanced framework to predict an additional class of inflammatory receptors that use a feature space of biological pathway enrichment analysis scores of co-expression networks and their eigengene correlations. These are fed into three machine learning classifiers-eXtreme Gradient Boosting (XGBoost), Support Vector Machines (SVM), and K-Nearest Neighbors (k-NN). We applied our methodology to subcutaneous and visceral adipose gene expression datasets derived from the GTEx (Genotype-Tissue Expression) project and compared the predictions. The XGBoost model demonstrated the best performance in predicting the pre-labeled receptors, with an accuracy of 0.89/0.8 in subcutaneous/visceral adipose. We analyzed ~700 receptors to predict eight new metabolic and 15 new inflammatory functions of receptors and four new metabolic functions for known inflammatory receptors in both adipose tissues. We cross-referenced multiple predictions using the published literature. Our results establish a picture of the changing functions of receptors for two adipose tissues that can be beneficial for drug development.
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Affiliation(s)
| | - Judith Somekh
- Information Systems, University of Haifa, Haifa, Israel
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41
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Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Commun Biol 2022; 5:1066. [PMID: 36207580 PMCID: PMC9546880 DOI: 10.1038/s42003-022-03975-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/12/2022] [Indexed: 02/01/2023] Open
Abstract
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
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Affiliation(s)
- Sean M. Gross
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Mark A. Dane
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Rebecca L. Smith
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kaylyn L. Devlin
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Ian C. McLean
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Daniel S. Derrick
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Caitlin E. Mills
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Kartik Subramanian
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Alexandra B. London
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Denis Torre
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - John Erol Evangelista
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel J. B. Clarke
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Zhuorui Xie
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Cemal Erdem
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Nicholas Lyons
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ted Natoli
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Sarah Pessa
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Xiaodong Lu
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - James Mullahoo
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jonathan Li
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Miriam Adam
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Brook Wassie
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Moqing Liu
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - David F. Kilburn
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Tiera A. Liby
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Elmar Bucher
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Crystal Sanchez-Aguila
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kenneth Daily
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Larsson Omberg
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Yunguan Wang
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Connor Jacobson
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Clarence Yapp
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Mirra Chung
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Dusica Vidovic
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Stephan Schurer
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Albert Lee
- grid.94365.3d0000 0001 2297 5165Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA
| | - Ajay Pillai
- grid.94365.3d0000 0001 2297 5165Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Aravind Subramanian
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Malvina Papanastasiou
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ernest Fraenkel
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Heidi S. Feiler
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Gordon B. Mills
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Division of Oncological Sciences, OHSU, Portland, OR USA
| | - Jake D. Jaffe
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Avi Ma’ayan
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Marc R. Birtwistle
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Peter K. Sorger
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - James E. Korkola
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Joe W. Gray
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Laura M. Heiser
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
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A multi-adenylate cyclase regulator at the flagellar tip controls African trypanosome transmission. Nat Commun 2022; 13:5445. [PMID: 36114198 PMCID: PMC9481589 DOI: 10.1038/s41467-022-33108-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Signaling from ciliary microdomains controls developmental processes in metazoans. Trypanosome transmission requires development and migration in the tsetse vector alimentary tract. Flagellar cAMP signaling has been linked to parasite social motility (SoMo) in vitro, yet uncovering control of directed migration in fly organs is challenging. Here we show that the composition of an adenylate cyclase (AC) complex in the flagellar tip microdomain is essential for tsetse salivary gland (SG) colonization and SoMo. Cyclic AMP response protein 3 (CARP3) binds and regulates multiple AC isoforms. CARP3 tip localization depends on the cytoskeletal protein FLAM8. Re-localization of CARP3 away from the tip microdomain is sufficient to abolish SoMo and fly SG colonization. Since intrinsic development is normal in carp3 and flam8 knock-out parasites, AC complex-mediated tip signaling specifically controls parasite migration and thereby transmission. Participation of several developmentally regulated receptor-type AC isoforms may indicate the complexity of the in vivo signals perceived. Trypanosomes can sense signal molecules and coordinate their movement in response to such signals, a phenomenon termed social motility (SoMo). Here, Bachmaier et al show that cyclic AMP response protein 3 (CARP3) localization to the flagellar tip and its interaction with a number of different adenylate cyclases is essential for migration to tsetse fly salivary glands and for SoMo, therewith linking SoMo and cAMP signaling to trypanosome transmission.
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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Pan W, Song K, Zhang Y, Yang C, Zhang Y, Ji F, Zhang J, Shi J, Wang K. The molecular subtypes of triple negative breast cancer were defined and a ligand-receptor pair score model was constructed by comprehensive analysis of ligand-receptor pairs. Front Immunol 2022; 13:982486. [PMID: 36119101 PMCID: PMC9470927 DOI: 10.3389/fimmu.2022.982486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
Background Intercellular communication mediated by ligand-receptor interactions in tumor microenvironment (TME) has a profound impact on tumor progression. This study aimed to explore the molecular subtypes mediated by ligand-receptor (LR) pairs in triple negative breast cancer (TNBC), identify the most important LR pairs to construct a prognostic risk model, and study their effect on TNBC immunotherapy. Methods LR pairs subclasses of TNBC were categorized by consensus clustering based on LR Pairs in METABRIC dataset. Least absolute shrinkage and selection operator (LASSO) Cox regression and stepwise Akaike information criterion (stepAIC) were conducted to build a LR pairs score model. The relationship between LR pairs score and immune cell infiltration, stromal score and immune score associated with TME was analyzed, and the prediction of drug therapy and immunotherapy efficacy by LR pairs score was evaluated. Results According to the expression pattern of 145 TNBC prognostic LR pairs, the samples were divided into three subclasses with different survival outcomes, copy number variation (CNV), TME immune cell infiltration, stromal score and immune score. The LR pairs score model constructed in the METABRIC dataset was composed of four LR pairs, and its predictive significance for TNBC prognosis was verified in GSE58812 and GSE21653 cohorts. In addition, LR pairs score was negatively correlated with several immune pathways regulating immunity and immune score, and related to the sensitivity of anti-neoplastic drugs and the effect of anti-PD-L1 therapy. Conclusion Our study confirmed the impact of LR pairs on the molecular heterogeneity of TNBC, characterized three LR pairs subtypes with different survival outcomes and TME patterns, and proposed a LR pairs score system with predictive significance for TNBC prognosis and anti-PD-L1 therapeutic effect, which provides a potential evaluation scheme for TNBC management.
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Affiliation(s)
- Weijun Pan
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kai Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yunli Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Ciqiu Yang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Fei Ji
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junsheng Zhang
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Shi
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
- *Correspondence: Kun Wang, ; Jian Shi,
| | - Kun Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Kun Wang, ; Jian Shi,
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45
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Navarro-Lérida I, Aragay AM, Asensio A, Ribas C. Gq Signaling in Autophagy Control: Between Chemical and Mechanical Cues. Antioxidants (Basel) 2022; 11:1599. [PMID: 36009317 PMCID: PMC9405508 DOI: 10.3390/antiox11081599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
All processes in human physiology relies on homeostatic mechanisms which require the activation of specific control circuits to adapt the changes imposed by external stimuli. One of the critical modulators of homeostatic balance is autophagy, a catabolic process that is responsible of the destruction of long-lived proteins and organelles through a lysosome degradative pathway. Identification of the mechanism underlying autophagic flux is considered of great importance as both protective and detrimental functions are linked with deregulated autophagy. At the mechanistic and regulatory levels, autophagy is activated in response to diverse stress conditions (food deprivation, hyperthermia and hypoxia), even a novel perspective highlight the potential role of physical forces in autophagy modulation. To understand the crosstalk between all these controlling mechanisms could give us new clues about the specific contribution of autophagy in a wide range of diseases including vascular disorders, inflammation and cancer. Of note, any homeostatic control critically depends in at least two additional and poorly studied interdependent components: a receptor and its downstream effectors. Addressing the selective receptors involved in autophagy regulation is an open question and represents a new area of research in this field. G-protein coupled receptors (GPCRs) represent one of the largest and druggable targets membrane receptor protein superfamily. By exerting their action through G proteins, GPCRs play fundamental roles in the control of cellular homeostasis. Novel studies have shown Gαq, a subunit of heterotrimeric G proteins, as a core modulator of mTORC1 and autophagy, suggesting a fundamental contribution of Gαq-coupled GPCRs mechanisms in the control of this homeostatic feedback loop. To address how GPCR-G proteins machinery integrates the response to different stresses including oxidative conditions and mechanical stimuli, could provide deeper insight into new signaling pathways and open potential and novel therapeutic strategies in the modulation of different pathological conditions.
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Affiliation(s)
- Inmaculada Navarro-Lérida
- Molecular Biology Department and Center of Molecular Biology “Severo Ochoa”, CSIC-UAM, 28049 Madrid, Spain
- Health Research Institute “La Princesa”, 28006 Madrid, Spain
- Center for Biomedical Research in Cardiovascular Diseases Network (CIBERCV), ISCIII, 28029 Madrid, Spain
- Connexion Cancer-CSIC, 28006 Madrid, Spain
| | - Anna M. Aragay
- Department of Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), 08028 Barcelona, Spain
| | - Alejandro Asensio
- Molecular Biology Department and Center of Molecular Biology “Severo Ochoa”, CSIC-UAM, 28049 Madrid, Spain
- Health Research Institute “La Princesa”, 28006 Madrid, Spain
- Center for Biomedical Research in Cardiovascular Diseases Network (CIBERCV), ISCIII, 28029 Madrid, Spain
- Connexion Cancer-CSIC, 28006 Madrid, Spain
| | - Catalina Ribas
- Molecular Biology Department and Center of Molecular Biology “Severo Ochoa”, CSIC-UAM, 28049 Madrid, Spain
- Health Research Institute “La Princesa”, 28006 Madrid, Spain
- Center for Biomedical Research in Cardiovascular Diseases Network (CIBERCV), ISCIII, 28029 Madrid, Spain
- Connexion Cancer-CSIC, 28006 Madrid, Spain
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Casello SM, Flores RJ, Yarur HE, Wang H, Awanyai M, Arenivar MA, Jaime-Lara RB, Bravo-Rivera H, Tejeda HA. Neuropeptide System Regulation of Prefrontal Cortex Circuitry: Implications for Neuropsychiatric Disorders. Front Neural Circuits 2022; 16:796443. [PMID: 35800635 PMCID: PMC9255232 DOI: 10.3389/fncir.2022.796443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
Abstract
Neuropeptides, a diverse class of signaling molecules in the nervous system, modulate various biological effects including membrane excitability, synaptic transmission and synaptogenesis, gene expression, and glial cell architecture and function. To date, most of what is known about neuropeptide action is limited to subcortical brain structures and tissue outside of the central nervous system. Thus, there is a knowledge gap in our understanding of neuropeptide function within cortical circuits. In this review, we provide a comprehensive overview of various families of neuropeptides and their cognate receptors that are expressed in the prefrontal cortex (PFC). Specifically, we highlight dynorphin, enkephalin, corticotropin-releasing factor, cholecystokinin, somatostatin, neuropeptide Y, and vasoactive intestinal peptide. Further, we review the implication of neuropeptide signaling in prefrontal cortical circuit function and use as potential therapeutic targets. Together, this review summarizes established knowledge and highlights unknowns of neuropeptide modulation of neural function underlying various biological effects while offering insights for future research. An increased emphasis in this area of study is necessary to elucidate basic principles of the diverse signaling molecules used in cortical circuits beyond fast excitatory and inhibitory transmitters as well as consider components of neuropeptide action in the PFC as a potential therapeutic target for neurological disorders. Therefore, this review not only sheds light on the importance of cortical neuropeptide studies, but also provides a comprehensive overview of neuropeptide action in the PFC to serve as a roadmap for future studies in this field.
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Affiliation(s)
- Sanne M. Casello
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Rodolfo J. Flores
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Hector E. Yarur
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Huikun Wang
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Monique Awanyai
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Miguel A. Arenivar
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Rosario B. Jaime-Lara
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
| | - Hector Bravo-Rivera
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Hugo A. Tejeda
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Hugo A. Tejeda,
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47
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Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys Rev 2022; 14:679-707. [DOI: 10.1007/s12551-022-00968-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/28/2022] [Indexed: 12/14/2022] Open
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48
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Engineered Allosteric Regulation of Protein Function. J Mol Biol 2022; 434:167620. [PMID: 35513109 DOI: 10.1016/j.jmb.2022.167620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
Allosteric regulation of proteins has been utilized to study various aspects of cell signaling, from unicellular events to organism-wide phenotypes. However, traditional methods of allosteric regulation, such as constitutively active mutants and inhibitors, lack tight spatiotemporal control. This often leads to unintended signaling consequences that interfere with data interpretation. To overcome these obstacles, researchers employed protein engineering approaches that enable tight control of protein function through allosteric mechanisms. These methods provide high specificity as well as spatial and temporal precision in regulation of protein activity in vitro and in vivo. In this review, we focus on the recent advancements in engineered allosteric regulation and discuss the various bioengineered allosteric techniques available now, from chimeric GPCRs to chemogenetic and optogenetic switches. We highlight the benefits and pitfalls of each of these techniques as well as areas in which future improvements can be made. Additionally, we provide a brief discussion on implementation of engineered allosteric regulation approaches, demonstrating that these tools can shed light on elusive biological events and have the potential to be utilized in precision medicine.
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49
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Ma N, Chen D, Lee JH, Kuri P, Hernandez EB, Kocan J, Mahmood H, Tichy ED, Rompolas P, Mourkioti F. Piezo1 regulates the regenerative capacity of skeletal muscles via orchestration of stem cell morphological states. SCIENCE ADVANCES 2022; 8:eabn0485. [PMID: 35302846 PMCID: PMC8932657 DOI: 10.1126/sciadv.abn0485] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/26/2022] [Indexed: 05/08/2023]
Abstract
Muscle stem cells (MuSCs) are essential for tissue homeostasis and regeneration, but the potential contribution of MuSC morphology to in vivo function remains unknown. Here, we demonstrate that quiescent MuSCs are morphologically heterogeneous and exhibit different patterns of cellular protrusions. We classified quiescent MuSCs into three functionally distinct stem cell states: responsive, intermediate, and sensory. We demonstrate that the shift between different stem cell states promotes regeneration and is regulated by the sensing protein Piezo1. Pharmacological activation of Piezo1 is sufficient to prime MuSCs toward more responsive cells. Piezo1 deletion in MuSCs shifts the distribution toward less responsive cells, mimicking the disease phenotype we find in dystrophic muscles. We further demonstrate that Piezo1 reactivation ameliorates the MuSC morphological and regenerative defects of dystrophic muscles. These findings advance our fundamental understanding of how stem cells respond to injury and identify Piezo1 as a key regulator for adjusting stem cell states essential for regeneration.
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Affiliation(s)
- Nuoying Ma
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Delia Chen
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ji-Hyung Lee
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paola Kuri
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edward Blake Hernandez
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jacob Kocan
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hamd Mahmood
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elisia D. Tichy
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Panteleimon Rompolas
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Regenerative Medicine, Musculoskeletal Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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50
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Schardt JS, Jhajj HS, O’Meara RL, Lwo TS, Smith MD, Tessier PM. Agonist antibody discovery: Experimental, computational, and rational engineering approaches. Drug Discov Today 2022; 27:31-48. [PMID: 34571277 PMCID: PMC8714685 DOI: 10.1016/j.drudis.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Agonist antibodies that activate cellular signaling have emerged as promising therapeutics for treating myriad pathologies. Unfortunately, the discovery of rare antibodies with the desired agonist functions is a major bottleneck during drug development. Nevertheless, there has been important recent progress in discovering and optimizing agonist antibodies against a variety of therapeutic targets that are activated by diverse signaling mechanisms. Herein, we review emerging high-throughput experimental and computational methods for agonist antibody discovery as well as rational molecular engineering methods for optimizing their agonist activity.
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Affiliation(s)
- John S. Schardt
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harkamal S. Jhajj
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryen L. O’Meara
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Timon S. Lwo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
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