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ZHANG Z, JIA Z, SONG Y, ZHANG X, WANG C, WANG S, ZHANG P, REN Q, WANG X, MAO J. Optimized new Shengmai powder inhibits myocardial fibrosis in heart failure by regulating the rat sarcoma/rapidly accelerated fibrosarcoma/mitogen-activated protein kinase kinase/extracellular regulated protein kinases signaling pathway. J TRADIT CHIN MED 2024; 44:448-457. [PMID: 38767628 PMCID: PMC11077160 DOI: 10.19852/j.cnki.jtcm.20240402.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/25/2023] [Indexed: 05/22/2024]
Abstract
OBJECTIVE Exploring the effect of Optimized New Shengmai powder (, ONSMP) on myocardial fibrosis in heart failure (HF) based on rat sarcoma (RAS)/rapidly accelerated fibrosarcoma (RAF)/mitogen-activated protein kinase kinase (MEK)/extracellular regulated protein kinases (ERK) signaling pathway. METHODS Randomized 70 Sprague-Dawley rats into sham (n = 10) and operation (n = 60) groups, then established the HF rat by ligating the left anterior descending branch of the coronary artery. We randomly divided the operation group rats into the model, ONSMP [including low (L), medium (M), and high (H) dose], and enalapril groups. After the 4-week drug intervention, echocardiography examines the cardiac function and calculates the ratios of the whole/left heart to the rat's body weight. Finally, we observed the degree of myocardial fibrosis by pathological sections, determined myocardium collagen (COL) I and COL Ⅲ content by enzyme-linked immunosorbent assay, detected the mRNA levels of COL I, COL Ⅲ, α-smooth muscle actin (α-SMA), and c-Fos proto-oncogene (c-Fos) by universal real-time, and detected the protein expression of p-RAS, p-RAF, p-MEK1/2, p-ERK1/2, p-ETS-like-1 transcription factor (p-ELK1), p-c-Fos, α-SMA, COL I, and COL Ⅲ by Western blot. RESULTS ONSMP can effectively improve HF rat's cardiac function, decrease cardiac organ coefficient, COL volume fraction, and COL I/Ⅲ content, down-regulate the mRNA of COL I/Ⅲ, α-SMA and c-Fos, and the protein of p-RAS, p-RAF, p-MEK1/ 2, p-ERK1/2, p-ELK1, c-Fos, COL Ⅰ/Ⅲ, and α-SMA. CONCLUSIONS ONSMP can effectively reduce myocardial fibrosis in HF rats, and the mechanism may be related to the inhibition of the RAS/RAF/MEK/ERK signaling pathway.
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Affiliation(s)
- Zeyu ZHANG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Zhuangzhuang JIA
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Yuwei SONG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Xuan ZHANG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Ci WANG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Shuai WANG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Peipei ZHANG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Qiuan REN
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Xianliang WANG
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Jingyuan MAO
- Department of Cardiovascular, the First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
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Lind DJ, Naidoo KC, Tomalin LE, Rohwer JM, Veal EA, Pillay CS. Quantifying redox transcription factor dynamics as a tool to investigate redox signalling. Free Radic Biol Med 2024; 218:16-25. [PMID: 38574974 DOI: 10.1016/j.freeradbiomed.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
A critical feature of the cellular antioxidant response is the induction of gene expression by redox-sensitive transcription factors. In many cells, activating these transcription factors is a dynamic process involving multiple redox steps, but it is unclear how these dynamics should be measured. Here, we show how the dynamic profile of the Schizosaccharomyces pombe Pap1 transcription factor is quantifiable by three parameters: signal amplitude, signal time and signal duration. In response to increasing hydrogen peroxide concentrations, the Pap1 amplitude decreased while the signal time and duration showed saturable increases. In co-response plots, these parameters showed a complex, non-linear relationship to the mRNA levels of four Pap1-regulated genes. We also demonstrate that hydrogen peroxide and tert-butyl hydroperoxide trigger quantifiably distinct Pap1 activation profiles and transcriptional responses. Based on these findings, we propose that different oxidants and oxidant concentrations modulate the Pap1 dynamic profile, leading to specific transcriptional responses. We further show how the effect of combination and pre-exposure stresses on Pap1 activation dynamics can be quantified using this approach. This method is therefore a valuable addition to the redox signalling toolbox that may illuminate the role of dynamics in determining appropriate responses to oxidative stress.
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Affiliation(s)
- Diane J Lind
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Kelisa C Naidoo
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Lewis E Tomalin
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Johann M Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Elizabeth A Veal
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Ché S Pillay
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa.
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Zhang Z, Yang Z, Wang S, Wang X, Mao J. Targeting MAPK-ERK/JNK pathway: A potential intervention mechanism of myocardial fibrosis in heart failure. Biomed Pharmacother 2024; 173:116413. [PMID: 38461687 DOI: 10.1016/j.biopha.2024.116413] [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: 12/24/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024] Open
Abstract
Myocardial fibrosis is a significant pathological basis of heart failure. Overactivation of the ERK1/2 and JNK1/2 signaling pathways of MAPK family members synergistically promotes the proliferation of myocardial fibroblasts and accelerates the development of myocardial fibrosis. In addition to some small molecule inhibitors and Western drugs, many Chinese medicines can also inhibit the activity of ERK1/2 and JNK1/2, thus slowing down the development of myocardial fibrosis, and are generally safe and effective. However, the specific biological mechanisms of ERK1/2 and JNK1/2 signaling pathways in myocardial fibrosis still need to be fully understood, and there is no systematic review of existing drugs and methods to inhibit them from improving myocardial fibrosis. This study aims to summarize the roles and cross-linking mechanisms of ERK1/2 and JNK1/2 signaling pathways in myocardial fibrosis and to systematically sort out the small-molecule inhibitors, Western drugs, traditional Chinese medicines, and non-pharmacological therapies that inhibit ERK1/2 and JNK1/2 to alleviate myocardial fibrosis. In the future, we hope to conduct more in-depth research from the perspective of precision-targeted therapy, using this as a basis for developing new drugs that provide new perspectives on the prevention and treatment of heart failure.
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Affiliation(s)
- Zeyu Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China; Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Zhihua Yang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China; Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Shuai Wang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China.
| | - Xianliang Wang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China.
| | - Jingyuan Mao
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China.
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Schmidt HN, Gaetjens TK, Leopin EE, Abel SM. Compartmental exchange regulates steady states and stochastic switching of a phosphorylation network. Biophys J 2024; 123:598-609. [PMID: 38317416 PMCID: PMC10938077 DOI: 10.1016/j.bpj.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
The phosphoregulation of proteins with multiple phosphorylation sites is governed by biochemical reaction networks that can exhibit multistable behavior. However, the behavior of such networks is typically studied in a single reaction volume, while cells are spatially organized into compartments that can exchange proteins. In this work, we use stochastic simulations to study the impact of compartmentalization on a two-site phosphorylation network. We characterize steady states and fluctuation-driven transitions between them as a function of the rate of protein exchange between two compartments. Surprisingly, the average time spent in a state before stochastically switching to another depends nonmonotonically on the protein exchange rate, with the most frequent switching occurring at intermediate exchange rates. At sufficiently small exchange rates, the state of the system and mean switching time are controlled largely by fluctuations in the balance of enzymes in each compartment. This leads to negatively correlated states in the compartments. For large exchange rates, the two compartments behave as a single effective compartment. However, when the compartmental volumes are unequal, the behavior differs from a single compartment with the same total volume. These results demonstrate that exchange of proteins between distinct compartments can regulate the emergent behavior of a common signaling motif.
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Affiliation(s)
- Hannah N Schmidt
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Thomas K Gaetjens
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Emily E Leopin
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee.
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5
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Zhang Z, Song Y, Zhang X, Wang S, Jia Z, Wang L, Wang C, Wang X, Mao J. Optimized new Shengmai powder ameliorates myocardial fibrosis in rats with heart failure by inhibition of the MAPK signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117210. [PMID: 37739104 DOI: 10.1016/j.jep.2023.117210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Optimized New Shengmai Powder (ONSMP) is a traditional Chinese medicine (TCM) formula for heart failure treatment. MAPK signaling pathway is the key driver of myocardial fibrosis in heart failure. However, the mechanism of ONSMP on myocardial fibrosis and MAPK signaling pathway remains unclear. AIM OF THE STUDY To evaluate the effect of ONSMP against myocardial fibrosis in heart failure and the underlying mechanisms. MATERIALS AND METHODS Firstly, UHPLC-Q-Exactive-MS/MS was used to identify the active components in ONSMP. Secondly, a rat model of heart failure was established by ligating the left anterior descending branch of the coronary artery. After four weeks of intragastric administration of ONSMP, we used various classic tests, including echocardiography, exhaustive swimming, cardiopulmonary coefficient, heart failure markers, and cardiac pathological section, to assess the prescription's anti-myocardial fibrosis in heart failure properties. AGEs, Ang Ⅱ, VEGF, CTGF, and TGFβ levels in rat serum were quantified using ELISA. The positive expression of p-ERK1/2 and p-JNK1/2 of rat myocardium was determined immunohistochemical. The protein and mRNA levels of genes involved in the MAPK signaling pathway and myocardial fibrosis were measured using western blotting or real-time PCR. RESULTS The main components of ONSMP that regulate the MAPK signaling pathway are isorhamnetin, kaempferol, quercetin, and tanshinone ⅡA. ONSMP ameliorated cardiac function and exercise tolerance and reduced cardiopulmonary coefficient, heart failure marker levels, and myocardial fibrosis in the heart failure rats. In addition, ONSMP diminished the serum MAPK pathway activator levels, positive expression level of p-ERK1/2 and p-JNK1/2, protein and mRNA levels of components of the MAPK signaling pathway in the myocardial tissue of heart failure rat, indicating that it inhibits MAPK signaling pathway. CONCLUSIONS ONSMP delayed heart failure by inhibiting myocardial fibrosis via the MAPK signaling pathway.
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Affiliation(s)
- Zeyu Zhang
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Yuwei Song
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Xuan Zhang
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Shuai Wang
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Zhuangzhuang Jia
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Lin Wang
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Ci Wang
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Xianliang Wang
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
| | - Jingyuan Mao
- Department of First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, PR China.
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Zhang JZ, Nguyen WH, Greenwood N, Rose JC, Ong SE, Maly DJ, Baker D. Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nat Biotechnol 2024:10.1038/s41587-023-02107-w. [PMID: 38273065 DOI: 10.1038/s41587-023-02107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
The utility of genetically encoded biosensors for sensing the activity of signaling proteins has been hampered by a lack of strategies for matching sensor sensitivity to the physiological concentration range of the target. Here we used computational protein design to generate intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity (Ras-LOCKR-S)) and proximity labelers of the Ras signaling environment (LOCKR-based, Ras activity-dependent Proximity Labeler (Ras-LOCKR-PL)). These tools allow the detection of endogenous Ras activity and labeling of the surrounding environment at subcellular resolution. Using these sensors in human cancer cell lines, we identified Ras-interacting proteins in oncogenic EML4-Alk granules and found that Src-Associated in Mitosis 68-kDa (SAM68) protein specifically enhances Ras activity in the granules. The ability to subcellularly localize endogenous Ras activity should deepen our understanding of Ras function in health and disease and may suggest potential therapeutic strategies.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - William H Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Greenwood
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Rose
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Fan J, Zhu J, Zhu H, Zhang Y, Xu H. Potential therapeutic target for polysaccharide inhibition of colon cancer progression. Front Med (Lausanne) 2024; 10:1325491. [PMID: 38264044 PMCID: PMC10804854 DOI: 10.3389/fmed.2023.1325491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
In recent years, colon cancer has become one of the most common malignant tumors worldwide, posing a great threat to human health. Studies have shown that natural polysaccharides have rich biological activities and medicinal value, such as anti-inflammatory, anti-cancer, anti-oxidation, and immune-enhancing effects, especially with potential anti-colon cancer mechanisms. Natural polysaccharides can not only protect and enhance the homeostasis of the intestinal environment but also exert a direct inhibition effect on cancer cells, making it a promising strategy for treating colon cancer. Preliminary clinical experiments have demonstrated that oral administration of low and high doses of citrus pectin polysaccharides can reduce tumor volume in mice by 38% (p < 0.02) and 70% (p < 0.001), respectively. These results are encouraging. However, there are relatively few clinical studies on the effectiveness of polysaccharide therapy for colon cancer, and ensuring the effective bioavailability of polysaccharides in the body remains a challenge. In this article, we elucidate the impact of the physicochemical factors of polysaccharides on their anticancer effects and then reveal the anti-tumor effects and mechanisms of natural polysaccharides on colon cancer. Finally, we emphasize the challenges of using polysaccharides in the treatment of colon cancer and discuss future applications.
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Affiliation(s)
- Jiawei Fan
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Jianshu Zhu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - He Zhu
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Yinmeng Zhang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Hong Xu
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
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Wither MJ, White WL, Pendyala S, Leanza PJ, Fowler DM, Kueh HY. Antigen perception in T cells by long-term Erk and NFAT signaling dynamics. Proc Natl Acad Sci U S A 2023; 120:e2308366120. [PMID: 38113261 PMCID: PMC10756264 DOI: 10.1073/pnas.2308366120] [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: 05/29/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023] Open
Abstract
Immune system threat detection hinges on T cells' ability to perceive varying peptide-major histocompatibility complex (pMHC) antigens. As the Erk and NFAT pathways link T cell receptor engagement to gene regulation, their signaling dynamics may convey information about pMHC inputs. To test this idea, we developed a dual reporter mouse strain and a quantitative imaging assay that, together, enable simultaneous monitoring of Erk and NFAT dynamics in live T cells over day-long timescales as they respond to varying pMHC inputs. Both pathways initially activate uniformly across various pMHC inputs but diverge only over longer (9+ h) timescales, enabling independent encoding of pMHC affinity and dose. These late signaling dynamics are decoded via multiple temporal and combinatorial mechanisms to generate pMHC-specific transcriptional responses. Our findings underscore the importance of long timescale signaling dynamics in antigen perception and establish a framework for understanding T cell responses under diverse contexts.
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Affiliation(s)
- Matthew J. Wither
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - William L. White
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - Sriram Pendyala
- University of Washington, Department of Genome Sciences, Seattle, WA98195
| | - Paul J. Leanza
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - Douglas M. Fowler
- University of Washington, Department of Genome Sciences, Seattle, WA98195
| | - Hao Yuan Kueh
- University of Washington, Department of Bioengineering, Seattle, WA98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98109
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 1: mechanisms and models. Biochem J 2023; 480:1887-1907. [PMID: 38038974 PMCID: PMC10754288 DOI: 10.1042/bcj20230276] [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: 07/09/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Extracellular signal-regulated kinase (ERK) has long been studied as a key driver of both essential cellular processes and disease. A persistent question has been how this single pathway is able to direct multiple cell behaviors, including growth, proliferation, and death. Modern biosensor studies have revealed that the temporal pattern of ERK activity is highly variable and heterogeneous, and critically, that these dynamic differences modulate cell fate. This two-part review discusses the current understanding of dynamic activity in the ERK pathway, how it regulates cellular decisions, and how these cell fates lead to tissue regulation and pathology. In part 1, we cover the optogenetic and live-cell imaging technologies that first revealed the dynamic nature of ERK, as well as current challenges in biosensor data analysis. We also discuss advances in mathematical models for the mechanisms of ERK dynamics, including receptor-level regulation, negative feedback, cooperativity, and paracrine signaling. While hurdles still remain, it is clear that higher temporal and spatial resolution provide mechanistic insights into pathway circuitry. Exciting new algorithms and advanced computational tools enable quantitative measurements of single-cell ERK activation, which in turn inform better models of pathway behavior. However, the fact that current models still cannot fully recapitulate the diversity of ERK responses calls for a deeper understanding of network structure and signal transduction in general.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
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Sokol DK, Lahiri DK. APPlications of amyloid-β precursor protein metabolites in macrocephaly and autism spectrum disorder. Front Mol Neurosci 2023; 16:1201744. [PMID: 37799731 PMCID: PMC10548831 DOI: 10.3389/fnmol.2023.1201744] [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: 04/07/2023] [Accepted: 07/17/2023] [Indexed: 10/07/2023] Open
Abstract
Metabolites of the Amyloid-β precursor protein (APP) proteolysis may underlie brain overgrowth in Autism Spectrum Disorder (ASD). We have found elevated APP metabolites (total APP, secreted (s) APPα, and α-secretase adamalysins in the plasma and brain tissue of children with ASD). In this review, we highlight several lines of evidence supporting APP metabolites' potential contribution to macrocephaly in ASD. First, APP appears early in corticogenesis, placing APP in a prime position to accelerate growth in neurons and glia. APP metabolites are upregulated in neuroinflammation, another potential contributor to excessive brain growth in ASD. APP metabolites appear to directly affect translational signaling pathways, which have been linked to single gene forms of syndromic ASD (Fragile X Syndrome, PTEN, Tuberous Sclerosis Complex). Finally, APP metabolites, and microRNA, which regulates APP expression, may contribute to ASD brain overgrowth, particularly increased white matter, through ERK receptor activation on the PI3K/Akt/mTOR/Rho GTPase pathway, favoring myelination.
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Affiliation(s)
- Deborah K. Sokol
- Department of Neurology, Section of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Debomoy K. Lahiri
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Indiana Alzheimer Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, United States
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Khamoshina MB, Artemenko YS, Bayramova AA, Ryabova VA, Orazov MR. Polycystic ovary syndrome and obesity: a modern paradigm. RUDN JOURNAL OF MEDICINE 2022. [DOI: 10.22363/2313-0245-2022-26-4-382-395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Polycystic ovary syndrome is a heterogeneous endocrine disease that affects women of childbearing age. The pathogenesis of polycystic ovary syndrome has not been fully studied to date, its paradigm considers the genetic determinism of the manifestation of hormonal and metabolic disorders, which are considered to be criteria for the verification of the disease (hyperandrogenism, oligo/anovulation and/or polycystic ovarian transformation during ultrasound examination (ultrasound). This review discusses the main ways of interaction between hyperandrogenism, insulin resistance and obesity and their role in the pathogenesis of polycystic ovary syndrome, as well as possible methods of treatment for this category of patients. The review analyzes the role of hyperandrogenism and insulin resistance in the implementation of the genetic scenario of polycystic ovary syndrome and finds out the reasons why women with polycystic ovary syndrome often demonstrate the presence of a «metabolic trio» - hyperinsulinemia, insulin resistance and type 2 diabetes mellitus. It is noted that obesity is not included in the criteria for the diagnosis of polycystic ovary syndrome, but epidemiological data confirm the existence of a relationship between these diseases. Obesity, especially visceral, which is often found in women with polycystic ovary syndrome, enhances and worsens metabolic and reproductive outcomes with polycystic ovary syndrome, as well as increases insulin resistance and compensatory hyperinsulinemia, which, in turn, stimulates adipogenesis and suppresses lipolysis. Obesity increases the sensitivity of tech cells to luteinizing hormone stimulation and enhances functional hyperandrogenism of the ovaries, increasing the production of androgens by the ovaries. Excess body weight is associated with a large number of inflammatory adipokines, which, in turn, contribute to the growth of insulin resistance and adipogenesis. Obesity and insulin resistance exacerbate the symptoms of hyperandrogenism, forming a vicious circle that contributes to the development of polycystic ovary syndrome. These data allow us to conclude that bariatric surgery can become an alternative to drugs (metformin, thiazolidinedione analogs of glucagon-like peptide-1), which has shown positive results in the treatment of patients with polycystic ovary syndrome and obesity.
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12
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Microscopic image-based classification of adipocyte differentiation by machine learning. Histochem Cell Biol 2022; 159:313-327. [PMID: 36504003 DOI: 10.1007/s00418-022-02168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Adipocyte differentiation is a sequential process involving increased expression of peroxisome proliferator-activated receptor gamma (PPARγ), adipocyte-specific gene expression, and accumulation of lipid droplets in the cytoplasm. Expression of the transcription factors involved is usually detected using canonical biochemical or biomolecular procedures such as Western blotting or qPCR of pooled cell lysates. While this provides a useful average index for adipogenesis for some populations, the precise stage of adipogenesis cannot be distinguished at the single-cell level, because the heterogenous nature of differentiation among cells limits the utility of averaged data. We have created a classifier to sort cells, and used it to determine the stage of adipocyte differentiation at the single-cell level. We used a machine learning method with microscopic images of cell stained for PPARγ and lipid droplets as input data. Our results show that the classifier can successfully determine the precise stage of differentiation. Stage classification and subsequent model fitting using the sequential reaction model revealed the action of pioglitazone and rosiglitazone to be promotion of transition from the stage of increased PPARγ expression to the next stage. This indicates that these drugs are PPARγ agonists, and that our classifier and model can accurately estimate drug action points and would be suitable for evaluating the stage/state of individual cells during differentiation or disease progression. The incorporation of both biochemical and morphological information derived from immunofluorescence image of cells and so overcomes limitations of current models.
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13
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Harnessing conserved signaling and metabolic pathways to enhance the maturation of functional engineered tissues. NPJ Regen Med 2022; 7:44. [PMID: 36057642 PMCID: PMC9440900 DOI: 10.1038/s41536-022-00246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
The development of induced-pluripotent stem cell (iPSC)-derived cell types offers promise for basic science, drug testing, disease modeling, personalized medicine, and translatable cell therapies across many tissue types. However, in practice many iPSC-derived cells have presented as immature in physiological function, and despite efforts to recapitulate adult maturity, most have yet to meet the necessary benchmarks for the intended tissues. Here, we summarize the available state of knowledge surrounding the physiological mechanisms underlying cell maturation in several key tissues. Common signaling consolidators, as well as potential synergies between critical signaling pathways are explored. Finally, current practices in physiologically relevant tissue engineering and experimental design are critically examined, with the goal of integrating greater decision paradigms and frameworks towards achieving efficient maturation strategies, which in turn may produce higher-valued iPSC-derived tissues.
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14
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Shahidi N, Pan M, Tran K, Crampin EJ, Nickerson DP. A semantics, energy-based approach to automate biomodel composition. PLoS One 2022; 17:e0269497. [PMID: 35657966 PMCID: PMC9165793 DOI: 10.1371/journal.pone.0269497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/20/2022] [Indexed: 11/19/2022] Open
Abstract
Hierarchical modelling is essential to achieving complex, large-scale models. However, not all modelling schemes support hierarchical composition, and correctly mapping points of connection between models requires comprehensive knowledge of each model's components and assumptions. To address these challenges in integrating biosimulation models, we propose an approach to automatically and confidently compose biosimulation models. The approach uses bond graphs to combine aspects of physical and thermodynamics-based modelling with biological semantics. We improved on existing approaches by using semantic annotations to automate the recognition of common components. The approach is illustrated by coupling a model of the Ras-MAPK cascade to a model of the upstream activation of EGFR. Through this methodology, we aim to assist researchers and modellers in readily having access to more comprehensive biological systems models.
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Affiliation(s)
- Niloofar Shahidi
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Michael Pan
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Victoria, Australia
| | - Kenneth Tran
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Edmund J. Crampin
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Victoria, Australia
- School of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - David P. Nickerson
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
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15
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Dessauges C, Mikelson J, Dobrzyński M, Jacques MA, Frismantiene A, Gagliardi PA, Khammash M, Pertz O. Optogenetic actuator - ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics. Mol Syst Biol 2022; 18:e10670. [PMID: 35694820 PMCID: PMC9189677 DOI: 10.15252/msb.202110670] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/12/2022] Open
Abstract
Combining single-cell measurements of ERK activity dynamics with perturbations provides insights into the MAPK network topology. We built circuits consisting of an optogenetic actuator to activate MAPK signaling and an ERK biosensor to measure single-cell ERK dynamics. This allowed us to conduct RNAi screens to investigate the role of 50 MAPK proteins in ERK dynamics. We found that the MAPK network is robust against most node perturbations. We observed that the ERK-RAF and the ERK-RSK2-SOS negative feedback operate simultaneously to regulate ERK dynamics. Bypassing the RSK2-mediated feedback, either by direct optogenetic activation of RAS, or by RSK2 perturbation, sensitized ERK dynamics to further perturbations. Similarly, targeting this feedback in a human ErbB2-dependent oncogenic signaling model increased the efficiency of a MEK inhibitor. The RSK2-mediated feedback is thus important for the ability of the MAPK network to produce consistent ERK outputs, and its perturbation can enhance the efficiency of MAPK inhibitors.
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Affiliation(s)
| | - Jan Mikelson
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | | | | | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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16
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A gene cluster with positive and negative elements controls bistability and hysteresis of the Crippled versus Normal growth in the fungus Podospora anserina. Fungal Genet Biol 2022; 161:103711. [PMID: 35597448 DOI: 10.1016/j.fgb.2022.103711] [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: 03/01/2022] [Revised: 05/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022]
Abstract
The Crippled Growth (CG) cell degeneration of the model ascomycete Podospora anserina (strain S) is controlled by a prion-like element and has been linked to the self-activation of the PaMpk1 MAP kinase cascade. Here, we report on the identification of the "86-11" locus containing twelve genes, ten of which are involved either in setting up the self-activation loop of CG or in inhibiting this loop, as demonstrated by targeted gene deletion. Interestingly, deletion of the whole locus results only in the elimination of CG and in no detectable additional physiological defect. Sequence comparison shows that these ten genes belong to four different families, each one endowed with a specific activity: two encode factors activating the loop, a third one encodes a factor crucial for inhibition of the loop and the fourth one participates in inhibiting the loop in a pathway parallel to the one controlled by the previously described PDC1 gene. Intriguingly, a very distant homologue of this "86-11" locus is present at the syntenic position in Podospora comata (strain T) that do not present Crippled Growth. Introgression of the P. comata strain T locus in P. anserina strain S and the P. anserina strain S in P. comata strain T showed that both drive CG in the P. anserina strain S genetic background, but not in the genetic background of strain P. comata T, indicating that genetic determinants outside the twelve-gene locus are responsible for lack of CG in P. comata strain T. Our data question the role of this twelve-gene locus in the physiology of P. anserina.
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17
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Tewari D, Priya A, Bishayee A, Bishayee A. Targeting transforming growth factor-β signalling for cancer prevention and intervention: Recent advances in developing small molecules of natural origin. Clin Transl Med 2022; 12:e795. [PMID: 35384373 PMCID: PMC8982327 DOI: 10.1002/ctm2.795] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/19/2022] Open
Abstract
Background Cancer is the world's second leading cause of death, but a significant advancement in cancer treatment has been achieved within the last few decades. However, major adverse effects and drug resistance associated with standard chemotherapy have led towards targeted treatment options. Objectives Transforming growth factor‐β (TGF‐β) signaling plays a key role in cell proliferation, differentiation, morphogenesis, regeneration, and tissue homeostasis. The prime objective of this review is to decipher the role of TGF‐β in oncogenesis and to evaluate the potential of various natural and synthetic agents to target this dysregulated pathway to confer cancer preventive and anticancer therapeutic effects. Methods Various authentic and scholarly databases were explored to search and obtain primary literature for this study. The Preferred Reporting Items for Systematic Reviews and Meta‐Analysis (PRISMA) criteria was followed for the review. Results Here we provide a comprehensive and critical review of recent advances on our understanding of the effect of various bioactive natural molecules on the TGF‐β signaling pathway to evaluate their full potential for cancer prevention and therapy. Conclusion Based on emerging evidence as presented in this work, TGF‐β‐targeting bioactive compounds from natural sources can serve as potential therapeutic agents for prevention and treatment of various human malignancies.
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Affiliation(s)
- Devesh Tewari
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anu Priya
- Department of Pharmacology, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | | | - Anupam Bishayee
- College of Osteopathic Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, Florida, USA
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18
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Wang C, Zhang Y. Endoplasmic Reticulum Stress: A New Research Direction for Polycystic Ovary Syndrome? DNA Cell Biol 2022; 41:356-367. [PMID: 35353637 DOI: 10.1089/dna.2021.1050] [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] [Indexed: 11/13/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common gynecological endocrine disorders, with sporadic ovulation, excessive androgens, and polycystic ovarian changes as the main clinical manifestations. Due to the high heterogeneity of its clinical manifestations, the discussion on its pathogenesis has not been unified. Current research has found that genetic factors, hyperandrogenism, chronic inflammation and oxidative stress, insulin resistance, and obesity are strongly associated with PCOS. Recently, when studying the specific mechanisms of the abovementioned factors in PCOS, the biological response process of endoplasmic reticulum stress (ERS) has gradually come to researchers' attention, and several studies have confirmed the involvement of ERS in the pathogenesis of PCOS and the improvement of a series of pathological manifestations of PCOS after the application of ERS inhibitors, which may be a new entry point for the treatment of PCOS. In this article, we review the relationship between ERS and various pathogenic factors of PCOS.
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Affiliation(s)
- Chengzhe Wang
- Department of Gynecology of traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan City, China
| | - Yingjie Zhang
- Department of Gynecology of traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan City, China
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19
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Jiménez A, Lu D, Kalocsay M, Berberich MJ, Balbi P, Jambhekar A, Lahav G. Time‐series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations. Mol Syst Biol 2022; 18:e10588. [PMID: 35285572 PMCID: PMC8919251 DOI: 10.15252/msb.202110588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/21/2022] Open
Affiliation(s)
- Alba Jiménez
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Dan Lu
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Marian Kalocsay
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Laboratory of Systems Pharmacology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Matthew J Berberich
- Laboratory of Systems Pharmacology Blavatnik Institute at Harvard Medical School Boston MA USA
- Center for Protein Degradation Dana‐Farber Cancer Institute Boston MA USA
| | - Petra Balbi
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
| | - Ashwini Jambhekar
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Ludwig Center at Harvard Medical School Boston MA USA
| | - Galit Lahav
- Department of Systems Biology Blavatnik Institute at Harvard Medical School Boston MA USA
- Ludwig Center at Harvard Medical School Boston MA USA
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20
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Lengyel CG, Hussain S, Seeber A, Jamil Nidhamalddin S, Trapani D, Habeeb BS, Elfaham E, Mazher SA, Seid F, Khan SZ, El Bairi K, Odhiambo A, Altuna SC, Petrillo A. FGFR Pathway Inhibition in Gastric Cancer: The Golden Era of an Old Target? Life (Basel) 2022; 12:81. [PMID: 35054474 PMCID: PMC8778800 DOI: 10.3390/life12010081] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-associated death worldwide. The majority of patients are diagnosed at an advanced/metastatic stage of disease due to a lack of specific symptoms and lack of screening programs, especially in Western countries. Thus, despite the improvement in GC therapeutic opportunities, the survival is disappointing, and the definition of the optimal treatment is still an unmet need. Novel diagnostic techniques were developed in clinical trials in order to characterize the genetic profile of GCs and new potential molecular pathways, such as the Fibroblast Growth Factor Receptor (FGFR) pathway, were identified in order to improve patient's survival by using target therapies. The aim of this review is to summarize the role and the impact of FGFR signaling in GC and to provide an overview regarding the potential effectiveness of anti-FGFR agents in GC treatment in the context of precision medicine.
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Affiliation(s)
- Csongor G. Lengyel
- Head and Neck Surgery, National Institute of Oncology, 1122 Budapest, Hungary;
| | - Sadaqat Hussain
- Oncology Department, University Hospital of Leicester, Leicester LE1 5WW, UK;
| | - Andreas Seeber
- Comprehensive Cancer Center Innsbruck, Department of Hematology and Oncology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | | | | | - Baker S. Habeeb
- Medical Oncology, Shaqlawa Teaching Hospital, Erbil 44001, Iraq;
| | - Essam Elfaham
- Department of Hematoncology, Kuwait Cancer Control Center (KCCC), Kuwait City 20001, Kuwait;
| | - Syed Ayub Mazher
- Division of Internal Medicine, UT Southwestern Clements University Hospital, Dallas, TX 75390, USA;
| | - Fahmi Seid
- Department of Oncology, College of Medicine and Health Sciences, Hawassa University, Hawassa 1560, Ethiopia;
| | - Shah Z. Khan
- Department of Clinical Oncology, BINOR Cancer Hospital, Bannu 28000, Pakistan;
| | | | - Andrew Odhiambo
- Unit of Medical Oncology, Department of Clinical Medicine, University of Nairobi, Nairobi 00202, Kenya;
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21
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Chen Y, Zhang Q, Ma J, Yu Y. Mapping research trends of insulin resistance in polycystic ovary syndrome from 2017 to 2021: A bibliometric analysis. Front Endocrinol (Lausanne) 2022; 13:963213. [PMID: 36589816 PMCID: PMC9797656 DOI: 10.3389/fendo.2022.963213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION To map publication trends and explore research hotspots of insulin resistance (IR) in polycystic ovary syndrome (PCOS) study. METHODS With the theme of "Polycystic ovary syndrome" AND "Insulin Resistance", the key data set of Science Core Literature Collection (WoSCC) web from 2017 to 2021 was extracted and bibliometric analysis was performed. Through VOSviewer v1.6.10 software, the research trend in this field is analyzed visually. RESULTS 2080 literatures about IR in PCOS from 2017 to 2021 were downloaded. The following basic information was collected for each article: country, author, institution, journal, references. The key words are divided into six categories: (1) The interaction between insulin resistance and chronic inflammation; (2) The relationship between insulin resistance and metabolic syndrome and nonalcoholic fatty liver disease; (3) The interaction between insulin resistance and hyperandrogenemia; (4) The relationship between insulin resistance and dyslipidemia; (5) Metformin may regulate insulin resistance in the treatment of PCOS; (6) The study of serum biomarkers in PCOS patients with insulin resistance. DISCUSSION The six key words extracted can provide an in-depth perspective for the study of IR in PCOS, and provide valuable information to help researchers identify potential research directions, collaborators and cooperative institutions.
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22
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Hager R, Müller U, Ollinger N, Weghuber J, Lanzerstorfer P. Subcellular Dynamic Immunopatterning of Cytosolic Protein Complexes on Microstructured Polymer Substrates. ACS Sens 2021; 6:4076-4088. [PMID: 34652152 PMCID: PMC8630788 DOI: 10.1021/acssensors.1c01574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Analysis of protein–protein
interactions in living cells
by protein micropatterning is currently limited to the spatial arrangement
of transmembrane proteins and their corresponding downstream molecules.
Here, we present a robust and straightforward method for dynamic immunopatterning
of cytosolic protein complexes by use of an artificial transmembrane
bait construct in combination with microstructured antibody arrays
on cyclic olefin polymer substrates. As a proof, the method was used
to characterize Grb2-mediated signaling pathways downstream of the
epidermal growth factor receptor (EGFR). Ternary protein complexes
(Shc1:Grb2:SOS1 and Grb2:Gab1:PI3K) were identified, and we found
that EGFR downstream signaling is based on constitutively bound (Grb2:SOS1
and Grb2:Gab1) as well as on agonist-dependent protein associations
with transient interaction properties (Grb2:Shc1 and Grb2:PI3K). Spatiotemporal
analysis further revealed significant differences in stability and
exchange kinetics of protein interactions. Furthermore, we could show
that this approach is well suited to study the efficacy and specificity
of SH2 and SH3 protein domain inhibitors in a live cell context. Altogether,
this method represents a significant enhancement of quantitative subcellular
micropatterning approaches as an alternative to standard biochemical
analyses.
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Affiliation(s)
- Roland Hager
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
| | - Ulrike Müller
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
| | - Nicole Ollinger
- Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Head Office: FFoQSI GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, Head Office: FFoQSI GmbH, Technopark 1C, 3430 Tulln, Austria
| | - Peter Lanzerstorfer
- University of Applied Sciences Upper Austria, School of Engineering, 4600 Wels, Austria
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23
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ERK: A Double-Edged Sword in Cancer. ERK-Dependent Apoptosis as a Potential Therapeutic Strategy for Cancer. Cells 2021; 10:cells10102509. [PMID: 34685488 PMCID: PMC8533760 DOI: 10.3390/cells10102509] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The RAF/MEK/ERK signaling pathway regulates diverse cellular processes as exemplified by cell proliferation, differentiation, motility, and survival. Activation of ERK1/2 generally promotes cell proliferation, and its deregulated activity is a hallmark of many cancers. Therefore, components and regulators of the ERK pathway are considered potential therapeutic targets for cancer, and inhibitors of this pathway, including some MEK and BRAF inhibitors, are already being used in the clinic. Notably, ERK1/2 kinases also have pro-apoptotic functions under certain conditions and enhanced ERK1/2 signaling can cause tumor cell death. Although the repertoire of the compounds which mediate ERK activation and apoptosis is expanding, and various anti-cancer compounds induce ERK activation while exerting their anti-proliferative effects, the mechanisms underlying ERK1/2-mediated cell death are still vague. Recent studies highlight the importance of dual-specificity phosphatases (DUSPs) in determining the pro- versus anti-apoptotic function of ERK in cancer. In this review, we will summarize the recent major findings in understanding the role of ERK in apoptosis, focusing on the major compounds mediating ERK-dependent apoptosis. Studies that further define the molecular targets of these compounds relevant to cell death will be essential to harnessing these compounds for developing effective cancer treatments.
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24
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Gómez-Gálvez P, Anbari S, Escudero LM, Buceta J. Mechanics and self-organization in tissue development. Semin Cell Dev Biol 2021; 120:147-159. [PMID: 34417092 DOI: 10.1016/j.semcdb.2021.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Self-organization is an all-important feature of living systems that provides the means to achieve specialization and functionality at distinct spatio-temporal scales. Herein, we review this concept by addressing the packing organization of cells, the sorting/compartmentalization phenomenon of cell populations, and the propagation of organizing cues at the tissue level through traveling waves. We elaborate on how different theoretical models and tools from Topology, Physics, and Dynamical Systems have improved the understanding of self-organization by shedding light on the role played by mechanics as a driver of morphogenesis. Altogether, by providing a historical perspective, we show how ideas and hypotheses in the field have been revisited, developed, and/or rejected and what are the open questions that need to be tackled by future research.
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Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Samira Anbari
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna, 46980 Valencia, Spain.
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25
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Leonce C, Saintigny P, Ortiz-Cuaran S. Cell-intrinsic mechanisms of drug tolerance to systemic therapies in cancer. Mol Cancer Res 2021; 20:11-29. [PMID: 34389691 DOI: 10.1158/1541-7786.mcr-21-0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/11/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
In cancer patients with metastatic disease, the rate of complete tumor response to systemic therapies is low, and residual lesions persist in the majority of patients due to early molecular adaptation in cancer cells. A growing body of evidence suggests that a subpopulation of drug-tolerant « persister » cells - a reversible phenotype characterized by reduced drug sensitivity and decreased cell proliferation - maintains residual disease and may serve as a reservoir for resistant phenotypes. The survival of these residual tumor cells can be caused by reactivation of specific signaling pathways, phenotypic plasticity (i.e., transdifferentiation), epigenetic or metabolic reprogramming, downregulation of apoptosis as well as transcriptional remodeling. In this review, we discuss the molecular mechanisms that enable adaptive survival in drug-tolerant cells. We describe the main characteristics and dynamic nature of this persistent state, and highlight the current therapeutic strategies that may be used to interfere with the establishment of drug-tolerant cells, as an alternative to improve objective response to systemic therapies and delay the emergence of resistance to improve long-term survival.
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Affiliation(s)
- Camille Leonce
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon
| | - Pierre Saintigny
- Department of Medical Oncology, Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon. Department of Medical Oncology, Centre Léon Bérard
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon
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26
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Watson J, Schwartz JM, Francavilla C. Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites. J Proteome Res 2021; 20:3532-3548. [PMID: 34164982 PMCID: PMC8256419 DOI: 10.1021/acs.jproteome.1c00150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Indexed: 01/23/2023]
Abstract
Mass spectrometry-based quantitative phosphoproteomics has become an essential approach in the study of cellular processes such as signaling. Commonly used methods to analyze phosphoproteomics datasets depend on generic, gene-centric annotations such as Gene Ontology terms, which do not account for the function of a protein in a particular phosphorylation state. Analysis of phosphoproteomics data is hampered by a lack of phosphorylated site-specific annotations. We propose a method that combines shotgun phosphoproteomics data, protein-protein interactions, and functional annotations into a heterogeneous multilayer network. Phosphorylation sites are associated to potential functions using a random walk on the heterogeneous network (RWHN) algorithm. We validated our approach against a model of the MAPK/ERK pathway and functional annotations from PhosphoSitePlus and were able to associate differentially regulated sites on the same proteins to their previously described specific functions. We further tested the algorithm on three previously published datasets and were able to reproduce their experimentally validated conclusions and to associate phosphorylation sites with known functions based on their regulatory patterns. Our approach provides a refinement of commonly used analysis methods and accurately predicts context-specific functions for sites with similar phosphorylation profiles.
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Affiliation(s)
- Joanne Watson
- Division
of Evolution & Genomic Sciences, School of Biological Sciences,
Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, U.K.
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, U.K.
| | - Jean-Marc Schwartz
- Division
of Evolution & Genomic Sciences, School of Biological Sciences,
Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, U.K.
| | - Chiara Francavilla
- Division
of Molecular and Cellular Function, School of Biological Sciences,
Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, U.K.
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Halder S, Ghosh S, Chattopadhyay J, Chatterjee S. Bistability in cell signalling and its significance in identifying potential drug targets. Bioinformatics 2021; 37:4156-4163. [PMID: 34021761 DOI: 10.1093/bioinformatics/btab395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/09/2021] [Accepted: 05/20/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Bistability is one of the salient dynamical features in various all-or-none kinds of decision-making processes. The presence of bistability in a cell signalling network plays a key role in input-output (I/O) relation. Our study is aiming to capture and emphasise the role of motif structure influencing the I/O relation between two nodes in the context of bistability. Here, a model-based analysis is made to investigate the critical conditions responsible for the emergence of different bistable protein-protein interaction (PPI) motifs and their possible applications to find the potential drug targets. RESULTS The global sensitivity analysis is used to identify sensitive parameters and their role in maintaining the bistability. Additionally, the bistable switching through hysteresis is explored to develop an understanding of the underlying mechanisms involved in the cell signalling processes, when significant motifs exhibiting bistability have emerged. Further, we elaborate the application of the results by the implication of the emerged PPI motifs to identify potential drug-targets in three cancer networks, which is validated with existing databases. The influence of stochastic perturbations that could hinder desired functionality of any signalling networks is also described here. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Suvankar Halder
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd milestone, Faridabad-Gurgaon Expressway, Faridabad-121001, India
| | - Sumana Ghosh
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd milestone, Faridabad-Gurgaon Expressway, Faridabad-121001, India
| | - Joydev Chattopadhyay
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata-700108, India
| | - Samrat Chatterjee
- Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd milestone, Faridabad-Gurgaon Expressway, Faridabad-121001, India
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Jayakumar P, Martínez-Moreno CG, Lorenson MY, Walker AM, Morales T. Prolactin Attenuates Neuroinflammation in LPS-Activated SIM-A9 Microglial Cells by Inhibiting NF-κB Pathways Via ERK1/2. Cell Mol Neurobiol 2021; 42:2171-2186. [PMID: 33821330 DOI: 10.1007/s10571-021-01087-2] [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: 07/16/2020] [Accepted: 03/27/2021] [Indexed: 10/21/2022]
Abstract
Prolactin (PRL) is a pleiotropic hormone with multiple functions in several tissues and organs, including the brain. PRL decreases lesion-induced microgliosis and modifies gene expression related to microglial functions in the hippocampus, thereby providing a possible mechanism through which it might participate in neuroimmune modulatory responses and prevent neuronal cell damage. However, the direct contribution of microglial cells to PRL-mediated neuroprotection is still unclear and no studies have yet documented whether PRL can directly activate cellular pathways in microglial cells. The aim of this study is to elucidate in vitro actions of PRL on the immortalized SIM-A9 microglia cell line in basal and LPS-stimulated conditions. PRL alone induced a time-dependent extracellular signal-regulated kinase 1/2 (ERK1/2) activation. Pretreatment with PRL attenuated LPS (200 ng/ml) stimulated pro-inflammatory markers: nitric oxide (NO) levels, inducible nitric oxide synthase (iNOS), interleukins (IL)-6, -1β and tumor necrosis factor (TNF-α) expression at 20 nM dosage. PRL suppressed LPS-induced nuclear factor (NF)-κappaB (NF-κB) p65 subunit phosphorylation and its upstream p-ERK1/2 activity. In conclusion, PRL exhibits anti-inflammatory effects in LPS-stimulated SIM-A9 microglia by downregulating pro-inflammatory mediators corresponding to suppression of LPS-activated ERK1/2 and NF-κB phosphorylation.
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Affiliation(s)
- Preethi Jayakumar
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carlos G Martínez-Moreno
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Mary Y Lorenson
- Department of Biomedical Sciences, University of California, Riverside, CA, USA
| | - Ameae M Walker
- Department of Biomedical Sciences, University of California, Riverside, CA, USA
| | - Teresa Morales
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico.
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Chen MJ, Ramesha S, Weinstock LD, Gao T, Ping L, Xiao H, Dammer EB, Duong DD, Levey AI, Lah JJ, Seyfried NT, Wood LB, Rangaraju S. Extracellular signal-regulated kinase regulates microglial immune responses in Alzheimer's disease. J Neurosci Res 2021; 99:1704-1721. [PMID: 33729626 DOI: 10.1002/jnr.24829] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/20/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
The importance of mitogen-activated protein kinase (MAPK) pathway signaling in regulating microglia-mediated neuroinflammation in Alzheimer's disease (AD) remains unclear. We examined the role of MAPK signaling in microglia using a preclinical model of AD pathology and quantitative proteomics studies of postmortem human brains. In multiplex immunoassay analyses of MAPK phosphoproteins in acutely isolated microglia and brain tissue from 5xFAD mice, we found phosphorylated extracellular signal-regulated kinase (ERK) was the most strongly upregulated phosphoprotein within the MAPK pathway in acutely isolated microglia, but not whole-brain tissue from 5xFAD mice. The importance of ERK signaling in primary microglia cultures was next investigated using transcriptomic profiling and functional assays of amyloid-β and neuronal phagocytosis, which confirmed that ERK is a critical regulator of IFNγ-mediated pro-inflammatory activation of microglia, although it was also partly important for constitutive microglial functions. Phospho-ERK was an upstream regulator of disease-associated microglial gene expression (Trem2, Tyrobp), as well as several human AD risk genes (Bin1, Cd33, Trem2, Cnn2), indicative of the importance of microglial ERK signaling in AD pathology. Quantitative proteomic analyses of postmortem human brain showed that ERK1 and ERK2 were the only MAPK proteins with increased protein expression and positive associations with neuropathological grade. In a human brain phosphoproteomic study, we found evidence for increased flux through the ERK signaling pathway in AD. Overall, our analyses strongly suggest that ERK phosphorylation, particularly in microglia in mouse models, is a regulator of pro-inflammatory immune responses in AD pathogenesis.
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Affiliation(s)
- Michael J Chen
- Department of Neurology, Emory University, Atlanta, GA, USA
| | | | - Laura D Weinstock
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.,The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tianwen Gao
- Department of Neurology, Emory University, Atlanta, GA, USA
| | - Lingyan Ping
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Hailian Xiao
- Department of Neurology, Emory University, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Duc D Duong
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory University, Atlanta, GA, USA
| | - James J Lah
- Department of Neurology, Emory University, Atlanta, GA, USA
| | | | - Levi B Wood
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.,The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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Modelling Cell Metabolism: A Review on Constraint-Based Steady-State and Kinetic Approaches. Processes (Basel) 2021. [DOI: 10.3390/pr9020322] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Studying cell metabolism serves a plethora of objectives such as the enhancement of bioprocess performance, and advancement in the understanding of cell biology, of drug target discovery, and in metabolic therapy. Remarkable successes in these fields emerged from heuristics approaches, for instance, with the introduction of effective strategies for genetic modifications, drug developments and optimization of bioprocess management. However, heuristics approaches have showed significant shortcomings, such as to describe regulation of metabolic pathways and to extrapolate experimental conditions. In the specific case of bioprocess management, such shortcomings limit their capacity to increase product quality, while maintaining desirable productivity and reproducibility levels. For instance, since heuristics approaches are not capable of prediction of the cellular functions under varying experimental conditions, they may lead to sub-optimal processes. Also, such approaches used for bioprocess control often fail in regulating a process under unexpected variations of external conditions. Therefore, methodologies inspired by the systematic mathematical formulation of cell metabolism have been used to address such drawbacks and achieve robust reproducible results. Mathematical modelling approaches are effective for both the characterization of the cell physiology, and the estimation of metabolic pathways utilization, thus allowing to characterize a cell population metabolic behavior. In this article, we present a review on methodology used and promising mathematical modelling approaches, focusing primarily to investigate metabolic events and regulation. Proceeding from a topological representation of the metabolic networks, we first present the metabolic modelling approaches that investigate cell metabolism at steady state, complying to the constraints imposed by mass conservation law and thermodynamics of reactions reversibility. Constraint-based models (CBMs) are reviewed highlighting the set of assumed optimality functions for reaction pathways. We explore models simulating cell growth dynamics, by expanding flux balance models developed at steady state. Then, discussing a change of metabolic modelling paradigm, we describe dynamic kinetic models that are based on the mathematical representation of the mechanistic description of nonlinear enzyme activities. In such approaches metabolic pathway regulations are considered explicitly as a function of the activity of other components of metabolic networks and possibly far from the metabolic steady state. We have also assessed the significance of metabolic model parameterization in kinetic models, summarizing a standard parameter estimation procedure frequently employed in kinetic metabolic modelling literature. Finally, some optimization practices used for the parameter estimation are reviewed.
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31
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Bunker EN, Wheeler GE, Chapnick DA, Liu X. Suppression of α-catenin and adherens junctions enhances epithelial cell proliferation and motility via TACE-mediated TGF-α autocrine/paracrine signaling. Mol Biol Cell 2020; 32:348-361. [PMID: 33378218 PMCID: PMC8098817 DOI: 10.1091/mbc.e19-08-0474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sustained cell migration is essential for wound healing and cancer metastasis. The epidermal growth factor receptor (EGFR) signaling cascade is known to drive cell migration and proliferation. While the signal transduction downstream of EGFR has been extensively investigated, our knowledge of the initiation and maintenance of EGFR signaling during cell migration remains limited. The metalloprotease TACE (tumor necrosis factor alpha converting enzyme) is responsible for producing active EGFR family ligands in the via ligand shedding. Sustained TACE activity may perpetuate EGFR signaling and reduce a cell’s reliance on exogenous growth factors. Using a cultured keratinocyte model system, we show that depletion of α-catenin perturbs adherens junctions, enhances cell proliferation and motility, and decreases dependence on exogenous growth factors. We show that the underlying mechanism for these observed phenotypical changes depends on enhanced autocrine/paracrine release of the EGFR ligand transforming growth factor alpha in a TACE-dependent manner. We demonstrate that proliferating keratinocyte epithelial cell clusters display waves of oscillatory extracellular signal–regulated kinase (ERK) activity, which can be eliminated by TACE knockout, suggesting that these waves of oscillatory ERK activity depend on autocrine/paracrine signals produced by TACE. These results provide new insights into the regulatory role of adherens junctions in initiating and maintaining autocrine/paracrine signaling with relevance to wound healing and cellular transformation.
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Affiliation(s)
- Eric N Bunker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Graycen E Wheeler
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | | | - Xuedong Liu
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
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32
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Koganti R, Suryawanshi R, Shukla D. Heparanase, cell signaling, and viral infections. Cell Mol Life Sci 2020; 77:5059-5077. [PMID: 32462405 PMCID: PMC7252873 DOI: 10.1007/s00018-020-03559-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/17/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
Heparanase (HPSE) is a multifunctional protein endowed with many non-enzymatic functions and a unique enzymatic activity as an endo-β-D-glucuronidase. The latter allows it to serve as a key modulator of extracellular matrix (ECM) via a well-regulated cleavage of heparan sulfate side chains of proteoglycans at cell surfaces. The cleavage and associated changes at the ECM cause release of multiple signaling molecules with important cellular and pathological functions. New and emerging data suggest that both enzymatic as well as non-enzymatic functions of HPSE are important for health and illnesses including viral infections and virally induced cancers. This review summarizes recent findings on the roles of HPSE in activation, inhibition, or bioavailability of key signaling molecules such as AKT, VEGF, MAPK-ERK, and EGFR, which are known regulators of common viral infections in immune and non-immune cell types. Altogether, our review provides a unique overview of HPSE in cell-survival signaling pathways and how they relate to viral infections.
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Affiliation(s)
- Raghuram Koganti
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, 1855 W. Taylor St, Chicago, IL, 60612, USA
| | - Rahul Suryawanshi
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, 1855 W. Taylor St, Chicago, IL, 60612, USA
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, 1855 W. Taylor St, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, 60612, USA.
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Kalotra S, Kaur G. PSA mimetic 5-nonyloxytryptamine protects cerebellar neurons against glutamate induced excitotoxicity: An in vitro perspective. Neurotoxicology 2020; 82:69-81. [PMID: 33197482 DOI: 10.1016/j.neuro.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 12/29/2022]
Abstract
PSA-NCAM is a molecule of therapeutic interest for its key role in promoting neuritogenesis and synaptic plasticity. The current study was aimed to investigate the neuroregenerative potential of 5-nonyloxytryptamine (5-NOT) as PSA mimetic compound against glutamate induced excitotoxicity. 2D and 3D cultures of cerebellar neurons challenged with glutamate were used to ascertain the effect of 5-NOT on neurite outgrowth, migration and expression of neuronal plasticity markers. Glutamate excitotoxicity is one of the major underlying pathological factor responsible for neurodegeneration in various neurological disorders such as trauma, stroke, ischemia, epilepsy and neurodegenerative diseases.5-NOT treatment was observed to promote axonal growth and defasiculation in glutamate challenged neurons as well as promoted the migration of cerebellar neurons in both wound scratched area and cerebellar explant cultures. Further, 5-NOT treatment upregulated the expression of synaptic plasticity and cell survival pathway proteins which showed reduced expression after glutamate induced excitotoxicity. Thus, this preliminary data reveals thatPSA-mimetic,5-NOT may prove to be a potential neuroprotective candidate for neurodegenerative diseases.
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Affiliation(s)
- Shikha Kalotra
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
| | - Gurcharan Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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Mahato AK, Sidorova YA. RET Receptor Tyrosine Kinase: Role in Neurodegeneration, Obesity, and Cancer. Int J Mol Sci 2020; 21:ijms21197108. [PMID: 32993133 PMCID: PMC7583994 DOI: 10.3390/ijms21197108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
Rearranged during transfection (RET) is the tyrosine kinase receptor that under normal circumstances interacts with ligand at the cell surface and mediates various essential roles in a variety of cellular processes such as proliferation, differentiation, survival, migration, and metabolism. RET plays a pivotal role in the development of both peripheral and central nervous systems. RET is expressed from early stages of embryogenesis and remains expressed throughout all life stages. Mutations either activating or inhibiting RET result in several aggressive diseases, namely cancer and Hirschsprung disease. However, the physiological ligand-dependent activation of RET receptor is important for the survival and maintenance of several neuronal populations, appetite, and weight gain control, thus providing an opportunity for the development of disease-modifying therapeutics against neurodegeneration and obesity. In this review, we describe the structure of RET, its signaling, and its role in both normal conditions as well as in several disorders. We highlight the differences in the signaling and outcomes of constitutive and ligand-induced RET activation. Finally, we review the data on recently developed small molecular weight RET agonists and their potential for the treatment of various diseases.
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35
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Saha P, Guha S, Biswas SC. P38K and JNK pathways are induced by amyloid-β in astrocyte: Implication of MAPK pathways in astrogliosis in Alzheimer's disease. Mol Cell Neurosci 2020; 108:103551. [PMID: 32896578 DOI: 10.1016/j.mcn.2020.103551] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Astrocyte activation is one of the crucial hallmarks of Alzheimer's disease (AD) along with amyloid-β (Aβ) plaques, neurofibrillary tangles and neuron death. Glial scar and factors secreted from activated astrocytes have important contribution on neuronal health in AD. In this study, we investigated the mechanisms of astrocyte activation both in in vitro and in vivo models of AD. In this regard, mitogen activated protein kinase (MAPK) signalling cascades that control several fundamental and stress related cellular events, has been implicated in astrocyte activation in various neurological diseases. We checked activation of different MAPKs by western blot and immunocytochemistry and found that both JNK and p38K, but not ERK pathways are activated in Aβ-treated astrocytes in culture and in Aβ-infused rat brain cortex. Next, to investigate the downstream consequences of these two MAPKs (JNK and p38K) in Aβ-induced astrocyte activation, we individually blocked these pathways by specific inhibitors in presence and absence of Aβ and checked Aβ-induced cellular proliferation, morphological changes and glial fibrillary acidic protein (GFAP) upregulation. We found that activation of both JNK and p38K signalling cascades are involved in astrocyte proliferation evoked by Aβ, whereas only p38K pathway is implicated in morphological changes and GFAP upregulation in astrocytes exposed to Aβ. To further validate the implication of p38K pathway in Aβ-induced astrocyte activation, we also observed that transcription factor ATF2, a downstream phosphorylation substrate of p38, is phosphorylated upon Aβ treatment. Taken together, our study indicates that p38K and JNK pathways mediate astrocyte activation and both the pathways are involved in cellular proliferation but only p38K pathway contributes in morphological changes triggered by Aβ.
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Affiliation(s)
- Pampa Saha
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Subhalakshmi Guha
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Subhas Chandra Biswas
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700 032, India.
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36
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Vališ K, Novák P. Targeting ERK-Hippo Interplay in Cancer Therapy. Int J Mol Sci 2020; 21:ijms21093236. [PMID: 32375238 PMCID: PMC7247570 DOI: 10.3390/ijms21093236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular signal-regulated kinase (ERK) is a part of the mitogen-activated protein kinase (MAPK) signaling pathway which allows the transduction of various cellular signals to final effectors and regulation of elementary cellular processes. Deregulation of the MAPK signaling occurs under many pathological conditions including neurodegenerative disorders, metabolic syndromes and cancers. Targeted inhibition of individual kinases of the MAPK signaling pathway using synthetic compounds represents a promising way to effective anti-cancer therapy. Cross-talk of the MAPK signaling pathway with other proteins and signaling pathways have a crucial impact on clinical outcomes of targeted therapies and plays important role during development of drug resistance in cancers. We discuss cross-talk of the MAPK/ERK signaling pathway with other signaling pathways, in particular interplay with the Hippo/MST pathway. We demonstrate the mechanism of cell death induction shared between MAPK/ERK and Hippo/MST signaling pathways and discuss the potential of combination targeting of these pathways in the development of more effective anti-cancer therapies.
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Affiliation(s)
- Karel Vališ
- Correspondence: (K.V.); (P.N.); Tel.: +420-325873610 (P.N.)
| | - Petr Novák
- Correspondence: (K.V.); (P.N.); Tel.: +420-325873610 (P.N.)
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Senatorov IS, Cheshmehkani A, Burns RN, Singh K, Moniri NH. Carboxy-Terminal Phosphoregulation of the Long Splice Isoform of Free-Fatty Acid Receptor-4 Mediates β-Arrestin Recruitment and Signaling to ERK1/2. Mol Pharmacol 2020; 97:304-313. [PMID: 32132133 DOI: 10.1124/mol.119.117697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Free-fatty acid receptor-4 (FFA4), previously termed GPR120, is a G protein-coupled receptor (GPCR) for medium and long-chained fatty acids, agonism of which can regulate a myriad of metabolic, sensory, inflammatory, and proliferatory signals. Two alternative splice isoforms of FFA4 exist that differ by the presence of an additional 16 amino acids in the longer (FFA4-L) transcript, which has been suggested to be an intrinsically β-arrestin-biased GPCR. Although the shorter isoform (FFA4-S) has been studied more extensively, very little is known about mechanisms of regulation or signaling of the longer isoform. Because β-arrestin recruitment is dependent on receptor phosphorylation, in the current study, we used the endogenous agonist docosahexaenoic acid (DHA) to examine the mechanisms of FFA4-L phosphorylation, as well as DHA-dependent β-arrestin recruitment and DHA-dependent extracellular-signal regulated kinase-1/2 (ERK1/2) signaling in human embryonic kidney 293 cells. Our results reveal differences in basal phosphorylation of the two FFA4 isoforms, and we show that DHA-mediated phosphorylation of FFA4-L is primarily regulated by G protein-coupled receptor kinase 6, whereas protein kinase-C can also contribute to agonist-induced and heterologous phosphorylation. Moreover, our data demonstrate that FFA4-L phosphorylation occurs on the distal C terminus and is directly responsible for recruitment and interactions with β-arrestin-2. Finally, using CRISPR/Cas9 genome-edited cells, our data reveal that unlike FFA4-S, the longer isoform is unable to facilitate phosphorylation of ERK1/2 in cells that are devoid of β-arrestin-1/2. Together, these results are the first to demonstrate phosphoregulation of FFA4-L as well as the effects of loss of phosphorylation sites on β-arrestin recruitment and ERK1/2 activation. SIGNIFICANCE STATEMENT: Free-fatty acid receptor-4 (FFA4) is a cell-surface G protein-coupled receptor for medium and long-chained fatty acids that can be expressed as distinct short (FFA4-S) or long (FFA4-L) isoforms. Although much is known about FFA4-S, the longer isoform remains virtually unstudied. Here, we reveal the mechanisms of docosahexaenoic acid-induced phosphorylation of FFA4-L and subsequent β-arrestin-2 recruitment and extracellular-signal regulated kinase-1/2 activity.
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Affiliation(s)
- Ilya S Senatorov
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, Georgia
| | - Ameneh Cheshmehkani
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, Georgia
| | - Rebecca N Burns
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, Georgia
| | - Kirti Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, Georgia
| | - Nader H Moniri
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, Georgia
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Poreba E, Durzynska J. Nuclear localization and actions of the insulin-like growth factor 1 (IGF-1) system components: Transcriptional regulation and DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108307. [PMID: 32430099 DOI: 10.1016/j.mrrev.2020.108307] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022]
Abstract
Insulin-like growth factor (IGF) system stimulates growth, proliferation, and regulates differentiation of cells in a tissue-specific manner. It is composed of two insulin-like growth factors (IGF-1 and IGF-2), six insulin-like growth factor-binding proteins (IGFBPs), and two insulin-like growth factor receptors (IGF-1R and IGF-2R). IGF actions take place mostly through the activation of the plasma membrane-bound IGF-Rs by the circulating ligands (IGFs) released from the IGFBPs that stabilize their levels in the serum. This review focuses on the IGF-1 part of the system. The IGF-1 gene, which is expressed mainly in the liver as well as in other tissues, comprises six alternatively spliced exons that code for three protein isoforms (pro-IGF-1A, pro-IGF-1B, and pro-IGF-1C), which are processed to mature IGF-1 and E-peptides. The IGF-1R undergoes autophosphorylation, resulting in a signaling cascade involving numerous cytoplasmic proteins such as AKT and MAPKs, which regulate the expression of target genes. However, a more complex picture of the axis has recently emerged with all its components being translocated to the nuclear compartment. IGF-1R takes part in the regulation of gene expression by forming transcription complexes, modifying the activity of chromatin remodeling proteins, and participating in DNA damage tolerance mechanisms. Four IGFBPs contain a nuclear localization signal (NLS), which targets them to the nucleus, where they regulate gene expression (IGFBP-2, IGFBP-3, IGFBP-5, IGFBP-6) and DNA damage repair (IGFBP-3 and IGFBP-6). Last but not least, the IGF-1B isoform has been reported to be localized in the nuclear compartment. However, no specific molecular actions have been assigned to the nuclear pro-IGF-1B or its derivative EB peptide. Therefore, further studies are needed to shed light on their nuclear activity. These recently uncovered nuclear actions of different components of the IGF-1 axis are relevant in cancer cell biology and are discussed in this review.
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Affiliation(s)
- Elzbieta Poreba
- Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Julia Durzynska
- Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Arkun Y. Modeling and Analysis of Gab1 Mediated Feedback Loops to Understand Gab's Role in Erk-Akt Signaling and Cancer .. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:2939-2942. [PMID: 31946506 DOI: 10.1109/embc.2019.8857855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A mathematical model is presented to study the dynamics of the docking protein Gab1 that plays an important role in the regulation of ERK and AKT signaling pathways. Model predictions can be used to understand the role of Gab1 in the development of cancer which can give insight into targeted therapy.
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Miningou N, Blackwell KT. The road to ERK activation: Do neurons take alternate routes? Cell Signal 2020; 68:109541. [PMID: 31945453 DOI: 10.1016/j.cellsig.2020.109541] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/11/2020] [Accepted: 01/12/2020] [Indexed: 01/29/2023]
Abstract
The ERK cascade is a central signaling pathway that regulates a wide variety of cellular processes including proliferation, differentiation, learning and memory, development, and synaptic plasticity. A wide range of inputs travel from the membrane through different signaling pathway routes to reach activation of one set of output kinases, ERK1&2. The classical ERK activation pathway beings with growth factor activation of receptor tyrosine kinases. Numerous G-protein coupled receptors and ionotropic receptors also lead to ERK through increases in the second messengers calcium and cAMP. Though both types of pathways are present in diverse cell types, a key difference is that most stimuli to neurons, e.g. synaptic inputs, are transient, on the order of milliseconds to seconds, whereas many stimuli acting on non-neural tissue, e.g. growth factors, are longer duration. The ability to consolidate these inputs to regulate the activation of ERK in response to diverse signals raises the question of which factors influence the difference in ERK activation pathways. This review presents both experimental studies and computational models aimed at understanding the control of ERK activation and whether there are fundamental differences between neurons and other cells. Our main conclusion is that differences between cell types are quite subtle, often related to differences in expression pattern and quantity of some molecules such as Raf isoforms. In addition, the spatial location of ERK is critical, with regulation by scaffolding proteins producing differences due to colocalization of upstream molecules that may differ between neurons and other cells.
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Affiliation(s)
- Nadiatou Miningou
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA 22030, United States of America
| | - Kim T Blackwell
- Interdisciplinary Program in Neuroscience and Bioengineering Department, George Mason University, Fairfax, VA 22030, United States of America.
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Arkun Y. Detection of biological switches using the method of Gröebner bases. BMC Bioinformatics 2019; 20:615. [PMID: 31779580 PMCID: PMC6883700 DOI: 10.1186/s12859-019-3155-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 10/14/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS In this work we show how the method of Gröebner bases can be used to detect bistability and output switchability. The method of Gröebner bases can be seen as a multivariate, non-linear generalization of the Gaussian elimination for linear systems which conveniently seperates the variables and drastically simplifies the simultaneous solution of polynomial equations. A necessary condition for fixed-point state bistability is for the Gröbner basis to have three distinct solutions for the state. A sufficient condition is provided by the eigenvalues of the local Jacobians. We also introduce the concept of output switchability which is defined as the ability of an output of a bistable system to switch between two different stable steady-state values. It is shown that bistability does not necessarily guarantee switchability of every state variable of the system. We further show that, for a bistable system, the necessary conditions for output switchability can be derived using the Gröebner basis. The theoretical results are incorporated into an analysis procedure and applied to several systems including the AKT (Protein kinase B), RAS (Rat Sarcoma) and MAPK (Mitogen-activated protein kinase) signal transduction pathways. Results demonstrate that the Gröebner bases can be conveniently used to analyze biological switches by simultaneously detecting bistability and output switchability. CONCLUSION The Gröebner bases provides a novel methodology to analyze bistability. Results clarify the distinction between bistability and output switchability which is lacking in the literature. We have shown that theoretically, it is possible to have an output subspace of an n-dimensional bistable system where certain variables cannot switch. It is possible to construct such systems as we have done with two reaction networks.
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Affiliation(s)
- Yaman Arkun
- Department of Chemical and Biological Engineering, Koc University, Rumeli Feneri Yolu, 34450, Sariyer, Istanbul, Turkey.
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42
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Ferreira HJ, de Almeida EM, da Silva WMB, Teixeira EH, do Nascimento Neto LG. Molecular Mechanisms Involved in the Antitumor Activity of Isolated Lectins from Marine Organisms: A Systematic Review. Curr Drug Targets 2019; 21:616-625. [PMID: 31763966 DOI: 10.2174/1389450120666191122113850] [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: 08/04/2019] [Revised: 09/27/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Tumor cells may present several molecular alterations that favor their malignancy, among which there is the expression of tumor-related antigens, such as truncated T-glycans, Thomsen-nouvelle, sialyl-Lewis X and sialyl Tn, which may help in the diagnosis and treatment using specific target molecules. Lectins are ubiquitous proteins capable of interacting with specific carbohydrates. Lectins isolated from marine organisms have important characteristics such as low immunogenicity and can bind to complex glycans compared to plant lectins. OBJECTIVE This work evaluated, through a systematic review, the molecular mechanisms of antitumor activity of lectins isolated from marine organisms. METHODOLOGY The Pubmed, Lilacs, Science Direct, Wiley and Scopus databases were reviewed using the descriptors: marine lectin and cancer. Articles in English, published between January 2008 and December 2018, which proposed the molecular mechanisms of anticancer activity of lectins from marine organisms were eligible for the study. RESULTS 17 articles were eligible. The lectins showed promising performance against cancer cells, presenting specific cytotoxicity for some types of malignant cells. The articles presented several lectins specific to different carbohydrates, modulating: pro and anti-apoptotic proteins, transcription factor E2F-1, via mitogen-activated protein kinase. In addition, exogenous lectin expression in cancer cells has been shown to be a promising way to treat cancer. CONCLUSION This review showed the various studies that described the molecular mechanisms caused by marine lectins with antineoplastic potential. This knowledge is relevant for the development and use of the next generations of lectins isolated from marine organisms, supporting their potential in cancer treatment.
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Affiliation(s)
- Hugo Jefferson Ferreira
- Biomedicine College, Christus University Center, Fortaleza - CE, Brazil.,Integrated Laboratory of Biomolecules (LIBS), Federal University of Ceara, Department of Pathology and Forensic Medicine, 60430-160, Fortaleza, CE, Brazil
| | - Evandro Moreira de Almeida
- Biomedicine College, Christus University Center, Fortaleza - CE, Brazil.,Integrated Laboratory of Biomolecules (LIBS), Federal University of Ceara, Department of Pathology and Forensic Medicine, 60430-160, Fortaleza, CE, Brazil
| | | | - Edson Holanda Teixeira
- Integrated Laboratory of Biomolecules (LIBS), Federal University of Ceara, Department of Pathology and Forensic Medicine, 60430-160, Fortaleza, CE, Brazil
| | - Luiz Gonzaga do Nascimento Neto
- Integrated Laboratory of Biomolecules (LIBS), Federal University of Ceara, Department of Pathology and Forensic Medicine, 60430-160, Fortaleza, CE, Brazil.,Federal Institute of Education, Science and Technology of Ceará, Limoeiro do Norte Campus, 62930-000, Limoeiro do Norte, Ceara, Brazil
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43
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Saroz Y, Kho DT, Glass M, Graham ES, Grimsey NL. Cannabinoid Receptor 2 (CB 2) Signals via G-alpha-s and Induces IL-6 and IL-10 Cytokine Secretion in Human Primary Leukocytes. ACS Pharmacol Transl Sci 2019; 2:414-428. [PMID: 32259074 DOI: 10.1021/acsptsci.9b00049] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 12/11/2022]
Abstract
Cannabinoid receptor 2 (CB2) is a promising therapeutic target for immunological modulation. There is, however, a deficit of knowledge regarding CB2 signaling and function in human primary immunocompetent cells. We applied an experimental paradigm which closely models the in situ state of human primary leukocytes (PBMC; peripheral blood mononuclear cells) to characterize activation of a number of signaling pathways in response to a CB2-selective ligand (HU308). We observed a "lag" phase of unchanged cAMP concentration prior to development of classically expected Gαi-mediated inhibition of cAMP synthesis. Application of G protein inhibitors revealed that this apparent lag was a result of counteraction of Gαi effects by concurrent Gαs activation. Monitoring downstream signaling events showed that activation of p38 was mediated by Gαi, whereas ERK1/2 and Akt phosphorylation were mediated by Gαi-coupled βγ. Activation of CREB integrated multiple components; Gαs and βγ mediated ∼85% of the response, while ∼15% was attributed to Gαi. Responses to HU308 had an important functional outcome-secretion of interleukins 6 (IL-6) and 10 (IL-10). IL-2, IL-4, IL-12, IL-13, IL-17A, MIP-1α, and TNF-α were unaffected. IL-6/IL-10 induction had a similar G protein coupling profile to CREB activation. All response potencies were consistent with that expected for HU308 acting via CB2. Additionally, signaling and functional effects were completely blocked by a CB2-selective inverse agonist, giving additional evidence for CB2 involvement. This work expands the current paradigm regarding cannabinoid immunomodulation and reinforces the potential utility of CB2 ligands as immunomodulatory therapeutics.
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Affiliation(s)
- Yurii Saroz
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.,Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand
| | - Dan T Kho
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.,Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand
| | - Michelle Glass
- Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, 9016, New Zealand
| | - Euan Scott Graham
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.,Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand
| | - Natasha Lillia Grimsey
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.,Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, Centre for Brain Research, Faculty of Medical and Health Sciences, and Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand
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El Khoury D, Matar R, Touma T. Curcumin and endometrial carcinoma: an old spice as a novel agent. Int J Womens Health 2019; 11:249-256. [PMID: 31354362 PMCID: PMC6586219 DOI: 10.2147/ijwh.s194262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
One of the clinically major gynecological cancers is endometrial carcinoma that develops from the lining of the uterus. During the past years, different approaches have been developed to treat endometrial carcinoma, among which natural herbal medicine has recently faired as an effective method. The yellow Indian spice known as curcumin has been extolled for its healing powers and has recently been adopted for investigation by the scientific community as a potent anti-cancerous agent. This review focuses on the effect of curcumin on endometrial cancer (EC) and its role in specific pathways involved in carcinogenesis.
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Affiliation(s)
- Diala El Khoury
- Department of Sciences, Notre Dame University-Louaize, Zouk Mosbeh, Lebanon,
| | - Rana Matar
- Department of Sciences, Notre Dame University-Louaize, Zouk Mosbeh, Lebanon,
| | - Tina Touma
- Department of Sciences, Notre Dame University-Louaize, Zouk Mosbeh, Lebanon,
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Zou ZG, Rios FJ, Montezano AC, Touyz RM. TRPM7, Magnesium, and Signaling. Int J Mol Sci 2019; 20:E1877. [PMID: 30995736 PMCID: PMC6515203 DOI: 10.3390/ijms20081877] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
The transient receptor potential melastatin-subfamily member 7 (TRPM7) is a ubiquitously expressed chanzyme that possesses an ion channel permeable to the divalent cations Mg2+, Ca2+, and Zn2+, and an α-kinase that phosphorylates downstream substrates. TRPM7 and its homologue TRPM6 have been implicated in a variety of cellular functions and is critically associated with intracellular signaling, including receptor tyrosine kinase (RTK)-mediated pathways. Emerging evidence indicates that growth factors, such as EGF and VEGF, signal through their RTKs, which regulate activity of TRPM6 and TRPM7. TRPM6 is primarily an epithelial-associated channel, while TRPM7 is more ubiquitous. In this review we focus on TRPM7 and its association with growth factors, RTKs, and downstream kinase signaling. We also highlight how interplay between TRPM7, Mg2+ and signaling kinases influences cell function in physiological and pathological conditions, such as cancer and preeclampsia.
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Affiliation(s)
- Zhi-Guo Zou
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Centre, University of Glasgow, Glasgow G12 8TA, UK.
| | - Francisco J Rios
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Centre, University of Glasgow, Glasgow G12 8TA, UK.
| | - Augusto C Montezano
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Centre, University of Glasgow, Glasgow G12 8TA, UK.
| | - Rhian M Touyz
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Centre, University of Glasgow, Glasgow G12 8TA, UK.
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46
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Sokol DK, Maloney B, Westmark CJ, Lahiri DK. Novel Contribution of Secreted Amyloid-β Precursor Protein to White Matter Brain Enlargement in Autism Spectrum Disorder. Front Psychiatry 2019; 10:165. [PMID: 31024350 PMCID: PMC6469489 DOI: 10.3389/fpsyt.2019.00165] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/06/2019] [Indexed: 12/27/2022] Open
Abstract
The most replicated neuroanatomical finding in autism is the tendency toward brain overgrowth, especially in younger children. Research shows that both gray and white matter are enlarged. Proposed mechanisms underlying brain enlargement include abnormal inflammatory and neurotrophic signals that lead to excessive, aberrant dendritic connectivity via disrupted pruning and cell adhesion, and enlargement of white matter due to excessive gliogenesis and increased myelination. Amyloid-β protein precursor (βAPP) and its metabolites, more commonly associated with Alzheimer's disease (AD), are also dysregulated in autism plasma and brain tissue samples. This review highlights findings that demonstrate how one βAPP metabolite, secreted APPα, and the ADAM family α-secretases, may lead to increased brain matter, with emphasis on increased white matter as seen in autism. sAPPα and the ADAM family α-secretases contribute to the anabolic, non-amyloidogenic pathway, which is in contrast to the amyloid (catabolic) pathway known to contribute to Alzheimer disease. The non-amyloidogenic pathway could produce brain enlargement via genetic mechanisms affecting mRNA translation and polygenic factors that converge on molecular pathways (mitogen-activated protein kinase/MAPK and mechanistic target of rapamycin/mTOR), promoting neuroinflammation. A novel mechanism linking the non-amyloidogenic pathway to white matter enlargement is proposed: α-secretase and/or sAPPα, activated by ERK receptor signaling activates P13K/AKt/mTOR and then Rho GTPases favoring myelination via oligodendrocyte progenitor cell (OPC) activation of cofilin. Applying known pathways in AD to autism should allow further understanding and provide options for new drug targets.
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Affiliation(s)
- Deborah K. Sokol
- Pediatrics Section, Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bryan Maloney
- Indiana Alzheimers Disease Center, Department of Psychiatry, Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Cara J. Westmark
- Department of Neurology, University of Wisconsin, Madison, WI, United States
| | - Debomoy K. Lahiri
- Indiana Alzheimers Disease Center, Department of Psychiatry, Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
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Goh GH, Maloney SK, Mark PJ, Blache D. Episodic Ultradian Events-Ultradian Rhythms. BIOLOGY 2019; 8:biology8010015. [PMID: 30875767 PMCID: PMC6466064 DOI: 10.3390/biology8010015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/24/2019] [Accepted: 03/09/2019] [Indexed: 11/16/2022]
Abstract
In the fast lane of chronobiology, ultradian events are short-term rhythms that have been observed since the beginning of modern biology and were quantified about a century ago. They are ubiquitous in all biological systems and found in all organisms, from unicellular organisms to mammals, and from single cells to complex biological functions in multicellular animals. Since these events are aperiodic and last for a few minutes to a few hours, they are better classified as episodic ultradian events (EUEs). Their origin is unclear. However, they could have a molecular basis and could be controlled by hormonal inputs-in vertebrates, they originate from the activity of the central nervous system. EUEs are receiving increasing attention but their aperiodic nature requires specific sampling and analytic tools. While longer scale rhythms are adaptations to predictable changes in the environment, in theory, EUEs could contribute to adaptation by preparing organisms and biological functions for unpredictability.
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Affiliation(s)
- Grace H Goh
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Shane K Maloney
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Peter J Mark
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
| | - Dominique Blache
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
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Abstract
Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss some lesser-known ones, mostly in filamentous fungi, while it will direct readers to additional literature in the case of well-known phenomena such as the amyloid prions or fungal senescence. It will present in depth the "white/opaque" switch of Candida albicans and the "crippled growth" degeneration of the model fungus Podospora anserina. These are two of the most thoroughly studied epigenetic phenotypic switches. I will also discuss the "sectors" presented by many filamentous ascomycetes, for which a prion-based model exists but is not demonstrated. Finally, I will also describe intriguing examples of phenotypic instability for which an explanation has yet to be provided.
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