1
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Li H, Li Y, Luo S, Zhang Y, Feng Z, Li S. The roles and mechanisms of the NF-κB signaling pathway in tendon disorders. Front Vet Sci 2024; 11:1382239. [PMID: 38978635 PMCID: PMC11228182 DOI: 10.3389/fvets.2024.1382239] [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: 02/05/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Both acute and chronic tendon injuries are the most frequently occurring musculoskeletal diseases in human and veterinary medicine, with a limited repertoire of successful and evidenced-based therapeutic strategies. Inflammation has been suggested as a key driver for the formation of scar and adhesion tissue following tendon acute injury, as well as pathological alternations of degenerative tendinopathy. However, prior efforts to completely block this inflammatory process have yet to be largely successful. Recent investigations have indicated that a more precise targeted approach for modulating inflammation is critical to improve outcomes. The nuclear factor-kappaB (NF-κB) is a typical proinflammatory signal transduction pathway identified as a key factor leading to tendon disorders. Therefore, a comprehensive understanding of the mechanism or regulation of NF-κB in tendon disorders will aid in developing targeted therapeutic strategies for human and veterinary tendon disorders. In this review, we discuss what is currently known about molecular components and structures of basal NF-κB proteins and two activation pathways: the canonical activation pathway and the non-canonical activation pathway. Furthermore, we summarize the underlying mechanisms of the NF-κB signaling pathway in fibrosis and adhesion after acute tendon injury, as well as pathological changes of degenerative tendinopathy in all species and highlight the effect of targeting this signaling pathway in tendon disorders. However, to gain a comprehensive understanding of its mechanisms underlying tendon disorders, further investigations are required. In the future, extensive scientific examinations are warranted to full characterize the NF-κB, the exact mechanisms of action, and translate findings into clinical human and veterinary practice.
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Affiliation(s)
- Hanyue Li
- School of Physical Education, Southwest Medical University, Luzhou, China
| | - Yini Li
- Department of Ultrasound, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Shengyu Luo
- School of Physical Education, Southwest Medical University, Luzhou, China
| | - Yan Zhang
- Luzhou Vocational and Technical College, Luzhou, China
| | - Zhenhua Feng
- Division of Spine Surgery, Department of Orthopedic Surgery, Affiliated Hospital of Medical School, Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
| | - Sen Li
- School of Physical Education, Southwest Medical University, Luzhou, China
- Division of Spine Surgery, Department of Orthopedic Surgery, Affiliated Hospital of Medical School, Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
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2
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Li Z, Yu Z, Cui S, Hu S, Li B, Chen T, Qu C, Yang B. AMPA receptor inhibition alleviates inflammatory response and myocardial apoptosis after myocardial infarction by inhibiting TLR4/NF-κB signaling pathway. Int Immunopharmacol 2024; 133:112080. [PMID: 38613882 DOI: 10.1016/j.intimp.2024.112080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
Myocardial infarction leads to myocardial inflammation and apoptosis, which are crucial factors leading to heart failure and cardiovascular dysfunction, eventually resulting in death. While the inhibition of AMPA receptors mitigates inflammation and tissue apoptosis, the effectiveness of this inhibition in the pathophysiological processes of myocardial infarction remains unclear. This study investigated the role of AMPA receptor inhibition in myocardial infarction and elucidated the underlying mechanisms. This study established a myocardial infarction model by ligating the left anterior descending branch of the coronary artery in Sprague-Dawley rats. The findings suggested that injecting the AMPA receptor antagonist NBQX into myocardial infarction rats effectively alleviated cardiac inflammation, myocardial necrosis, and apoptosis and improved their cardiac contractile function. Conversely, injecting the AMPA receptor agonist CX546 into infarcted rats exacerbated the symptoms and tissue damage, as reflected by histopathology. This agonist also stimulated the TLR4/NF-κB pathway, further deteriorating cardiac function. Furthermore, the investigations revealed that AMPA receptor inhibition hindered the nuclear translocation of P65, blocking its downstream signaling pathway and attenuating tissue inflammation. In summary, this study affirmed the potential of AMPA receptor inhibition in countering inflammation and tissue apoptosis after myocardial infarction, making it a promising therapeutic target for mitigating myocardial infarction.
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Affiliation(s)
- Zixuan Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China
| | - Zhili Yu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China
| | - Shengyu Cui
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China
| | - Shan Hu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China
| | - Bin Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China
| | - Tao Chen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China
| | - Chuan Qu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China.
| | - Bo Yang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, China; Hubei Key Laboratory of Cardiology, Wuhan 430060, China.
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3
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Mu DP, Scharer CD, Kaminski NE, Zhang Q. A multiscale spatial modeling framework for the germinal center response. Front Immunol 2024; 15:1377303. [PMID: 38881901 PMCID: PMC11179717 DOI: 10.3389/fimmu.2024.1377303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymphoid organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework - integrating molecular, cellular, and tissue-level responses - is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-κB, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events, including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanistic and applied research questions on the adaptive humoral immune response in the future.
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Affiliation(s)
- Derek P. Mu
- Montgomery Blair High School, Silver Spring, MD, United States
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Norbert E. Kaminski
- Department of Pharmacology & Toxicology, Institute for Integrative Toxicology, Center for Research on Ingredient Safety, Michigan State University, East Lansing, MI, United States
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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4
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Ginley-Hidinger M, Abewe H, Osborne K, Richey A, Kitchen N, Mortenson KL, Wissink EM, Lis J, Zhang X, Gertz J. Cis-regulatory control of transcriptional timing and noise in response to estrogen. CELL GENOMICS 2024; 4:100542. [PMID: 38663407 PMCID: PMC11099348 DOI: 10.1016/j.xgen.2024.100542] [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: 03/16/2023] [Revised: 10/26/2023] [Accepted: 03/27/2024] [Indexed: 05/07/2024]
Abstract
Cis-regulatory elements control transcription levels, temporal dynamics, and cell-cell variation or transcriptional noise. However, the combination of regulatory features that control these different attributes is not fully understood. Here, we used single-cell RNA-seq during an estrogen treatment time course and machine learning to identify predictors of expression timing and noise. We found that genes with multiple active enhancers exhibit faster temporal responses. We verified this finding by showing that manipulation of enhancer activity changes the temporal response of estrogen target genes. Analysis of transcriptional noise uncovered a relationship between promoter and enhancer activity, with active promoters associated with low noise and active enhancers linked to high noise. Finally, we observed that co-expression across single cells is an emergent property associated with chromatin looping, timing, and noise. Overall, our results indicate a fundamental tradeoff between a gene's ability to quickly respond to incoming signals and maintain low variation across cells.
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Affiliation(s)
- Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Hosiana Abewe
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kyle Osborne
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandra Richey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Noel Kitchen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Katelyn L Mortenson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Erin M Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xiaoyang Zhang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
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5
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Fischer AAM, Robertson HB, Kong D, Grimm MM, Grether J, Groth J, Baltes C, Fliegauf M, Lautenschläger F, Grimbacher B, Ye H, Helms V, Weber W. Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311834. [PMID: 38573961 DOI: 10.1002/smll.202311834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. However, the impact of the material properties of biomolecular condensates on important processes, such as the control of gene expression, remains largely elusive. Here, the material properties of optogenetically induced transcription factor condensates are systematically tuned, and probed for their impact on the activation of target promoters. It is demonstrated that transcription factors in rather liquid condensates correlate with increased gene expression levels, whereas stiffer transcription factor condensates correlate with the opposite effect, reduced activation of gene expression. The broad nature of these findings is demonstrated in mammalian cells and mice, as well as by using different synthetic and natural transcription factors. These effects are observed for both transgenic and cell-endogenous promoters. The findings provide a novel materials-based layer in the control of gene expression, which opens novel opportunities in optogenetic engineering and synthetic biology.
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Affiliation(s)
- Alexandra A M Fischer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 21a, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Hanah B Robertson
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Merlin M Grimm
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Jakob Grether
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Biberach University of Applied Sciences, Karlstraße 6-11, 88400, Biberach an der Riß, Germany
| | - Johanna Groth
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Carsten Baltes
- Department of Experimental Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Manfred Fliegauf
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Franziska Lautenschläger
- Department of Experimental Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 115, 79106, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- DZIF - German Center for Infection Research, Deutsches Zentrum für Infektionsforschung e.V., Inhoffenstr. 7, 38124, Braunschweig, Germany
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 21a, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Department of Materials Science and Engineering, Campus D2 2, Saarland University, 66123, Saarbrücken, Germany
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6
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Ginley-Hidinger M, Abewe H, Osborne K, Richey A, Kitchen N, Mortenson KL, Wissink EM, Lis J, Zhang X, Gertz J. Cis-regulatory control of transcriptional timing and noise in response to estrogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.14.532457. [PMID: 36993565 PMCID: PMC10054948 DOI: 10.1101/2023.03.14.532457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cis-regulatory elements control transcription levels, temporal dynamics, and cell-cell variation or transcriptional noise. However, the combination of regulatory features that control these different attributes is not fully understood. Here, we used single cell RNA-seq during an estrogen treatment time course and machine learning to identify predictors of expression timing and noise. We find that genes with multiple active enhancers exhibit faster temporal responses. We verified this finding by showing that manipulation of enhancer activity changes the temporal response of estrogen target genes. Analysis of transcriptional noise uncovered a relationship between promoter and enhancer activity, with active promoters associated with low noise and active enhancers linked to high noise. Finally, we observed that co-expression across single cells is an emergent property associated with chromatin looping, timing, and noise. Overall, our results indicate a fundamental tradeoff between a gene's ability to quickly respond to incoming signals and maintain low variation across cells.
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Affiliation(s)
- Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Hosiana Abewe
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kyle Osborne
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandra Richey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Noel Kitchen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Katelyn L. Mortenson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Erin M. Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xiaoyang Zhang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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7
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Mu DP, Scharer CD, Kaminski NE, Zhang Q. A Multiscale Spatial Modeling Framework for the Germinal Center Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577491. [PMID: 38501122 PMCID: PMC10945589 DOI: 10.1101/2024.01.26.577491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymph organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework - integrating molecular, cellular, and tissue-level responses - is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-κB, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanic and applied research questions in future.
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8
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Vlahopoulos S, Pan L, Varisli L, Dancik GM, Karantanos T, Boldogh I. OGG1 as an Epigenetic Reader Affects NFκB: What This Means for Cancer. Cancers (Basel) 2023; 16:148. [PMID: 38201575 PMCID: PMC10778025 DOI: 10.3390/cancers16010148] [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: 11/22/2023] [Revised: 12/16/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
8-oxoguanine glycosylase 1 (OGG1), which was initially identified as the enzyme that catalyzes the first step in the DNA base excision repair pathway, is now also recognized as a modulator of gene expression. What is important for cancer is that OGG1 acts as a modulator of NFκB-driven gene expression. Specifically, oxidant stress in the cell transiently halts enzymatic activity of substrate-bound OGG1. The stalled OGG1 facilitates DNA binding of transactivators, such as NFκB to their cognate sites, enabling the expression of cytokines and chemokines, with ensuing recruitment of inflammatory cells. Recently, we highlighted chief aspects of OGG1 involvement in regulation of gene expression, which hold significance in lung cancer development. However, OGG1 has also been implicated in the molecular underpinning of acute myeloid leukemia. This review analyzes and discusses how these cells adapt through redox-modulated intricate connections, via interaction of OGG1 with NFκB, which provides malignant cells with alternative molecular pathways to transform their microenvironment, enabling adjustment, promoting cell proliferation, metastasis, and evading killing by therapeutic agents.
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Affiliation(s)
- Spiros Vlahopoulos
- First Department of Pediatrics, National and Kapodistrian University of Athens, Thivon & Levadeias 8, Goudi, 11527 Athens, Greece
| | - Lang Pan
- Department of Microbiology and Immunology, School of Medicine, University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555, USA;
| | - Lokman Varisli
- Department of Molecular Biology and Genetics, Science Faculty, Dicle University, Diyarbakir 21280, Turkey;
| | - Garrett M. Dancik
- Department of Computer Science, Eastern Connecticut State University, Willimantic, CT 06226, USA;
| | - Theodoros Karantanos
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA;
| | - Istvan Boldogh
- Department of Microbiology and Immunology, School of Medicine, University of Texas Medical Branch at Galveston, 301 University Blvd., Galveston, TX 77555, USA;
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9
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Singh A, Kaileh M, De S, Mazan-Mamczarz K, Bayarsaihan D, Sen R, Roy AL. Transcription factor TFII-I fine tunes innate properties of B lymphocytes. Front Immunol 2023; 14:1067459. [PMID: 36756127 PMCID: PMC9900109 DOI: 10.3389/fimmu.2023.1067459] [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: 10/11/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
The ubiquitously expressed transcription factor TFII-I is a multifunctional protein with pleiotropic roles in gene regulation. TFII-I associated polymorphisms are implicated in Sjögren's syndrome and Lupus in humans and, germline deletion of the Gtf2i gene in mice leads to embryonic lethality. Here we report a unique role for TFII-I in homeostasis of innate properties of B lymphocytes. Loss of Gtf2i in murine B lineage cells leads to an alteration in transcriptome, chromatin landscape and associated transcription factor binding sites, which exhibits myeloid-like features and coincides with enhanced sensitivity to LPS induced gene expression. TFII-I deficient B cells also show increased switching to IgG3, a phenotype associated with inflammation. These results demonstrate a role for TFII-I in maintaining immune homeostasis and provide clues for GTF2I polymorphisms associated with B cell dominated autoimmune diseases in humans.
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Affiliation(s)
- Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics & Genomics, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics & Genomics, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, United States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Ananda L Roy
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
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10
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Wen Y, Ma J. Phase separation drives the formation of biomolecular condensates in the immune system. Front Immunol 2022; 13:986589. [PMID: 36439121 PMCID: PMC9685520 DOI: 10.3389/fimmu.2022.986589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/19/2022] [Indexed: 08/12/2023] Open
Abstract
When the external conditions change, such as the temperature or the pressure, the multi-component system sometimes separates into several phases with different components and structures, which is called phase separation. Increasing studies have shown that cells condense related biomolecules into independent compartments in order to carry out orderly and efficient biological reactions with the help of phase separation. Biomolecular condensates formed by phase separation play a significant role in a variety of cellular processes, including the control of signal transduction, the regulation of gene expression, and the stress response. In recent years, many phase separation events have been discovered in the immune response process. In this review, we provided a comprehensive and detailed overview of the role and mechanism of phase separation in the innate and adaptive immune responses, which will help the readers to appreciate the advance and importance of this field.
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Affiliation(s)
- Yuqing Wen
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
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