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Schuldt C, Khudayberdiev S, Chandra BD, Linne U, Rust MB. Cyclase-associated protein (CAP) inhibits inverted formin 2 (INF2) to induce dendritic spine maturation. Cell Mol Life Sci 2024; 81:353. [PMID: 39154297 PMCID: PMC11335277 DOI: 10.1007/s00018-024-05393-y] [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: 03/12/2024] [Revised: 07/09/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]
Abstract
The morphology of dendritic spines, the postsynaptic compartment of most excitatory synapses, decisively modulates the function of neuronal circuits as also evident from human brain disorders associated with altered spine density or morphology. Actin filaments (F-actin) form the backbone of spines, and a number of actin-binding proteins (ABP) have been implicated in shaping the cytoskeleton in mature spines. Instead, only little is known about the mechanisms that control the reorganization from unbranched F-actin of immature spines to the complex, highly branched cytoskeleton of mature spines. Here, we demonstrate impaired spine maturation in hippocampal neurons upon genetic inactivation of cyclase-associated protein 1 (CAP1) and CAP2, but not of CAP1 or CAP2 alone. We found a similar spine maturation defect upon overactivation of inverted formin 2 (INF2), a nucleator of unbranched F-actin with hitherto unknown synaptic function. While INF2 overactivation failed in altering spine density or morphology in CAP-deficient neurons, INF2 inactivation largely rescued their spine defects. From our data we conclude that CAPs inhibit INF2 to induce spine maturation. Since we previously showed that CAPs promote cofilin1-mediated cytoskeletal remodeling in mature spines, we identified them as a molecular switch that control transition from filopodia-like to mature spines.
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Affiliation(s)
- Cara Schuldt
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany
| | - Sharof Khudayberdiev
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany
| | - Ben-David Chandra
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany.
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany.
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2
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Li X, Luo M, Xu H, Jia L, Liang Y, Xu Q, Wang Y. CAP2 contributes to Parkinson's disease diagnosed by neutrophil extracellular trap-related immune activity. Front Immunol 2024; 15:1377409. [PMID: 38846945 PMCID: PMC11153744 DOI: 10.3389/fimmu.2024.1377409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Introduction Neutrophil extracellular traps (NETs) constitute a crucial element of the immune system, and dysfunction in immune responses is implicated in the susceptibility and progression of Parkinson's disease (PD). Nevertheless, the mechanism connecting PD and NETs remains unclear. This study aims to uncover potential NETs-related immune biomarkers and elucidate their role in PD pathogenesis. Methods Through differential gene analysis of PD and NETs in GSE7621 datasets, we identified two PD subtypes and explored potential biological pathways. Subsequently, using ClusterWGCNA, we pinpointed pertinent genes and developed clinical diagnostic models. We then optimized the chosen model and evaluated its association with immune infiltration. Validation was conducted using the GSE20163 dataset. Screening the single-cell dataset GSE132758 revealed cell populations associated with the identified gene. Results Our findings identified XGB as the optimal diagnostic model, with CAP2 identified as a pivotal gene. The risk model effectively predicted overall diagnosis rates, demonstrating a robust correlation between infiltrating immune cells and genes related to the XGB model. Discussion In conclusions, we identified PD subtypes and diagnostic genes associated with NETs, highlighting CAP2 as a pivotal gene. These findings have significant implications for understanding potential molecular mechanisms and treatments for PD.
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Affiliation(s)
| | | | | | | | | | | | - Yonghui Wang
- Rehabilitation Center, Qilu Hospital of Shandong University, Jinan, China
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3
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Khudayberdiev S, Weiss K, Heinze A, Colombaretti D, Trausch N, Linne U, Rust MB. The actin-binding protein CAP1 represses MRTF-SRF-dependent gene expression in mouse cerebral cortex. Sci Signal 2024; 17:eadj0032. [PMID: 38713765 DOI: 10.1126/scisignal.adj0032] [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: 05/31/2023] [Accepted: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Serum response factor (SRF) is an essential transcription factor for brain development and function. Here, we explored how an SRF cofactor, the actin monomer-sensing myocardin-related transcription factor MRTF, is regulated in mouse cortical neurons. We found that MRTF-dependent SRF activity in vitro and in vivo was repressed by cyclase-associated protein CAP1. Inactivation of the actin-binding protein CAP1 reduced the amount of actin monomers in the cytoplasm, which promoted nuclear MRTF translocation and MRTF-SRF activation. This function was independent of cofilin1 and actin-depolymerizing factor, and CAP1 loss of function in cortical neurons was not compensated by endogenous CAP2. Transcriptomic and proteomic analyses of cerebral cortex lysates from wild-type and Cap1 knockout mice supported the role of CAP1 in repressing MRTF-SRF-dependent signaling in vivo. Bioinformatic analysis identified likely MRTF-SRF target genes, which aligned with the transcriptomic and proteomic results. Together with our previous studies that implicated CAP1 in axonal growth cone function as well as the morphology and plasticity of excitatory synapses, our findings establish CAP1 as a crucial actin regulator in the brain relevant for formation of neuronal networks.
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Affiliation(s)
- Sharof Khudayberdiev
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Kerstin Weiss
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Anika Heinze
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Dalila Colombaretti
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Nathan Trausch
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
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4
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Wen-Jing Z, Rui-Zhi T, Si-Yuan H, Xiao-Mei D, Qiong-Dan H, Xiao-Qian Z, Wen-Hua H, Hong-Wei S, Jian L, Qiong Z, Li W. Data independent acquisition reveals in-depth serum proteome changes in uremic pruritus. Front Physiol 2024; 15:1287072. [PMID: 38577622 PMCID: PMC10991838 DOI: 10.3389/fphys.2024.1287072] [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: 09/01/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction: Uremic pruritus (UP) is a prevalent symptom in patients suffering from uremia, yet its underlying etiology and mechanisms remain incompletely elucidated. Given the significant incidence of UP, identifying specific alterations in proteins present in the blood of UP patients could offer insights into the potential biological pathways associated with UP and facilitate the exploration of biomarkers. Methods: In this study, we employed LC-MS/MS-based data-independent acquisition (DIA) mode to analyze serum samples obtained from 54 UP patients categorized as DKD-UP, HN-UP, and GN-UP (n = 18 for each subgroup), along with 18 uremic patients without pruritus (Negative) and 18 CKD patients without pruritus (CKD). Through DIA mode analysis, a total of 7075 peptides and 959 proteins were quantified. Within these, we identified four upregulated and 13 downregulated Differentially Expressed Proteins (DEPs) in DKD-UP versus Negative, five upregulated and 22 downregulated DEPs in HN-UP versus Negative, and three upregulated and 23 downregulated DEPs in GN-UP versus Negative. Furthermore, we conducted an intersection analysis of the DEPs across these three comparison groups to derive a set of common DEPs (COMP). Subsequently, a total of 67 common DEPs were identified in the three UP groups when compared to the CKD group, with 40 DEPs showing upregulation and 27 DEPs displaying downregulation. Results: Following Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein-Protein Interaction (PPI) analyses, we observed that the DEPs distinguishing UP from CKD were primarily associated with mitochondrial function (MT-CYB, PRDX2, TOMM22), inflammation (CD59, CSF1), renal injury (WFDC2), and neural function (CAP1, VGF). Discussion: Our findings contribute to a potential molecular comprehension of UP pathogenesis, shedding light on the identification of these DEPs as plausible biomarkers for UP.
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Affiliation(s)
- Zhao Wen-Jing
- Research Center of Intergated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
- Department of Nephrology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Tan Rui-Zhi
- Research Center of Intergated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - He Si-Yuan
- School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Du Xiao-Mei
- Department of Nephrology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Hu Qiong-Dan
- Research Center of Intergated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
- Department of Nephrology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Zhang Xiao-Qian
- Research Center of Intergated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
- Department of Nephrology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Huang Wen-Hua
- School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Su Hong-Wei
- Department of Urology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Liu Jian
- Department of Nephrology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Zhang Qiong
- Department of Nephrology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Wang Li
- Research Center of Intergated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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Heinze A, Rust MB. Loss of the actin regulator cyclase-associated protein 1 (CAP1) modestly affects dendritic spine remodeling during synaptic plasticity. Eur J Cell Biol 2023; 102:151357. [PMID: 37634312 DOI: 10.1016/j.ejcb.2023.151357] [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: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023] Open
Abstract
Dendritic spines form the postsynaptic compartment of most excitatory synapses in the vertebrate brain. Morphological changes of dendritic spines contribute to major forms of synaptic plasticity such as long-term potentiation (LTP) or depression (LTD). Synaptic plasticity underlies learning and memory, and defects in synaptic plasticity contribute to the pathogeneses of human brain disorders. Hence, deciphering the molecules that drive spine remodeling during synaptic plasticity is critical for understanding the neuronal basis of physiological and pathological brain function. Since actin filaments (F-actin) define dendritic spine morphology, actin-binding proteins (ABP) that accelerate dis-/assembly of F-actin moved into the focus as critical regulators of synaptic plasticity. We recently identified cyclase-associated protein 1 (CAP1) as a novel actin regulator in neurons that cooperates with cofilin1, an ABP relevant for synaptic plasticity. We therefore hypothesized a crucial role for CAP1 in structural synaptic plasticity. By exploiting mouse hippocampal neurons, we tested this hypothesis in the present study. We found that induction of both forms of synaptic plasticity oppositely altered concentration of exogenous, myc-tagged CAP1 in dendritic spines, with chemical LTP (cLTP) decreasing and chemical LTD (cLTD) increasing it. cLTP induced spine enlargement in CAP1-deficient neurons. However, it did not increase the density of large spines, different from control neurons. cLTD induced spine retraction and spine size reduction in control neurons, but not in CAP1-KO neurons. Together, we report that postsynaptic myc-CAP1 concentration oppositely changed during cLTP and cTLD and that CAP1 inactivation modestly affected structural plasticity.
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Affiliation(s)
- Anika Heinze
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany; Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032 Marburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany; Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032 Marburg, Germany.
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7
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Alimov N, Hoeprich GJ, Padrick SB, Goode BL. Cyclase-associated protein interacts with actin filament barbed ends to promote depolymerization and formin displacement. J Biol Chem 2023; 299:105367. [PMID: 37863260 PMCID: PMC10692737 DOI: 10.1016/j.jbc.2023.105367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023] Open
Abstract
Cyclase-associated protein (CAP) has emerged as a central player in cellular actin turnover, but its molecular mechanisms of action are not yet fully understood. Recent studies revealed that the N terminus of CAP interacts with the pointed ends of actin filaments to accelerate depolymerization in conjunction with cofilin. Here, we use in vitro microfluidics-assisted TIRF microscopy to show that the C terminus of CAP promotes depolymerization at the opposite (barbed) ends of actin filaments. In the absence of actin monomers, full-length mouse CAP1 and C-terminal halves of CAP1 (C-CAP1) and CAP2 (C-CAP2) accelerate barbed end depolymerization. Using mutagenesis and structural modeling, we show that these activities are mediated by the WH2 and CARP domains of CAP. In addition, we observe that CAP collaborates with profilin to accelerate barbed end depolymerization and that these effects depend on their direct interaction, providing the first known example of CAP-profilin collaborative effects in regulating actin. In the presence of actin monomers, CAP1 attenuates barbed end growth and promotes formin dissociation. Overall, these findings demonstrate that CAP uses distinct domains and mechanisms to interact with opposite ends of actin filaments and drive turnover. Further, they contribute to the emerging view of actin barbed ends as sites of dynamic molecular regulation, where numerous proteins compete and cooperate with each other to tune polymer dynamics, similar to the rich complexity seen at microtubule ends.
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Affiliation(s)
- Nikita Alimov
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Gregory J Hoeprich
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Shae B Padrick
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Bruce L Goode
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA.
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8
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Wales-McGrath B, Mercer H, Piontkivska H. Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections. BMC Genomics 2023; 24:685. [PMID: 37968596 PMCID: PMC10652522 DOI: 10.1186/s12864-023-09778-4] [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: 06/18/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND RNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data. RESULTS We found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding. CONCLUSIONS Our findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
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Affiliation(s)
- Benjamin Wales-McGrath
- University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA
- Children's Hospital of Philadelphia, Division of Cancer Pathobiology, Philadelphia, PA, USA
| | - Heather Mercer
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
- School of Biomedical Sciences, Kent State University, Kent, OH, USA.
- Brain Health Research Institute, Kent State University, Kent, OH, USA.
- Healthy Communities Research Institute, Kent State University, Kent, OH, USA.
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Gomila Pelegri N, Stanczak AM, Bottomley AL, Milthorpe BK, Gorrie CA, Padula MP, Santos J. Adipose-Derived Stem Cells Spontaneously Express Neural Markers When Grown in a PEG-Based 3D Matrix. Int J Mol Sci 2023; 24:12139. [PMID: 37569515 PMCID: PMC10418654 DOI: 10.3390/ijms241512139] [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: 07/03/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Neurological diseases are among the leading causes of disability and death worldwide and remain difficult to treat. Tissue engineering offers avenues to test potential treatments; however, the development of biologically accurate models of brain tissues remains challenging. Given their neurogenic potential and availability, adipose-derived stem cells (ADSCs) are of interest for creating neural models. While progress has been made in differentiating ADSCs into neural cells, their differentiation in 3D environments, which are more representative of the in vivo physiological conditions of the nervous system, is crucial. This can be achieved by modulating the 3D matrix composition and stiffness. Human ADSCs were cultured for 14 days in a 1.1 kPa polyethylene glycol-based 3D hydrogel matrix to assess effects on cell morphology, cell viability, proteome changes and spontaneous neural differentiation. Results showed that cells continued to proliferate over the 14-day period and presented a different morphology to 2D cultures, with the cells elongating and aligning with one another. The proteome analysis revealed 439 proteins changed in abundance by >1.5 fold. Cyclic nucleotide 3'-phosphodiesterase (CNPase) markers were identified using immunocytochemistry and confirmed with proteomics. Findings indicate that ADSCs spontaneously increase neural marker expression when grown in an environment with similar mechanical properties to the central nervous system.
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Affiliation(s)
- Neus Gomila Pelegri
- Advanced Tissue Engineering and Stem Cell Biology Group, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.G.P.); (B.K.M.)
- Neural Injury Research Unit, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Aleksandra M. Stanczak
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (A.M.S.); (M.P.P.)
| | - Amy L. Bottomley
- Microbial Imaging Facility, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Bruce K. Milthorpe
- Advanced Tissue Engineering and Stem Cell Biology Group, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.G.P.); (B.K.M.)
| | - Catherine A. Gorrie
- Neural Injury Research Unit, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia;
| | - Matthew P. Padula
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (A.M.S.); (M.P.P.)
| | - Jerran Santos
- Advanced Tissue Engineering and Stem Cell Biology Group, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (N.G.P.); (B.K.M.)
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10
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Schneider F, Metz I, Rust MB. Regulation of actin filament assembly and disassembly in growth cone motility and axon guidance. Brain Res Bull 2023; 192:21-35. [PMID: 36336143 DOI: 10.1016/j.brainresbull.2022.10.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Directed outgrowth of axons is fundamental for the establishment of neuronal networks. Axon outgrowth is guided by growth cones, highly motile structures enriched in filamentous actin (F-actin) located at the axons' distal tips. Growth cones exploit F-actin-based protrusions to scan the environment for guidance cues, and they contain the sensory apparatus to translate guidance cue information into intracellular signaling cascades. These cascades act upstream of actin-binding proteins (ABP) and thereby control assembly and disassembly of F-actin. Spatiotemporally controlled F-actin dis-/assembly in growth cones steers the axon towards attractants and away from repellents, and it thereby navigates the axon through the developing nervous system. Hence, ABP that control F-actin dynamics emerged as critical regulators of neuronal network formation. In the present review article, we will summarize and discuss current knowledge of the mechanisms that control remodeling of the actin cytoskeleton in growth cones, focusing on recent progress in the field. Further, we will introduce tools and techniques that allow to study actin regulatory mechanism in growth cones.
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Affiliation(s)
- Felix Schneider
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany; DFG Research Training Group 'Membrane Plasticity in Tissue Development and Remodeling', GRK 2213, Philipps-University of Marburg, 35032 Marburg, Germany; Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Isabell Metz
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany; DFG Research Training Group 'Membrane Plasticity in Tissue Development and Remodeling', GRK 2213, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany; DFG Research Training Group 'Membrane Plasticity in Tissue Development and Remodeling', GRK 2213, Philipps-University of Marburg, 35032 Marburg, Germany; Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032 Marburg, Germany.
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11
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Biswas D, Kumari N, Lachén-Montes M, Dutta S, Agrawal I, Samanta D, Shenoy SV, Halder A, Fernández-Irigoyen J, Padhye AR, Santamaría E, Srivastava S. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. J Proteome Res 2022; 22:1043-1055. [PMID: 36317652 DOI: 10.1021/acs.jproteome.2c00244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal (https://www.brainprot.org/) for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Neha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sampurna Dutta
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ishita Agrawal
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi221005, India
| | - Debabrata Samanta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal721302, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Advait Rahul Padhye
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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12
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Heinze A, Schuldt C, Khudayberdiev S, van Bommel B, Hacker D, Schulz TG, Stringhi R, Marcello E, Mikhaylova M, Rust MB. Functional interdependence of the actin regulators CAP1 and cofilin1 in control of dendritic spine morphology. Cell Mol Life Sci 2022; 79:558. [PMID: 36264429 PMCID: PMC9585016 DOI: 10.1007/s00018-022-04593-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 12/01/2022]
Abstract
The vast majority of excitatory synapses are formed on small dendritic protrusions termed dendritic spines. Dendritic spines vary in size and density that are crucial determinants of excitatory synaptic transmission. Aberrations in spine morphogenesis can compromise brain function and have been associated with neuropsychiatric disorders. Actin filaments (F-actin) are the major structural component of dendritic spines, and therefore, actin-binding proteins (ABP) that control F-actin dis-/assembly moved into the focus as critical regulators of brain function. Studies of the past decade identified the ABP cofilin1 as a key regulator of spine morphology, synaptic transmission, and behavior, and they emphasized the necessity for a tight control of cofilin1 to ensure proper brain function. Here, we report spine enrichment of cyclase-associated protein 1 (CAP1), a conserved multidomain protein with largely unknown physiological functions. Super-resolution microscopy and live cell imaging of CAP1-deficient hippocampal neurons revealed impaired synaptic F-actin organization and dynamics associated with alterations in spine morphology. Mechanistically, we found that CAP1 cooperates with cofilin1 in spines and that its helical folded domain is relevant for this interaction. Moreover, our data proved functional interdependence of CAP1 and cofilin1 in control of spine morphology. In summary, we identified CAP1 as a novel regulator of the postsynaptic actin cytoskeleton that is essential for synaptic cofilin1 activity.
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Affiliation(s)
- Anika Heinze
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany
| | - Cara Schuldt
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany
| | - Sharof Khudayberdiev
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany
| | - Bas van Bommel
- AG Optobiology, Institute of Biology, Humboldt-University, 10115, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Daniela Hacker
- AG Optobiology, Institute of Biology, Humboldt-University, 10115, Berlin, Germany
- Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany
| | - Toni G Schulz
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany
| | - Ramona Stringhi
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133, Milan, Italy
| | - Elena Marcello
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133, Milan, Italy
| | - Marina Mikhaylova
- AG Optobiology, Institute of Biology, Humboldt-University, 10115, Berlin, Germany
- Guest Group 'Neuronal Protein Transport', Institute for Molecular Neurogenetics, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032, Marburg, Germany.
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032, Marburg, Germany.
- DFG Research Training Group 'Membrane Plasticity in Tissue Development and Remodeling', GRK 2213, Philipps-University of Marburg, 35032, Marburg, Germany.
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13
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Wurz AI, Schulz AM, O’Bryant CT, Sharp JF, Hughes RM. Cytoskeletal dysregulation and neurodegenerative disease: Formation, monitoring, and inhibition of cofilin-actin rods. Front Cell Neurosci 2022; 16:982074. [PMID: 36212686 PMCID: PMC9535683 DOI: 10.3389/fncel.2022.982074] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/31/2022] [Indexed: 12/04/2022] Open
Abstract
The presence of atypical cytoskeletal dynamics, structures, and associated morphologies is a common theme uniting numerous diseases and developmental disorders. In particular, cytoskeletal dysregulation is a common cellular feature of Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease. While the numerous activators and inhibitors of dysregulation present complexities for characterizing these elements as byproducts or initiators of the disease state, it is increasingly clear that a better understanding of these anomalies is critical for advancing the state of knowledge and plan of therapeutic attack. In this review, we focus on the hallmarks of cytoskeletal dysregulation that are associated with cofilin-linked actin regulation, with a particular emphasis on the formation, monitoring, and inhibition of cofilin-actin rods. We also review actin-associated proteins other than cofilin with links to cytoskeleton-associated neurodegenerative processes, recognizing that cofilin-actin rods comprise one strand of a vast web of interactions that occur as a result of cytoskeletal dysregulation. Our aim is to present a current perspective on cytoskeletal dysregulation, connecting recent developments in our understanding with emerging strategies for biosensing and biomimicry that will help shape future directions of the field.
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Affiliation(s)
- Anna I. Wurz
- Department of Chemistry, East Carolina University, Greenville, NC, United States
| | - Anna M. Schulz
- Department of Chemistry, East Carolina University, Greenville, NC, United States
| | - Collin T. O’Bryant
- Department of Chemistry, East Carolina University, Greenville, NC, United States
| | - Josephine F. Sharp
- Department of Chemistry, Notre Dame College, South Euclid, OH, United States
| | - Robert M. Hughes
- Department of Chemistry, East Carolina University, Greenville, NC, United States
- *Correspondence: Robert M. Hughes,
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14
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Xie Y, Liu Y, Ding J, Li G, Ni B, Pang H, Hu X, Wu L. Identification of DDX31 as a Potential Oncogene of Invasive Metastasis and Proliferation in PDAC. Front Cell Dev Biol 2022; 10:762372. [PMID: 35237592 PMCID: PMC8883474 DOI: 10.3389/fcell.2022.762372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/11/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignant tumors worldwide and has poor prognosis. DEAD box proteins31 (DDX31) participate in cellular processes involving RNA secondary structure changes. However, the functions of DDX31 in PDAC remain to be elucidated. Methods: The key gene DDX31 was identified using a combination of a risk model and weighted gene co-expression network analysis (WGCNA) with R software. The biological functions of DDX31 in PDAC were investigated through bioinformatics analysis and in vitro experiments. Results: Combining with WGCNA and risk model, DDX31 was identified as a potential factor of the invasive metastasis properties of PDAC, and its expression was closely related to the malignant differentiation of PDAC. The results of gene set enrichment analysis (GSEA) showed that DDX31 was correlated with cell invasive metastasis and proliferation by activating MAPK signaling pathway. The inhibition of DDX31 inhibited the invasion and migration of PDAC cells. Survival analysis showed that DDX31 expression was negatively associated with the poor prognosis in patients with PDAC. Interpretation:DDX31 may be a potential factor for PDAC. The inhibition of DDX31 may be a potential way to treat PDAC.
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Affiliation(s)
- Yongjie Xie
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Yang Liu
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Jinsheng Ding
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Guangming Li
- Department of General Surgery, Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Ni
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Huifang Pang
- Department of Gastroenterology, Digestive Endoscopy Unit, Tongliao City Hospital, Tongliao, China
| | - Xin Hu
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, China
| | - Liangliang Wu
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention, Department of Gastric Cancer, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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15
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Rust MB, Marcello E. Disease association of cyclase-associated protein (CAP): Lessons from gene-targeted mice and human genetic studies. Eur J Cell Biol 2022; 101:151207. [PMID: 35150966 DOI: 10.1016/j.ejcb.2022.151207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/03/2022] Open
Abstract
Cyclase-associated protein (CAP) is an actin binding protein that has been initially described as partner of the adenylyl cyclase in yeast. In all vertebrates and some invertebrate species, two orthologs, named CAP1 and CAP2, have been described. CAP1 and CAP2 are characterized by a similar multidomain structure, but different expression patterns. Several molecular studies clarified the biological function of the different CAP domains, and they shed light onto the mechanisms underlying CAP-dependent regulation of actin treadmilling. However, CAPs are crucial elements not only for the regulation of actin dynamics, but also for signal transduction pathways. During recent years, human genetic studies and the analysis of gene-targeted mice provided important novel insights into the physiological roles of CAPs and their involvement in the pathogenesis of several diseases. In the present review, we summarize and discuss recent progress in our understanding of CAPs' physiological functions, focusing on heart, skeletal muscle and central nervous system as well as their involvement in the mechanisms controlling metabolism. Remarkably, loss of CAPs or impairment of CAPs-dependent pathways can contribute to the pathogenesis of different diseases. Overall, these studies unraveled CAPs complexity highlighting their capability to orchestrate structural and signaling pathways in the cells.
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Affiliation(s)
- Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany; Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, 35032 Marburg, Germany; DFG Research Training Group 'Membrane Plasticity in Tissue Development and Remodeling', GRK 2213, Philipps-University of Marburg, 35032 Marburg, Germany.
| | - Elena Marcello
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy.
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