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El Sharkawy M, Felix JF, Grote V, Voortman T, Jaddoe VWV, Koletzko B, Küpers LK. Animal and plant protein intake during infancy and childhood DNA methylation: a meta-analysis in the NutriPROGRAM consortium. Epigenetics 2024; 19:2299045. [PMID: 38198623 PMCID: PMC10793674 DOI: 10.1080/15592294.2023.2299045] [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: 03/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Higher early-life animal protein intake is associated with a higher childhood obesity risk compared to plant protein intake. Differential DNA methylation may represent an underlying mechanism. METHODS We analysed associations of infant animal and plant protein intakes with DNA methylation in early (2-6 years, N = 579) and late (7̄-12 years, N = 604) childhood in two studies. Study-specific robust linear regression models adjusted for relevant confounders were run, and then meta-analysed using a fixed-effects model. We also performed sex-stratified meta-analyses. Follow-up analyses included pathway analysis and eQTM look-up. RESULTS Infant animal protein intake was not associated with DNA methylation in early childhood, but was associated with late-childhood DNA methylation at cg21300373 (P = 4.27 × 10¯8, MARCHF1) and cg10633363 (P = 1.09 × 10¯7, HOXB9) after FDR correction. Infant plant protein intake was associated with early-childhood DNA methylation at cg25973293 (P = 2.26 × 10-7, C1orf159) and cg15407373 (P = 2.13 × 10-7, MBP) after FDR correction. There was no overlap between the findings from the animal and plant protein analyses. We did not find enriched functional pathways at either time point using CpGs associated with animal and plant protein. These CpGs were not previously associated with childhood gene expression. Sex-stratified meta-analyses showed sex-specific DNA methylation associations for both animal and plant protein intake. CONCLUSION Infant animal protein intake was associated with DNA methylation at two CpGs in late childhood. Infant plant protein intake was associated with DNA methylation in early childhood at two CpGs. A potential mediating role of DNA methylation at these CpGs between infant protein intake and health outcomes requires further investigation.
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Affiliation(s)
- Mohammed El Sharkawy
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
- Munich Medical Research School, Faculty of Medicine, LMU - Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Leanne K. Küpers
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Lu Y, Berenson A, Lane R, Guelin I, Li Z, Chen Y, Shah S, Yin M, Soto-Ugaldi LF, Fiszbein A, Fuxman Bass JI. A large-scale cancer-specific protein-DNA interaction network. Life Sci Alliance 2024; 7:e202402641. [PMID: 39013578 PMCID: PMC11252446 DOI: 10.26508/lsa.202402641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
Cancer development and progression are generally associated with gene dysregulation, often resulting from changes in the transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network, as well as an extensive promoter clone resource for future studies. Highly connected TFs bind to promoters of genes associated with either good or poor cancer prognosis, suggesting that strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene-targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activators or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF ESR1 in DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study broadens our knowledge of the TFs involved in cancer gene regulation and provides a valuable resource for future studies and therapeutics.
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Affiliation(s)
- Yunwei Lu
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Anna Berenson
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Ryan Lane
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Isabelle Guelin
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Zhaorong Li
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
| | - Yilin Chen
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Sakshi Shah
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | - Meimei Yin
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
| | | | - Ana Fiszbein
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
| | - Juan Ignacio Fuxman Bass
- https://ror.org/05qwgg493 Biology Department, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- https://ror.org/05qwgg493 Bioinformatics Program, Boston University, Boston, MA, USA
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3
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Sagredo GT, Tanglay O, Shahdadpuri S, Fu Y, Halliday GM. ⍺-Synuclein levels in Parkinson's disease - Cell types and forms that contribute to pathogenesis. Exp Neurol 2024; 379:114887. [PMID: 39009177 DOI: 10.1016/j.expneurol.2024.114887] [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: 04/02/2024] [Revised: 06/28/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024]
Abstract
Parkinson's disease (PD) has two main pathological hallmarks, the loss of nigral dopamine neurons and the proteinaceous aggregations of ⍺-synuclein (⍺Syn) in neuronal Lewy pathology. These two co-existing features suggest a causative association between ⍺Syn aggregation and the underpinning mechanism of neuronal degeneration in PD. Both increased levels and post-translational modifications of ⍺Syn can contribute to the formation of pathological aggregations of ⍺Syn in neurons. Recent studies have shown that the protein is also expressed by multiple types of non-neuronal cells in the brain and peripheral tissues, suggesting additional roles of the protein and potential diversity in non-neuronal pathogenic triggers. It is important to determine (1) the threshold levels triggering ⍺Syn to convert from a biological to a pathologic form in different brain cells in PD; (2) the dominant form of pathologic ⍺Syn and the associated post-translational modification of the protein in each cell type involved in PD; and (3) the cell type associated biological processes impacted by pathologic ⍺Syn in PD. This review integrates these aspects and speculates on potential pathological mechanisms and their impact on neuronal and non-neuronal ⍺Syn in the brains of patients with PD.
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Affiliation(s)
- Giselle Tatiana Sagredo
- The University of Sydney, Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, Sydney, NSW, Australia; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, United States of America
| | - Onur Tanglay
- The University of Sydney, Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, Sydney, NSW, Australia
| | - Shrey Shahdadpuri
- The University of Sydney, Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, Sydney, NSW, Australia
| | - YuHong Fu
- The University of Sydney, Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, Sydney, NSW, Australia; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, United States of America
| | - Glenda M Halliday
- The University of Sydney, Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, Sydney, NSW, Australia; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, United States of America.
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Ma Q, Chen G, Li Y, Guo Z, Zhang X. The molecular genetics of PI3K/PTEN/AKT/mTOR pathway in the malformations of cortical development. Genes Dis 2024; 11:101021. [PMID: 39006182 PMCID: PMC11245990 DOI: 10.1016/j.gendis.2023.04.041] [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: 12/07/2022] [Revised: 04/07/2023] [Accepted: 04/30/2023] [Indexed: 07/16/2024] Open
Abstract
Malformations of cortical development (MCD) are a group of developmental disorders characterized by abnormal cortical structures caused by genetic or harmful environmental factors. Many kinds of MCD are caused by genetic variation. MCD is the common cause of intellectual disability and intractable epilepsy. With rapid advances in imaging and sequencing technologies, the diagnostic rate of MCD has been increasing, and many potential genes causing MCD have been successively identified. However, the high genetic heterogeneity of MCD makes it challenging to understand the molecular pathogenesis of MCD and to identify effective targeted drugs. Thus, in this review, we outline important events of cortical development. Then we illustrate the progress of molecular genetic studies about MCD focusing on the PI3K/PTEN/AKT/mTOR pathway. Finally, we briefly discuss the diagnostic methods, disease models, and therapeutic strategies for MCD. The information will facilitate further research on MCD. Understanding the role of the PI3K/PTEN/AKT/mTOR pathway in MCD could lead to a novel strategy for treating MCD-related diseases.
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Affiliation(s)
- Qing Ma
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Guang Chen
- Department of Urology, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Ying Li
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150000, China
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Zhenming Guo
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xue Zhang
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150000, China
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Martins P, D'Souza RCJ, Skarne N, Lekieffre L, Horsefield S, Ranjankumar M, Li X, Le TT, Smith F, Smith C, Burrows J, Day BW, Khanna R. EphA3 CAR T cells are effective against glioblastoma in preclinical models. J Immunother Cancer 2024; 12:e009403. [PMID: 39111832 DOI: 10.1136/jitc-2024-009403] [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] [Accepted: 07/18/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Adoptive T-cell therapy targeting antigens expressed in glioblastoma has emerged as a potential therapeutic strategy to prevent or delay recurrence and prolong overall survival in this aggressive disease setting. Ephrin receptor A3 (EphA3), which is highly expressed in glioblastoma; in particular, on the tumor vasculature and brain cancer stem cells, is an ideal target for immune-based therapies. METHODS We have designed an EphA3-targeted chimeric antigen receptor (CAR) using the single chain variable fragment of a novel monoclonal antibody, and assessed its therapeutic potential against EphA3-expressing patient-derived glioblastoma neurospheres, organoids and xenografted glioblastoma tumors in immunodeficient mice. RESULTS In vitro expanded EphA3 CAR T cells from healthy individuals efficiently recognize and kill EphA3-positive glioblastoma cells in vitro. Furthermore, these effector cells demonstrated curative efficacy in an orthotopic xenograft model of glioblastoma. EphA3 CAR T cells were equally effective in targeting patient-derived neurospheres and infiltrate, disaggregate, and induce apoptosis in glioblastoma-derived organoids. CONCLUSIONS This study provides compelling evidence supporting the therapeutic potential of EphA3 CAR T-cell therapy against glioblastoma by targeting EphA3 associated with brain cancer stem cells and the tumor vasculature. The ability to target patient-derived glioblastoma underscores the translational significance of this EphA3 CAR T-cell therapy in the pursuit of effective and targeted glioblastoma treatment strategies.
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Affiliation(s)
- Paulo Martins
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- The University of Queensland, Brisbane, Queensland, Australia
| | | | - Niclas Skarne
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Lea Lekieffre
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Shane Horsefield
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xiang Li
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Thuy T Le
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Fiona Smith
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Corey Smith
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jacqueline Burrows
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Bryan W Day
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Sid Faithfull Brain Cancer Laboratory, Brisbane, Queensland, Australia
| | - Rajiv Khanna
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- The University of Queensland, Brisbane, Queensland, Australia
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6
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Cho BPH, Auckland K, Gräf S, Markus HS. Rare Sequence Variation Underlying Suspected Familial Cerebral Small-Vessel Disease. J Am Heart Assoc 2024; 13:e035771. [PMID: 39082428 DOI: 10.1161/jaha.123.035771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Cerebral small-vessel disease (cSVD) is the leading monogenic cause of stroke. Despite genetic screening in routine diagnosis, many cases remain without a known causative variant. Using a cohort with suspected familial cSVD and whole-genome sequencing, we screened for variants in genes associated with monogenic cSVD and searched for novel variants associated with the disease. METHODS AND RESULTS Rare variants were identified in whole-genome sequencing data from the NBR (National Institute for Health Research BioResource Rare Disease) study. Pathogenic variants in known monogenic cSVD genes were identified. Gene-based burden tests and family analysis were performed to identify novel variants associated with familial cSVD. A total of 257 suspected cSVD cases (mean ± SD age, 56.2 ± 16.1 years), and 13 086 controls with other nonstroke diseases (5874 [44.9%] men) were studied. A total of 8.9% of the cases carried a variant in known cSVD genes. Excluding these known causes, 23.6% of unrelated subjects with cSVD carried predicted deleterious variants in the Genomics England gene panel, but no association was found with cSVD in burden tests. We identified potential associations with cSVD in noncoding genes, including RP4-568F9.3 (adjusted P = 7.1 × 10-25), RP3-466I7.1 (adjusted P = 8.9 × 10-16), and ZNF209P (adjusted P = 1.0 × 10-15), and matrisomal genes (adjusted P = 5.1 × 10-6), including FAM20C, INHA, LAMC1, and VWA5B2. CONCLUSIONS Predicted deleterious variants in known cSVD genes were present in 23.6% of unrelated cases with cSVD, but none of the genes were associated with the disease. Rare variants in noncoding and matrisomal genes could potentially contribute to cSVD development. These genes could play a role in tissue development and brain endothelial cell function. However, further studies are needed to confirm their pathophysiological roles.
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Affiliation(s)
- Bernard P H Cho
- Stroke Research Group Department of Clinical Neurosciences University of Cambridge Cambridge UK
| | - Kate Auckland
- Department of Medicine University of Cambridge Victor Phillip Dahdaleh Heart and Lung Research Institute Cambridge UK
| | - Stefan Gräf
- Department of Medicine University of Cambridge Victor Phillip Dahdaleh Heart and Lung Research Institute Cambridge UK
| | - Hugh S Markus
- Stroke Research Group Department of Clinical Neurosciences University of Cambridge Cambridge UK
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7
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Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024; 20:972-995. [PMID: 38907068 PMCID: PMC11297287 DOI: 10.1038/s44320-024-00050-9] [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: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
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Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
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8
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Fareed SA, Yousef EM, Abd El-Moneam SM. Effects of prolonged hydroxychloroquine use on the pancreatic tissue and expected ameliorative effect of lactoferrin in rats (biochemical, histological, and morphometric study). Tissue Cell 2024; 89:102439. [PMID: 38889555 DOI: 10.1016/j.tice.2024.102439] [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: 01/07/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
Hydroxychloroquine (HCQ), an antimalarial drug widely used in treating rheumatoid disorders. Many side effects have been reported with HCQ administration indicating its hazardous effects on various organs. No previous studies reported the effect of long-term administration of oral HCQ on pancreatic tissue. Our study assessed pancreatic tissues functional and histopathological alterations following prolonged oral administration of HCQ. We also investigated the possible ameliorative effects of the lactoferrin (LF) coadministration with HCQ in adult male albino rats. Forty adult male Wister albino rats were divided into: negative control, LF positive control (2 g/kg), HCQ-treated (200 mg/kg), and HCQ+LF treated. Biochemical, histological, immunohistochemical, and morphometric analyses of the pancreatic tissues were conducted. Our findings revealed that prolonged oral administration of HCQ induced significant disruption of the pancreatic acinar architecture, enlarged congested islets of Langerhans, and elevated plasma insulin, amylase, and lipase levels. Interestingly, LF administration ameliorated the deleterious effects of prolonged HCQ administration on pancreatic tissue of adult male albino rats. In conclusion, prolonged oral administration of HCQ induced pancreatic tissue damage in rats, while LF attenuates HCQ-induced pancreatic injury. Our results emphasized the necessity of prescribing HCQ with caution, considering both dosage and treatment duration.
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Affiliation(s)
- Shimaa Antar Fareed
- Department of Human Anatomy & Embryology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Einas Mohamed Yousef
- Department of Histology and Cell Biology, Faculty of Medicine, Menoufia University, Menoufia, Egypt.
| | - Samar M Abd El-Moneam
- Department of Human Anatomy & Embryology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
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Hirata K, Matsuoka K, Tagai K, Endo H, Tatebe H, Ono M, Kokubo N, Kataoka Y, Oyama A, Shinotoh H, Takahata K, Obata T, Dehghani M, Near J, Kawamura K, Zhang MR, Shimada H, Shimizu H, Kakita A, Yokota T, Tokuda T, Higuchi M, Takado Y. In Vivo Assessment of Astrocyte Reactivity in Patients with Progressive Supranuclear Palsy. Ann Neurol 2024; 96:247-261. [PMID: 38771066 DOI: 10.1002/ana.26962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/12/2024] [Accepted: 04/16/2024] [Indexed: 05/22/2024]
Abstract
OBJECTIVE Although astrocytic pathology is a pathological hallmark of progressive supranuclear palsy (PSP), its pathophysiological role remains unclear. This study aimed to assess astrocyte reactivity in vivo in patients with PSP. Furthermore, we investigated alterations in brain lactate levels and their relationship with astrocyte reactivity. METHODS We included 30 patients with PSP-Richardson syndrome and 30 healthy controls; in patients, tau deposition was confirmed through 18F-florzolotau positron emission tomography. Myo-inositol, an astroglial marker, and lactate were quantified in the anterior cingulate cortex through magnetic resonance spectroscopy. We measured plasma biomarkers, including glial fibrillary acidic protein as another astrocytic marker. The anterior cingulate cortex was histologically assessed in postmortem samples of another 3 patients with PSP with comparable disease durations. RESULTS The levels of myo-inositol and plasma glial fibrillary acidic protein were significantly higher in patients than those in healthy controls (p < 0.05); these increases were significantly associated with PSP rating scale and cognitive function scores (p < 0.05). The lactate level was high in patients, and correlated significantly with high myo-inositol levels. Histological analysis of the anterior cingulate cortex in patients revealed reactive astrocytes, despite mild tau deposition, and no marked synaptic loss. INTERPRETATION We discovered high levels of astrocyte biomarkers in patients with PSP, suggesting astrocyte reactivity. The association between myo-inositol and lactate levels suggests a link between reactive astrocytes and brain energy metabolism changes. Our results indicate that astrocyte reactivity in the anterior cingulate cortex precedes pronounced tau pathology and neurodegenerative processes in that region, and affects brain function in PSP. ANN NEUROL 2024;96:247-261.
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Affiliation(s)
- Kosei Hirata
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kiwamu Matsuoka
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Kenji Tagai
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Hironobu Endo
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Harutsugu Tatebe
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Maiko Ono
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naomi Kokubo
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yuko Kataoka
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Asaka Oyama
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Hitoshi Shinotoh
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Neurology Clinic Chiba, Chiba, Japan
| | - Keisuke Takahata
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takayuki Obata
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | | | - Jamie Near
- Physical Sciences, Sunnybrook Research Institute, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Kazunori Kawamura
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Ming-Rong Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Hitoshi Shimada
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Center for integrated human brain science, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroshi Shimizu
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Tokuda
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Makoto Higuchi
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yuhei Takado
- Advanced Neuroimaging Center, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
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10
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Radivojević I, Stojilković N, Antonijević-Miljaković E, Đorđević AB, Baralić K, Ćurčić M, Marić Đ, Đukić-Ćosić D, Bulat Z, Durgo K, Antonijević B. In silico attempt to reveal the link between cancer development and combined exposure to the maize herbicides: Glyphosate, nicosulfuron, S-metolachlor and terbuthylazine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175187. [PMID: 39094656 DOI: 10.1016/j.scitotenv.2024.175187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/27/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Pesticides are crucial for crop protection and have seen a 50 % increase in use in the last decade. Besides preventing significant crop losses their use has raised health concerns due to consumer exposure through residues in food and water. The toxicity data from individual components is often used to assess overall mixture toxicity, but uncertainty persists in understanding the behaviors of individual chemicals within these mixtures. Assessing the risk of pesticide mixture exposure remains challenging, potentially leading to overestimation or underestimation of toxicity. This study aims to establish a possible link between exposure to a herbicide mixture and genotoxic effects, focusing on cancer development. Our analysis was focused on four herbicides glyphosate, nicosulfuron, S-metolachlor and terbuthylazine. To determine the link between genes associated with cancer development due to exposure to herbicide mixture, a CTD database tools were used. Through the ToppFun tool molecular function and biological process associated with genes common to the disease of interest and selected herbicides were evaluated. And finally, GeneMANIA was used in order to analyze the function and interaction between common genes of herbicide mixture. Among the 7 common genes for herbicide mixture and cancer development coexpression characteristics were dominant at 65.41 %, 22.14 % of annotated genes shared the same pathway and 7.88 % showed co-localization. Among six target genes involved in genetic disease development co-expression was dominant at 87.34 %, colocalization at 8.03 % and shared protein domains at 4.52 %. Comprehensive molecular analyses, encompassing genomics, proteomics, and pathway analysis, are essential to unravel the specific mechanisms involved in the context of the studied mixture and its potential carcinogenic effects.
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Affiliation(s)
- Ivana Radivojević
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia.
| | - Nikola Stojilković
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Evica Antonijević-Miljaković
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Aleksandra Buha Đorđević
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Katarina Baralić
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Marijana Ćurčić
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Đurđica Marić
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Danijela Đukić-Ćosić
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Zorica Bulat
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Ksenija Durgo
- Faculty of food technology and biotechnology, University of Zagreb, Pierottijeva street 6, 10000 Zagreb, Croatia
| | - Biljana Antonijević
- Department of Toxicology "Akademik Danilo Soldatović", Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
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11
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Mondal A, Munan S, Saxena I, Mukherjee S, Upadhyay P, Gupta N, Dar W, Samanta A, Singh S, Pati S. G6PD deficiency mediated impairment of iNOS and lysosomal acidification affecting phagocytotic clearance in microglia in response to SARS-CoV-2. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167444. [PMID: 39074627 DOI: 10.1016/j.bbadis.2024.167444] [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: 01/24/2024] [Revised: 06/30/2024] [Accepted: 07/25/2024] [Indexed: 07/31/2024]
Abstract
The glucose-6-phosphate dehydrogenase (G6PD) deficiency is X-linked and is the most common enzymatic deficiency disorder globally. It is a crucial enzyme for the pentose phosphate pathway and produces NADPH, which plays a vital role in regulating the oxidative stress of many cell types. The deficiency of G6PD primarily causes hemolytic anemia under oxidative stress triggered by food, drugs, or infection. G6PD-deficient patients infected with SARS-CoV-2 showed an increase in hemolysis and thrombosis. Patients also exhibited prolonged COVID-19 symptoms, ventilation support, neurological impacts, and high mortality. However, the mechanism of COVID-19 severity in G6PD deficient patients and its neurological manifestation is still ambiguous. Here, using a CRISPR-edited G6PD deficient human microglia cell culture model, we observed a significant reduction in NADPH level and an increase in basal reactive oxygen species (ROS) in microglia. Interestingly, the deficiency of the G6PD-NAPDH axis impairs induced nitric oxide synthase (iNOS) mediated nitric oxide (NO) production, which plays a fundamental role in inhibiting viral replication. Surprisingly, we also observed that the deficiency of the G6PD-NADPH axis reduced lysosomal acidification and free radical production, further abrogating the lysosomal clearance of viral particles. Thus, impairment of NO production, lysosomal functions, and redox dysregulation in G6PD deficient microglia altered innate immune response, promoting the severity of SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Abir Mondal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Subrata Munan
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Isha Saxena
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Soumyadeep Mukherjee
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Prince Upadhyay
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Nutan Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Waseem Dar
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Animesh Samanta
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
| | - Soumya Pati
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida UP-201301, India.
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12
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Zhao X, Zhao Y, Zhang Y, Fan Q, Ke H, Chen X, Jin L, Tang H, Jiang Y, Ma J. Unraveling pathogenesis, biomarkers and potential therapeutic agents for endometriosis associated with disulfidptosis based on bioinformatics analysis, machine learning and experiment validation. J Biol Eng 2024; 18:42. [PMID: 39061076 PMCID: PMC11282767 DOI: 10.1186/s13036-024-00437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Endometriosis (EMs) is an enigmatic disease of yet-unknown pathogenesis. Disulfidptosis, a novel identified form of programmed cell death resulting from disulfide stress, stands a chance of treating diverse ailments. However, the potential roles of disulfidptosis-related genes (DRGs) in EMs remain elusive. This study aims to thoroughly explore the key disulfidptosis genes involved in EMs, and probe novel diagnostic markers and candidate therapeutic compounds from the aspect of disulfidptosis based on bioinformatics analysis, machine learning, and animal experiments. RESULTS Enrichment analysis on key module genes and differentially expressed genes (DEGs) of eutopic and ectopic endometrial tissues in EMs suggested that EMs was closely related to disulfidptosis. And then, we obtained 20 and 16 disulfidptosis-related DEGs in eutopic and ectopic endometrial tissue, respectively. The protein-protein interaction (PPI) network revealed complex interactions between genes, and screened nine and ten hub genes in eutopic and ectopic endometrial tissue, respectively. Furthermore, immune infiltration analysis uncovered distinct differences in the immunocyte, human leukocyte antigen (HLA) gene set, and immune checkpoints in the eutopic and ectopic endometrial tissues when compared with health control. Besides, the hub genes mentioned above showed a close correlation with the immune microenvironment of EMs. Furthermore, four machine learning algorithms were applied to screen signature genes in eutopic and ectopic endometrial tissue, including the binary logistic regression (BLR), the least absolute shrinkage and selection operator (LASSO), the support vector machine-recursive feature elimination (SVM-RFE), and the extreme gradient boosting (XGBoost). Model training and hyperparameter tuning were implemented on 80% of the data using a ten-fold cross-validation method, and tested in the testing sets which determined the excellent diagnostic performance of these models by six indicators (Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, Accuracy, and Area Under Curve). And seven eutopic signature genes (ACTB, GYS1, IQGAP1, MYH10, NUBPL, SLC7A11, TLN1) and five ectopic signature genes (CAPZB, CD2AP, MYH10, OXSM, PDLIM1) were finally identified based on machine learning. The independent validation dataset also showed high accuracy of the signature genes (IQGAP1, SLC7A11, CD2AP, MYH10, PDLIM1) in predicting EMs. Moreover, we screened 12 specific compounds for EMs based on ectopic signature genes and the pharmacological impact of tretinoin on signature genes was further verified in the ectopic lesion in the EMs murine model. CONCLUSION This study verified a close association between disulfidptosis and EMs based on bioinformatics analysis, machine learning, and animal experiments. Further investigation on the biological mechanism of disulfidptosis in EMs is anticipated to yield novel advancements for searching for potential diagnostic biomarkers and revolutionary therapeutic approaches in EMs.
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Affiliation(s)
- Xiaoxuan Zhao
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
- Research Institute of Women's Reproductive Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yang Zhao
- The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanyuan Zhang
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingnan Fan
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Huanxiao Ke
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaowei Chen
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Linxi Jin
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hongying Tang
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuepeng Jiang
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Jing Ma
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China.
- Research Institute of Women's Reproductive Health, Zhejiang Chinese Medical University, Hangzhou, China.
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13
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Fernandes EFA, Palner M, Raval NR, Jeppesen TE, Danková D, Bærentzen SL, Werner C, Eilts J, Maric HM, Doose S, Aripaka SS, Kaalund SS, Aznar S, Kjaer A, Schlosser A, Haugaard-Kedström LM, Knudsen GM, Herth MM, Stro Mgaard K. Development of Peptide-Based Probes for Molecular Imaging of the Postsynaptic Density in the Brain. J Med Chem 2024; 67:11975-11988. [PMID: 38981131 DOI: 10.1021/acs.jmedchem.4c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The postsynaptic density (PSD) comprises numerous scaffolding proteins, receptors, and signaling molecules that coordinate synaptic transmission in the brain. Postsynaptic density protein 95 (PSD-95) is a master scaffold protein within the PSD and one of its most abundant proteins and therefore constitutes a very attractive biomarker of PSD function and its pathological changes. Here, we exploit a high-affinity inhibitor of PSD-95, AVLX-144, as a template for developing probes for molecular imaging of the PSD. AVLX-144-based probes were labeled with the radioisotopes fluorine-18 and tritium, as well as a fluorescent tag. Tracer binding showed saturable, displaceable, and uneven distribution in rat brain slices, proving effective in quantitative autoradiography and cell imaging studies. Notably, we observed diminished tracer binding in human post-mortem Parkinson's disease (PD) brain slices, suggesting postsynaptic impairment in PD. We thus offer a suite of translational probes for visualizing and understanding PSD-related pathologies.
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Affiliation(s)
- Eduardo F A Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Mikael Palner
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Nakul Ravi Raval
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, Connecticut 06520, United States
| | - Troels E Jeppesen
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Daniela Danková
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Simone L Bærentzen
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Christian Werner
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Janna Eilts
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Hans M Maric
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University, Josef-Schneider-Str. 2, Würzburg 97080, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Sanjay Sagar Aripaka
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Sanne Simone Kaalund
- Center for Neuroscience and Stereology, Bispebjerg University Hospital, Nielsine Nielsens Vej 6B, Copenhagen DK-2400, Denmark
| | - Susana Aznar
- Center for Neuroscience and Stereology, Bispebjerg University Hospital, Nielsine Nielsens Vej 6B, Copenhagen DK-2400, Denmark
- Center for Translational Research, Bispebjerg University Hospital, Nielsine Nielsens Vej 4B, Copenhagen DK-2400, Denmark
| | - Andreas Kjaer
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Andreas Schlosser
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Linda M Haugaard-Kedström
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Gitte M Knudsen
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Matthias M Herth
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Kristian Stro Mgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
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14
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Zheng X, Wang Y, Qiu X. Comprehensive analysis of MAPK genes in the prognosis, immune characteristics, and drug treatment of renal clear cell carcinoma using bioinformatic analysis and Mendelian randomization. Eur J Pharmacol 2024; 980:176840. [PMID: 39038636 DOI: 10.1016/j.ejphar.2024.176840] [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: 01/23/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
Mitogen-activated protein kinase (MAPK) signalling is vitally important in tumour development and progression. This study is the first to comprehensively analyse the role of MAPK-family genes in the progression, prognosis, immune-cell infiltration, methylation, and potential therapeutic value drug candidates in ccRCC. We identified a novel prognostic panel of six MAPK-signature genes (MAP3K12, MAP3K1, MAP3K5, MAPK1, MAPK8, MAPK9), and introduced a robust MAPK-signature risk model for predicting ccRCC prognosis. Model construction, evaluation, and external validation using datasets from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database demonstrated its stability, as well as high sensitivity and specificity. Enrichment analysis suggested the participation of immune-mediated mechanism in MAPK dysregulation in ccRCC. Immune-infiltration analysis confirmed the relationship and revealed that the MAPK-signature risk model might stratify immunotherapy response in ccRCC, which was verified in drug sensitivity analysis and validated in external ccRCC immunotherapy dataset (GSE67501). Potential therapeutic drug predictions for key MAPKs using DSigDB, Network Analyst, CTD, and DGIdb were subsequently verified by molecular docking with AutoDock Vina and PyMol. Mendelian randomization further demonstrated the possibilities of the MAPK-signature genes as targets for therapeutic drugs in ccRCC. Methylation analysis using UALCAN and MethSurv revealed the participation of epigenetic modifications in dysregulation and survival difference of MAPK pathway in ccRCC. Among the key MAPKs, MAP3K12 exhibited the highest significance, indicating its independent prognostic value as single gene in ccRCC. Knockout and overexpression validation experiments in vitro and in vivo found that MAP3K12 acted as a promoter of tumour progression in RCC, suggesting a pivotal role for MAP3K12 in the proliferation, migration, and invasion of RCC cells. Our findings proposed the potential of MAPK-signature genes as biomarkers for prognosis and therapy response, as well as targets for therapeutic drugs in ccRCC.
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Affiliation(s)
- Xinyi Zheng
- Department of Pharmacy, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, China
| | - Yiqiu Wang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; State Key Laboratory of Oncogenes and Related Genes, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xiaoyan Qiu
- Department of Pharmacy, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, China.
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15
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Harris ES, McIntire HJ, Mazur M, Schulz-Hildebrandt H, Leung HM, Tearney GJ, Krick S, Rowe SM, Barnes JW. Reduced sialylation of airway mucin impairs mucus transport by altering the biophysical properties of mucin. Sci Rep 2024; 14:16568. [PMID: 39019950 PMCID: PMC11255327 DOI: 10.1038/s41598-024-66510-2] [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: 05/14/2024] [Accepted: 07/02/2024] [Indexed: 07/19/2024] Open
Abstract
Mucus stasis is a pathologic hallmark of muco-obstructive diseases, including cystic fibrosis (CF). Mucins, the principal component of mucus, are extensively modified with hydroxyl (O)-linked glycans, which are largely terminated by sialic acid. Sialic acid is a negatively charged monosaccharide and contributes to the biochemical/biophysical properties of mucins. Reports suggest that mucin sialylation may be altered in CF; however, the consequences of reduced sialylation on mucus clearance have not been fully determined. Here, we investigated the consequences of reduced sialylation on the charge state and conformation of the most prominent airway mucin, MUC5B, and defined the functional consequences of reduced sialylation on mucociliary transport (MCT). Reduced sialylation contributed to a lower charged MUC5B form and decreased polymer expansion. The inhibition of total mucin sialylation de novo impaired MCT in primary human bronchial epithelial cells and rat airways, and specific α-2,3 sialylation blockade was sufficient to recapitulate these findings. Finally, we show that ST3 beta-galactoside alpha-2,3-sialyltransferase (ST3Gal1) expression is downregulated in CF and partially restored by correcting CFTR via Elexacaftor/Tezacaftor/Ivacaftor treatment. Overall, this study demonstrates the importance of mucin sialylation in mucus clearance and identifies decreased sialylation by ST3Gal1 as a possible therapeutic target in CF and potentially other muco-obstructive diseases.
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Affiliation(s)
- Elex S Harris
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1900 University Blvd. Tinsley Harrison Tower, Suite 422, Birmingham, AL, 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hannah J McIntire
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1900 University Blvd. Tinsley Harrison Tower, Suite 422, Birmingham, AL, 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marina Mazur
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1900 University Blvd. Tinsley Harrison Tower, Suite 422, Birmingham, AL, 35294, USA
| | | | - Hui Min Leung
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Guillermo J Tearney
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Stefanie Krick
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1900 University Blvd. Tinsley Harrison Tower, Suite 422, Birmingham, AL, 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven M Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1900 University Blvd. Tinsley Harrison Tower, Suite 422, Birmingham, AL, 35294, USA.
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Departments of Pediatrics and Cell Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Jarrod W Barnes
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, 1900 University Blvd. Tinsley Harrison Tower, Suite 422, Birmingham, AL, 35294, USA.
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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16
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Alshammari MA, Alshehri AO, Alqahtani F, Khan MR, Bakhrebah MA, Alasmari F, Alshammari TK, Alsharari SD. Increased Permeability of the Blood-Brain Barrier in a Diabetic Mouse Model ( Leprdb/db Mice). Int J Mol Sci 2024; 25:7768. [PMID: 39063010 PMCID: PMC11276738 DOI: 10.3390/ijms25147768] [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: 05/18/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Type 2 Diabetes Mellitus (T2DM) is linked to multiple complications, including cognitive impairment, and the prevalence of memory-related neurodegenerative diseases is higher in T2DM patients. One possible theory is the alteration of the microvascular and macrovascular environment of the blood-brain barrier (BBB). In this study, we employed different approaches, including RT-PCR, functional pharmacokinetic studies using sodium fluorescein (NaFL), and confocal microscopy, to characterize the functional and molecular integrity of the BBB in a T2DM animal model, leptin receptor-deficient mutant mice (Leprdb/db mice). As a result, VCAM-1, ICAM-1, MMP-9, and S100b (BBB-related markers) dysregulation was observed in the Leprdb/db animal model compared to littermate wild-type mice. The brain concentration of sodium fluorescein (NaFL) increased significantly in Leprdb/db untreated mice compared to insulin-treated mice. Therefore, the permeability of NaFL was higher in Leprdb/db control mice than in all remaining groups. Identifying the factors that increase the BBB in Leprdb/db mice will provide a better understanding of the BBB microvasculature and present previously undescribed findings of T2DM-related brain illnesses, filling knowledge gaps in this emerging field of research.
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Affiliation(s)
- Musaad A. Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia; (F.A.); (M.R.K.); (F.A.); (T.K.A.); (S.D.A.)
| | - Abdulaziz O. Alshehri
- Department of Pharmacology and Toxicology (Graduate Student), Pharmacy College, King Saud University, Riyadh 11495, Saudi Arabia;
| | - Faleh Alqahtani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia; (F.A.); (M.R.K.); (F.A.); (T.K.A.); (S.D.A.)
| | - Mohammad R. Khan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia; (F.A.); (M.R.K.); (F.A.); (T.K.A.); (S.D.A.)
| | - Muhammed A. Bakhrebah
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia;
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia; (F.A.); (M.R.K.); (F.A.); (T.K.A.); (S.D.A.)
| | - Tahani K. Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia; (F.A.); (M.R.K.); (F.A.); (T.K.A.); (S.D.A.)
| | - Shakir D. Alsharari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia; (F.A.); (M.R.K.); (F.A.); (T.K.A.); (S.D.A.)
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17
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Liu Y, Theil S, Ibach M, Walter J. DAP12 interacts with RER1 and is retained in the secretory pathway before assembly with TREM2. Cell Mol Life Sci 2024; 81:302. [PMID: 39008111 DOI: 10.1007/s00018-024-05298-w] [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: 12/11/2023] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 07/16/2024]
Abstract
DNAX-activating protein of 12 kDa (DAP12) is a transmembrane adapter protein expressed in lymphoid and myeloid lineage cells. It interacts with several immunoreceptors forming functional complexes that trigger intracellular signaling pathways. One of the DAP12 associated receptors is the triggering receptor expressed on myeloid cells 2 (TREM2). Mutations in both DAP12 and TREM2 have been linked to neurodegenerative diseases. However, mechanisms involved in the regulation of subcellular trafficking and turnover of these proteins are not well understood. Here, we demonstrate that proteasomal degradation of DAP12 is increased in the absence of TREM2. Interestingly, unassembled DAP12 is also retained in early secretory compartments, including the endoplasmic reticulum (ER) and the ER-Golgi intermediate compartment (ERGIC), thereby preventing its transport to the plasma membrane. We also show that unassembled DAP12 interacts with the retention in ER sorting receptor 1 (RER1). The deletion of endogenous RER1 decreases expression of functional TREM2-DAP12 complexes and membrane proximal signaling, and resulted in almost complete inhibition of phagocytic activity in THP-1 differentiated macrophage-like cells. These results indicate that RER1 acts as an important regulator of DAP12 containing immunoreceptor complexes and immune cell function.
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Affiliation(s)
- Yanxia Liu
- Department of Neurology, University of Bonn, Bonn, 53127, Germany
| | - Sandra Theil
- Department of Neurology, University of Bonn, Bonn, 53127, Germany
| | - Melanie Ibach
- Department of Neurology, University of Bonn, Bonn, 53127, Germany
| | - Jochen Walter
- Department of Neurology, University of Bonn, Bonn, 53127, Germany.
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18
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Gutiérrez Rico E, Joseph P, Noutsos C, Poon K. Hypothalamic and hippocampal transcriptome changes in App NL-G-F mice as a function of metabolic and inflammatory dysfunction. Neuroscience 2024; 554:107-117. [PMID: 39002757 DOI: 10.1016/j.neuroscience.2024.07.007] [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: 08/13/2023] [Revised: 05/20/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
The progression of Alzheimer's disease (AD) has a silent phase that predates characteristic cognitive decline and eventually leads to active cognitive deficits. Metabolism, diet, and obesity have been correlated to the development of AD but is poorly understood. The hypothalamus is a brain region that exerts homeostatic control on food intake and metabolism and has been noted to be impacted during the active phase of Alzheimer's disease. This study, in using an amyloid overexpression AppNL-G-F mouse model under normal metabolic conditions, examines blood markers in young and old male AppNL-G-F mice (n = 5) that corresponds to the silent and active phases of AD, and bulk gene expression changes in the hypothalamus and the hippocampus. The results show a large panel of inflammatory mediators, leptin, and other proteins that may be involved in weakening the blood brain barrier, to be increased in the young AppNL-G-F mice but not in the old AppNL-G-F mice. There were also several differentially expressed genes in both the hypothalamus and the hippocampus in the young AppNL-G-F mice prior to amyloid plaque formation and cognitive decline that persisted in the old AppNL-G-F mice, including GABRa2 receptor, Wdfy1, and several pseudogenes with unknown function. These results suggests that a larger panel of inflammatory mediators may be used as blood markers to detect silent AD, and that a change in leptin and gene expression in the hypothalamus exist prior to cognitive effects, suggesting a coupling of metabolism with amyloid plaque induced cognitive decline.
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Affiliation(s)
- Evelyn Gutiérrez Rico
- Tohoku University, Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
| | - Patricia Joseph
- SUNY Old Westbury, 223 Store Hill Rd, Old Westbury, NY 11568, USA
| | - Christos Noutsos
- SUNY Old Westbury, 223 Store Hill Rd, Old Westbury, NY 11568, USA
| | - Kinning Poon
- SUNY Old Westbury, 223 Store Hill Rd, Old Westbury, NY 11568, USA.
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19
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Wälchli T, Ghobrial M, Schwab M, Takada S, Zhong H, Suntharalingham S, Vetiska S, Gonzalez DR, Wu R, Rehrauer H, Dinesh A, Yu K, Chen ELY, Bisschop J, Farnhammer F, Mansur A, Kalucka J, Tirosh I, Regli L, Schaller K, Frei K, Ketela T, Bernstein M, Kongkham P, Carmeliet P, Valiante T, Dirks PB, Suva ML, Zadeh G, Tabar V, Schlapbach R, Jackson HW, De Bock K, Fish JE, Monnier PP, Bader GD, Radovanovic I. Single-cell atlas of the human brain vasculature across development, adulthood and disease. Nature 2024:10.1038/s41586-024-07493-y. [PMID: 38987604 DOI: 10.1038/s41586-024-07493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/30/2024] [Indexed: 07/12/2024]
Abstract
A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood1. Here we performed single-cell RNA sequencing analysis of 606,380 freshly isolated endothelial cells, perivascular cells and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We identify extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumours and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict substantial endothelial-to-perivascular cell ligand-receptor cross-talk, including immune-related and angiogenic pathways, thereby revealing a central role for the endothelium within brain neurovascular unit signalling networks. Our single-cell brain atlas provides insights into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.
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Affiliation(s)
- Thomas Wälchli
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland.
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland.
| | - Moheb Ghobrial
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Marc Schwab
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
| | - Shigeki Takada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Hang Zhong
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Samuel Suntharalingham
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sandra Vetiska
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | | | - Ruilin Wu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Anuroopa Dinesh
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
| | - Kai Yu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Edward L Y Chen
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jeroen Bisschop
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Fiona Farnhammer
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ann Mansur
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Luca Regli
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Karl Schaller
- Department of Neurosurgery, University of Geneva Medical Center & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Frei
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Troy Ketela
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Paul Kongkham
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB & Department of Oncology, KU Leuven, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, P. R. China
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Taufik Valiante
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Krembil Brain Institute, Division of Clinical and Computational Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering and Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Peter B Dirks
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Departments of Surgery and Molecular Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Hartland W Jackson
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Katrien De Bock
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jason E Fish
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe P Monnier
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Ivan Radovanovic
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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20
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Yuan X, Ma Y, Gao R, Cui S, Wang Y, Fa B, Ma S, Wei T, Ma S, Yu Z. HEARTSVG: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics. Nat Commun 2024; 15:5700. [PMID: 38972896 PMCID: PMC11228050 DOI: 10.1038/s41467-024-49846-1] [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: 06/29/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Identifying spatially variable genes (SVGs) is crucial for understanding the spatiotemporal characteristics of diseases and tissue structures, posing a distinctive challenge in spatial transcriptomics research. We propose HEARTSVG, a distribution-free, test-based method for fast and accurately identifying spatially variable genes in large-scale spatial transcriptomic data. Extensive simulations demonstrate that HEARTSVG outperforms state-of-the-art methods with higherF 1 scores (averageF 1 Score=0.948), improved computational efficiency, scalability, and reduced false positives (FPs). Through analysis of twelve real datasets from various spatial transcriptomic technologies, HEARTSVG identifies a greater number of biologically significant SVGs (average AUC = 0.792) than other comparative methods without prespecifying spatial patterns. Furthermore, by clustering SVGs, we uncover two distinct tumor spatial domains characterized by unique spatial expression patterns, spatial-temporal locations, and biological functions in human colorectal cancer data, unraveling the complexity of tumors.
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Affiliation(s)
- Xin Yuan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yanran Ma
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruitian Gao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuya Cui
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Wang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Botao Fa
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Shiyang Ma
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangge Ma
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Department of Biostatistics, Yale University, New Haven, USA.
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Center for Biostatistics and Data Science Organization, Shanghai Jiao Tong University, Shanghai, China.
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Center for Biomedical Data Science, Translational Science Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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21
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Caputo M, Ivanova D, Chasserot-Golaz S, Doussau F, Haeberlé AM, Royer C, Ozkan S, Ecard J, Vitale N, Cousin MA, Tóth P, Gasman S, Ory S. Phospholipid Scramblase 1 Controls Efficient Neurotransmission and Synaptic Vesicle Retrieval at Cerebellar Synapses. J Neurosci 2024; 44:e0042242024. [PMID: 38839301 PMCID: PMC11223464 DOI: 10.1523/jneurosci.0042-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
Phospholipids (PLs) are asymmetrically distributed at the plasma membrane. This asymmetric lipid distribution is transiently altered during calcium-regulated exocytosis, but the impact of this transient remodeling on presynaptic function is currently unknown. As phospholipid scramblase 1 (PLSCR1) randomizes PL distribution between the two leaflets of the plasma membrane in response to calcium activation, we set out to determine its role in neurotransmission. We report here that PLSCR1 is expressed in cerebellar granule cells (GrCs) and that PLSCR1-dependent phosphatidylserine egress occurred at synapses in response to neuron stimulation. Synaptic transmission is impaired at GrC Plscr1 -/- synapses, and both PS egress and synaptic vesicle (SV) endocytosis are inhibited in Plscr1 -/- cultured neurons from male and female mice, demonstrating that PLSCR1 controls PL asymmetry remodeling and SV retrieval following neurotransmitter release. Altogether, our data reveal a novel key role for PLSCR1 in SV recycling and provide the first evidence that PL scrambling at the plasma membrane is a prerequisite for optimal presynaptic performance.
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Affiliation(s)
- Margherita Caputo
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Daniela Ivanova
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Sylvette Chasserot-Golaz
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Frédéric Doussau
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Anne-Marie Haeberlé
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Cathy Royer
- Plateforme Imagerie In Vitro, Centre National de la Recherche Scientifique UPS3256, Strasbourg F-67000, France
| | - Sebahat Ozkan
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Jason Ecard
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Nicolas Vitale
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Petra Tóth
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Stéphane Gasman
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
| | - Stéphane Ory
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg F-67000, France
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22
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Pellerin D, Méreaux JL, Boluda S, Danzi MC, Dicaire MJ, Davoine CS, Genis D, Spurdens G, Ashton C, Hammond JM, Gerhart BJ, Chelban V, Le PU, Safisamghabadi M, Yanick C, Lee H, Nageshwaran SK, Matos-Rodrigues G, Jaunmuktane Z, Petrecca K, Akbarian S, Nussenzweig A, Usdin K, Renaud M, Bonnet C, Ravenscroft G, Saporta MA, Napierala JS, Houlden H, Deveson IW, Napierala M, Brice A, Molina Porcel L, Seilhean D, Zuchner S, Durr A, Brais B. Somatic instability of the FGF14 -SCA27B GAA•TTC repeat reveals a marked expansion bias in the cerebellum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.01.24309777. [PMID: 39006414 PMCID: PMC11245061 DOI: 10.1101/2024.07.01.24309777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Spinocerebellar ataxia 27B (SCA27B) is a common autosomal dominant ataxia caused by an intronic GAA•TTC repeat expansion in FGF14 . Neuropathological studies have shown that neuronal loss is largely restricted to the cerebellum. Although the repeat locus is highly unstable during intergenerational transmission, it remains unknown whether it exhibits cerebral mosaicism and progressive instability throughout life. We conducted an analysis of the FGF14 GAA•TTC repeat somatic instability across 156 serial blood samples from 69 individuals, fibroblasts, induced pluripotent stem cells, and post-mortem brain tissues from six controls and six patients with SCA27B, alongside methylation profiling using targeted long-read sequencing. Peripheral tissues exhibited minimal somatic instability, which did not significantly change over periods of more than 20 years. In post-mortem brains, the GAA•TTC repeat was remarkably stable across all regions, except in the cerebellar hemispheres and vermis. The levels of somatic expansion in the cerebellar hemispheres and vermis were, on average, 3.15 and 2.72 times greater relative to other examined brain regions, respectively. Additionally, levels of somatic expansion in the brain increased with repeat length and tissue expression of FGF14 . We found no significant difference in methylation of wild-type and expanded FGF14 alleles in post-mortem cerebellar hemispheres between patients and controls. In conclusion, our study revealed that the FGF14 GAA•TTC repeat exhibits a cerebellar-specific expansion bias, which may explain the pure and late-onset cerebellar involvement in SCA27B.
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23
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El Daibani A, Madasu MK, Al-Hasani R, Che T. Limitations and potential of κOR biased agonists for pain and itch management. Neuropharmacology 2024; 258:110061. [PMID: 38960136 DOI: 10.1016/j.neuropharm.2024.110061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024]
Abstract
The concept of ligand bias is based on the premise that different agonists can elicit distinct responses by selectively activating the same receptor. These responses often determine whether an agonist has therapeutic or undesirable effects. Therefore, it would be highly advantageous to have agonists that specifically trigger the therapeutic response. The last two decades have seen a growing trend towards the consideration of ligand bias in the development of ligands to target the κ-opioid receptor (κOR). Most of these ligands selectively favor G-protein signaling over β-arrestin signaling to potentially provide effective pain and itch relief without adverse side effects associated with κOR activation. Importantly, the specific role of β-arrestin 2 in mediating κOR agonist-induced side effects remains unknown, and similarly the therapeutic and side-effect profiles of G-protein-biased κOR agonists have not been established. Furthermore, some drugs previously labeled as G-protein-biased may not exhibit true bias but may instead be either low-intrinsic-efficacy or partial agonists. In this review, we discuss the established methods to test ligand bias, their limitations in measuring bias factors for κOR agonists, as well as recommend the consideration of other systematic factors to correlate the degree of bias signaling and pharmacological effects.
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Affiliation(s)
- Amal El Daibani
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Manish K Madasu
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ream Al-Hasani
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Tao Che
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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24
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van der Westhuizen ET. Single nucleotide variations encoding missense mutations in G protein-coupled receptors may contribute to autism. Br J Pharmacol 2024; 181:2158-2181. [PMID: 36787962 DOI: 10.1111/bph.16057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/21/2022] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
Autism is a neurodevelopmental condition with a range of symptoms that vary in intensity and severity from person to person. Genetic sequencing has identified thousands of genes containing mutations in autistic individuals, which may contribute to the development of autistic symptoms. Several of these genes encode G protein-coupled receptors (GPCRs), which are cell surface expressed proteins that transduce extracellular messages to the intracellular space. Mutations in GPCRs can impact their function, resulting in aberrant signalling within cells and across neurotransmitter systems in the brain. This review summarises the current knowledge on autism-associated single nucleotide variations encoding missense mutations in GPCRs and the impact of these genetic mutations on GPCR function. For some autism-associated mutations, changes in GPCR expression levels, ligand affinity, potency and efficacy have been observed. However, for many the functional consequences remain unknown. Thus, further work to characterise the functional impacts of the genetically identified mutations is required. LINKED ARTICLES: This article is part of a themed issue Therapeutic Targeting of G Protein-Coupled Receptors: hot topics from the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists 2021 Virtual Annual Scientific Meeting. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.14/issuetoc.
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25
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Ren M, Zhang J, Zong R, Sun H. A Novel Pancreatic Cancer Hypoxia Status Related Gene Signature for Prognosis and Therapeutic Responses. Mol Biotechnol 2024; 66:1684-1703. [PMID: 37405638 DOI: 10.1007/s12033-023-00807-x] [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: 02/16/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
Pancreatic cancer (PAC) is a highly fatal and aggressive type of cancer. Hypoxia is a common feature of PAC. The aim of this study was to develop a hypoxia status-related prognostic model for predicting the survival outcomes in PAC. The data sets of PAC from The Cancer Genome Atlas and the International Cancer Genome Consortium were used to construct and validate the signature. A 6 hypoxia status-related differential expression genes prognostic model for predicting the survival outcomes was established. The Kaplan-Meier analysis and Received operating characteristic curve indicated the good performance of the signature at predicting overall survival. Univariate and Multivariate Cox regression revealed that the signature was an independent prognostic factor in PAC. Weighted Gene Co-expression Network Analysis and immune infiltration analysis indicated that Immune-related pathways and immune cell infiltration was mostly enriched in the low-risk group, which presented a better prognosis. We also evaluated the predictive of the signature for immunotherapy and chemoradiotherapy. Risk gene LY6D may be a potential prognostic predictor of PAC. This model can be used as an independent prognostic factor for predicting clinical outcomes and a possible classifier for response to chemotherapy.
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Affiliation(s)
- Min Ren
- College of Life Science, Yan'an University, Yan'an, 716000, China.
| | - Jianing Zhang
- College of Life Science, Yan'an University, Yan'an, 716000, China
| | - Rongrong Zong
- College of Life Science, Yan'an University, Yan'an, 716000, China
| | - Huiru Sun
- College of Life Science, Yan'an University, Yan'an, 716000, China.
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26
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Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nat Rev Gastroenterol Hepatol 2024; 21:493-516. [PMID: 38575682 DOI: 10.1038/s41575-024-00914-3] [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] [Accepted: 02/14/2024] [Indexed: 04/06/2024]
Abstract
Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The observation that there are hundreds of bile acids, especially many amidated bile acids, necessitates a revision of many of the classical descriptions of bile acids and bile acid enzyme functions. For example, bile salt hydrolases also have transferase activity. There are now hundreds of known modifications to bile acids and thousands of bile acid-associated genes, especially when including the microbiome, distributed throughout the human body (for example, there are >2,400 bile salt hydrolases alone). The fact that so much of our genetic and small-molecule repertoire, in both amount and diversity, is dedicated to bile acid function highlights the centrality of bile acids as key regulators of metabolism and immune homeostasis, which is, in large part, communicated via the gut microbiome.
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Affiliation(s)
- Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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27
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Qing L, Li Q, Yang Y, Xu W, Wang Y, Li R, You C, Dong Z. Hypoxia-mediated attenuation of EGLN2 inhibition of the NF-κB signaling pathway leads to the formation of a loop between HIF-1α and MUC1-C promoting chemoresistance in bladder cancer. Mol Carcinog 2024; 63:1303-1318. [PMID: 38634741 DOI: 10.1002/mc.23725] [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: 10/17/2023] [Revised: 01/30/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
The expression pattern of MUC1-C in tumors is closely linked to tumor progression; however, its specific mechanism remains unclear. The expression of MUC1-C in cancer and adjacent normal tissues was detected using immunohistochemistry and Western blot. The IC50 of cells to gemcitabine was determined using the CCK8 assay. The effects of hypoxia and MUC1-C on the behavioral and metabolic characteristics of bladder cancer cells were investigated. Gene expression was assessed through Western blot and polymerase chain reaction. The relationship between the genes was analyzed by co-immunoprecipitation, immunofluorescence and Western blot. Finally, the role of the EGLN2 and NF-κB signaling pathways in the interaction between MUC1-C and hypoxia-inducible factor-1α (HIF-1α) was investigated. MUC1-C expression is significantly higher in bladder cancer tissues than in adjacent normal tissues, particularly in large-volume tumors, and is closely correlated with clinical features such as tumor grade. Tumor volume-mediated hypoxia resulted in increased expression of MUC1-C and HIF-1α in bladder cancer cells. Under stimulation of hypoxia, the inhibitory effect of EGLN2 on the NF-κB signaling pathway was weakened, allowing NF-κB to promote the positive feedback formation of MUC1-C and HIF-1α. Simultaneously, EGLN2-mediated degradation of HIF-1α was reduced. This ultimately led to elevated HIF-1α-mediated downstream gene expression, promoting increased glucose uptake and glycolysis, and ultimately resulting in heightened chemotherapy resistance and malignancy.
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Affiliation(s)
- Liangliang Qing
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Qingchao Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yongjin Yang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Wenbo Xu
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yanan Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Rongxing Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Chengyu You
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhilong Dong
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
- Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
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28
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Vecellio Reane D, Serna JDC, Raffaello A. Unravelling the complexity of the mitochondrial Ca 2+ uniporter: regulation, tissue specificity, and physiological implications. Cell Calcium 2024; 121:102907. [PMID: 38788256 DOI: 10.1016/j.ceca.2024.102907] [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: 04/23/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Calcium (Ca2+) signalling acts a pleiotropic message within the cell that is decoded by the mitochondria through a sophisticated ion channel known as the Mitochondrial Ca2+ Uniporter (MCU) complex. Under physiological conditions, mitochondrial Ca2+ signalling is crucial for coordinating cell activation with energy production. Conversely, in pathological scenarios, it can determine the fine balance between cell survival and death. Over the last decade, significant progress has been made in understanding the molecular bases of mitochondrial Ca2+ signalling. This began with the elucidation of the MCU channel components and extended to the elucidation of the mechanisms that regulate its activity. Additionally, increasing evidence suggests molecular mechanisms allowing tissue-specific modulation of the MCU complex, tailoring channel activity to the specific needs of different tissues or cell types. This review aims to explore the latest evidence elucidating the regulation of the MCU complex, the molecular factors controlling the tissue-specific properties of the channel, and the physiological and pathological implications of mitochondrial Ca2+ signalling in different tissues.
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Affiliation(s)
- Denis Vecellio Reane
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HDC), Helmholtz Zentrum Munich, Germany.
| | - Julian D C Serna
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Anna Raffaello
- Department of Biomedical Sciences, University of Padova, Italy.
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29
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Padilla-Ferrer A, Carrete A, Simon A, Meffre D, Jafarian-Tehrani M. A Disintegrin And Metalloprotease 10 expression within the murine central nervous system. Brain Res 2024; 1834:148888. [PMID: 38548249 DOI: 10.1016/j.brainres.2024.148888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
A Disintegrin And Metalloprotease 10 (ADAM10), is able to control several important physiopathological processes through the shedding of a large number of protein substrates. Although ADAM10 plays a crucial role in the central nervous system (CNS) development and function, its protein distribution in the CNS has not been fully addressed. Here, we described the regional and cellular ADAM10 protein expression in C57BL/6 mice examined by immunofluorescence 1) throughout the adult mouse brain, cerebellum and spinal cord in vivo and 2) in different cell types as neurons, astrocytes, oligodendrocytes and microglia in vitro. We observed ADAM10 expression through the whole CNS, with a strong expression in the hippocampus, in the hypothalamus and in the cerebral and piriform cortex in the brain, in the Purkinje and in granular cell layers in the cerebellum and in the spinal cord to a lower extent. In vivo, ADAM10 protein expression was mainly found in neurons and in some oligodendroglial cell populations. However, in primary cultures we observed ADAM10 expression in neurons, oligodendrocytes, astrocytes and microglia. Interestingly, ADAM10 was not only found in the membrane but also in cytoplasmic vesicles and in the nucleus of primary cultured cells. Overall, this work highlights a wide distribution of ADAM10 throughout the CNS. The nuclear localization of ADAM10, probably due to its intracellular domain, emphasizes its role in cell signalling in physiological and pathological conditions. Further investigations are required to better elucidate the role of ADAM10 in glial cells.
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Affiliation(s)
| | - Alex Carrete
- Université Paris Cité and Inserm, UMR-S 1124, Paris, France
| | - Anne Simon
- Université Paris Cité and Inserm, UMR-S 1124, Paris, France
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Ren Z, Jiang L, Di Y, Zhang D, Gong J, Gong J, Jiang Q, Fu Z, Sun P, Zhou B, Ni M. CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism. Bioinformatics 2024; 40:btae330. [PMID: 38788220 PMCID: PMC11226863 DOI: 10.1093/bioinformatics/btae330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/17/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024] Open
Abstract
MOTIVATION Due to the varying delivery methods of mRNA vaccines, codon optimization plays a critical role in vaccine design to improve the stability and expression of proteins in specific tissues. Considering the many-to-one relationship between synonymous codons and amino acids, the number of mRNA sequences encoding the same amino acid sequence could be enormous. Finding stable and highly expressed mRNA sequences from the vast sequence space using in silico methods can generally be viewed as a path-search problem or a machine translation problem. However, current deep learning-based methods inspired by machine translation may have some limitations, such as recurrent neural networks, which have a weak ability to capture the long-term dependencies of codon preferences. RESULTS We develop a BERT-based architecture that uses the cross-attention mechanism for codon optimization. In CodonBERT, the codon sequence is randomly masked with each codon serving as a key and a value. In the meantime, the amino acid sequence is used as the query. CodonBERT was trained on high-expression transcripts from Human Protein Atlas mixed with different proportions of high codon adaptation index codon sequences. The result showed that CodonBERT can effectively capture the long-term dependencies between codons and amino acids, suggesting that it can be used as a customized training framework for specific optimization targets. AVAILABILITY AND IMPLEMENTATION CodonBERT is freely available on https://github.com/FPPGroup/CodonBERT.
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Affiliation(s)
- Zilin Ren
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Lili Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Yaxin Di
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China
| | - Dufei Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Jianli Gong
- School of Artificial Intelligence, Wuhan Technology and Business University, Wuhan 340000, China
| | - Jianting Gong
- Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Qiwei Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Zhiguo Fu
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Bo Zhou
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Ming Ni
- Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
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31
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Gray M, Nash KR, Yao Y. Adenylyl cyclase 2 expression and function in neurological diseases. CNS Neurosci Ther 2024; 30:e14880. [PMID: 39073001 PMCID: PMC11284242 DOI: 10.1111/cns.14880] [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: 05/09/2024] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
Adenylyl cyclases (Adcys) catalyze the formation of cAMP, a secondary messenger essential for cell survival and neurotransmission pathways in the CNS. Adcy2, one of ten Adcy isoforms, is highly expressed in the CNS. Abnormal Adcy2 expression and mutations have been reported in various neurological disorders in both rodents and humans. However, due to the lack of genetic tools, loss-of-function studies of Adcy2 are scarce. In this review, we summarize recent findings on Adcy2 expression and function in neurological diseases. Specifically, we first introduce the biochemistry, structure, and function of Adcy2 briefly. Next, the expression and association of Adcy2 in human patients and rodent models of neurodegenerative diseases (Alzheimer's disease and Parkinson's disease), psychiatric disorders (Tourette syndrome, schizophrenia, and bipolar disorder), and other neurological conditions (stress-associated disorders, stroke, epilepsy, and Lesch-Nyhan Syndrome) are elaborated. Furthermore, we discuss the pros and cons of current studies as well as key questions that need to be answered in the future. We hope to provide a focused review on Adcy2 that promotes future research in the field.
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Affiliation(s)
- Marsilla Gray
- Department of Molecular Pharmacology and Physiology, Morsani College of MedicineUniversity of South FloridaTampaFloridaUSA
| | - Kevin R. Nash
- Department of Molecular Pharmacology and Physiology, Morsani College of MedicineUniversity of South FloridaTampaFloridaUSA
| | - Yao Yao
- Department of Molecular Pharmacology and Physiology, Morsani College of MedicineUniversity of South FloridaTampaFloridaUSA
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32
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Dyrkheeva NS, Zakharenko AL, Malakhova AA, Okorokova LS, Shtokalo DN, Medvedev SP, Tupikin AA, Kabilov MR, Lavrik OI. Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout. Biochim Biophys Acta Gen Subj 2024; 1868:130616. [PMID: 38621596 DOI: 10.1016/j.bbagen.2024.130616] [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: 12/25/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | | | - Dmitry N Shtokalo
- AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; A.P. Ershov Institute of Informatics Systems, SB RAS, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexey A Tupikin
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
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González D, Peña MJ, Bernal C, García-Acero M, Manotas MC, Suarez-Obando F, Rojas A. Epigenetic control of SOX9 gene by the histone acetyltransferase P300 in human Sertoli cells. Heliyon 2024; 10:e33173. [PMID: 39022079 PMCID: PMC11252772 DOI: 10.1016/j.heliyon.2024.e33173] [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: 01/01/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
Background The transcription factor SOX9 is a key regulator of male sexual development and Sertoli cell differentiation. Altered SOX9 expression has been implicated in the pathogenesis of disorders of sexual development (DSD) in mammals. However, limited information exists regarding the epigenetic mechanisms governing its transcriptional control during sexual development. Methods This study employed real-time PCR (qPCR), immunofluorescence (IIF), and chromatin immunoprecipitation (ChIP) assays to investigate the epigenetic mechanisms associated with SOX9 gene transcriptional control in human and mouse Sertoli cell lines. To identify the specific epigenetic enzymes involved in SOX9 epigenetic control, functional assays using siRNAs for P300, GCN5, and WDR5 were performed. Results The transcriptional activation of SOX9 was associated with selective deposition of active histone modifications, such as H3K4me3 and H3K27ac, at its enhancer and promoter regions. Importantly, the histone acetyltransferase P300 was found to be significantly enriched at the SOX9 enhancers, co-localizing with the H3K27ac and the SOX9 transcription factor. Silencing of P300 led to decreased SOX9 expression and reduced H3K27ac levels at the eSR-A and e-ALDI enhancers, demonstrating the crucial role of P300-mediated histone acetylation in SOX9 transcriptional activation. Interestingly, another histone lysine acetyltransferases like GNC5 and methyltransferases as the Trithorax/COMPASS-like may also have a relevant role in male sexual differentiation. Conclusions Histone acetylation by P300 at SOX9 enhancers, is a key mechanism governing the transcriptional control of this essential regulator of male sexual development. These findings provide important insights into the epigenetic basis of sexual differentiation and the potential pathogenesis of DSDs.
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Affiliation(s)
- Daniel González
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
| | - María José Peña
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
| | - Camila Bernal
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
| | - Mary García-Acero
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
| | - Maria Carolina Manotas
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
| | - Fernando Suarez-Obando
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
| | - Adriana Rojas
- Institute of Human Genetics, Faculty of Medicine, Pontificia Universidad Javeriana. Carrera 7 No. 40-62, 110231, Bogotá, Colombia
- Department of Genetics, University of Córdoba, 14071, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain
- Reina Sofía University Hospital, 14071 Córdoba, Spain
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34
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Gardner OFW, Bai T, Baillie GS, Ferretti P. Phosphodiesterase 4D activity in acrodysostosis-associated neural pathology: too much or too little? Brain Commun 2024; 6:fcae225. [PMID: 38983619 PMCID: PMC11232698 DOI: 10.1093/braincomms/fcae225] [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: 03/08/2024] [Revised: 05/09/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
Members of the phosphodiesterase 4 (PDE4) enzyme family regulate the availability of the secondary messenger cyclic adenosine monophosphate (cAMP) and, by doing so, control cellular processes in health and disease. In particular, PDE4D has been associated with Alzheimer's disease and the intellectual disability seen in fragile X syndrome. Furthermore, single point mutations in critical PDE4D regions cause acrodysostosis type 2(ACRDYS2, also referred to as inactivating PTH/PTHrP signalling disorder 5 or iPPSD5), where intellectual disability is seen in ∼90% of patients alongside the skeletal dysmorphologies that are characteristic of acrodysostosis type 1 (ACRDYS1/iPPSD4) and ACRDYS2. Two contrasting mechanisms have been proposed to explain how mutations in PDE4D cause iPPSD5. The first mechanism, the 'over-activation hypothesis', suggests that cAMP/PKA (cyclic adenosine monophosphate/protein kinase A) signalling is reduced by the overactivity of mutant PDE4D, whilst the second, the 'over-compensation hypothesis' suggests that mutations reduce PDE4D activity. That reduction in activity is proposed to cause an increase in cellular cAMP, triggering the overexpression of other PDE isoforms. The resulting over-compensation then reduces cellular cAMP and the levels of cAMP/PKA signalling. However, neither of these proposed mechanisms accounts for the fine control of PDE activation and localization, which are likely to play a role in the development of iPPSD5. This review will draw together our understanding of the role of PDE4D in iPPSD5 and present a novel perspective on possible mechanisms of disease.
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Affiliation(s)
- Oliver F W Gardner
- Developmental Biology and Cancer Department, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Tianshu Bai
- Developmental Biology and Cancer Department, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - George S Baillie
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Patrizia Ferretti
- Developmental Biology and Cancer Department, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
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Punt LD, van der Kaay DCM, van Setten PA, de Groote K, Kruijsen AR, Bocca G, de Munnik SA, Renes JS, de Bruin C, Losekoot M, van Duyvenvoorde HA, Wit JM, Joustra SD. IGF1 Haploinsufficiency: Phenotype and Response to Growth Hormone Treatment in 9 Patients. Horm Res Paediatr 2024:1-11. [PMID: 38952118 DOI: 10.1159/000540053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024] Open
Abstract
INTRODUCTION The clinical features of bi-allelic IGF1 defects are well established, i.e., severe growth failure and microcephaly, delayed psychomotor development, and sensorineural deafness. However, information on clinical and endocrine consequences of heterozygous IGF1 variants and treatment options is scarce. We aimed at extending the knowledge base of the clinical presentation and growth response to recombinant human growth hormone (rhGH) of patients carrying such variants. METHODS Retrospective case series of patients with pathogenic heterozygous IGF1 variants. RESULTS Nine patients from six families were included, harbouring five whole or partial gene deletions and one frameshift variant resulting in a premature stop codon (three de novo, one unknown inheritance). In the other two families, variants segregated with short stature. Mean (SD) birth length was -1.9 (1.3) SDS (n = 7), height -3.8 (0.6) SDS, head circumference -2.5 (0.6) SDS, serum IGF-I -1.9 (0.7) SDS, serum IGFBP-3 1.1 (0.4) SDS (n = 7), and GH peak range 5-31 μg/L (n = 4). Five patients showed feeding problems in infancy. Average height increased after 1 and 2 years of rhGH treatment by 0.8 SDS (range 0.3-1.3 SDS) and 1.3 SDS (range 0.5-2.0 SDS), respectively. Adult height in 2 patients was -2.8 and -1.3 SDS, which was, respectively, 1.3 and 2.9 SDS taller than predicted before start of treatment. CONCLUSION Haploinsufficiency of IGF1 causes a variable phenotype of prenatal and postnatal growth failure, microcephaly, feeding difficulties, low/low-normal serum IGF-I values in contrast to serum IGFBP-3 in the upper-normal range. Treatment with rhGH increased growth in the first 2 years of treatment, and in 2 patients adult height after treatment was higher than predicted at treatment initiation.
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Affiliation(s)
- Lauren D Punt
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, The Netherlands
| | - Daniëlle C M van der Kaay
- Division of Paediatric Endocrinology, Department of Paediatrics, Erasmus University Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Petra A van Setten
- Department of Paediatrics, Amalia Childrens Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Kirsten de Groote
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, The Netherlands
| | - Anne R Kruijsen
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gianni Bocca
- Division of Paediatric Endocrinology, Department of Paediatrics, Beatrix Children's Hospital, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Judith S Renes
- Dutch Growth Research Foundation, Rotterdam, The Netherlands
- Department of Paediatrics, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - Christiaan de Bruin
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, The Netherlands
| | - Monique Losekoot
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Jan M Wit
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sjoerd D Joustra
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, The Netherlands
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Parag RR, Yamamoto T, Saito K, Zhu D, Yang L, Van Meir EG. Novel Isoforms of Adhesion G Protein-Coupled Receptor B1 (ADGRB1/BAI1) Generated from an Alternative Promoter in Intron 17. Mol Neurobiol 2024:10.1007/s12035-024-04293-3. [PMID: 38941066 DOI: 10.1007/s12035-024-04293-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
Brain-specific angiogenesis inhibitor 1 (BAI1) belongs to the adhesion G-protein-coupled receptors, which exhibit large multi-domain extracellular N termini that mediate cell-cell and cell-matrix interactions. To explore the existence of BAI1 isoforms, we queried genomic datasets for markers of active chromatin and new transcript variants in the ADGRB1 (adhesion G-protein-coupled receptor B1) gene. Two major types of mRNAs were identified in human/mouse brain, those with a start codon in exon 2 encoding a full-length protein of a predicted size of 173.5/173.3 kDa and shorter transcripts starting from alternative exons at the intron 17/exon 18 boundary with new or exon 19 start codons, predicting two shorter isoforms of 76.9/76.4 and 70.8/70.5 kDa, respectively. Immunoblots on wild-type and Adgrb1 exon 2-deleted mice, reverse transcription PCR, and promoter-luciferase reporter assay confirmed that the shorter isoforms originate from an alternative promoter in intron 17. The shorter BAI1 isoforms lack most of the N terminus and are very close in structure to the truncated BAI1 isoform generated through GPS processing from the full-length receptor. The cleaved BAI1 isoform has a 19 amino acid extracellular stalk that may serve as a receptor agonist, while the alternative transcripts generate BAI1 isoforms with extracellular N termini of 5 or 60 amino acids. Further studies are warranted to compare the functions of these isoforms and examine the distinct roles they play in different tissues and cell types.
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Affiliation(s)
- Rashed Rezwan Parag
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA
- Graduate Biomedical Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Takahiro Yamamoto
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan
| | - Kiyotaka Saito
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA
| | - Dan Zhu
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Liquan Yang
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham (UAB), WTI 520E, 1824 6th Avenue South, Birmingham, AL, 35233, USA.
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.
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Gao M, Ooms JF, Leurs R, Vischer HF. Histamine H 3 Receptor Isoforms: Insights from Alternative Splicing to Functional Complexity. Biomolecules 2024; 14:761. [PMID: 39062475 PMCID: PMC11274711 DOI: 10.3390/biom14070761] [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: 05/31/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing significantly enhances the diversity of the G protein-coupled receptor (GPCR) family, including the histamine H3 receptor (H3R). This post-transcriptional modification generates multiple H3R isoforms with potentially distinct pharmacological and physiological profiles. H3R is primarily involved in the presynaptic inhibition of neurotransmitter release in the central nervous system. Despite the approval of pitolisant for narcolepsy (Wakix®) and daytime sleepiness in adults with obstructive sleep apnea (Ozawade®) and ongoing clinical trials for other H3R antagonists/inverse agonists, the functional significance of the numerous H3R isoforms remains largely enigmatic. Recent publicly available RNA sequencing data have confirmed the expression of multiple H3R isoforms in the brain, with some isoforms exhibiting unique tissue-specific distribution patterns hinting at isoform-specific functions and interactions within neural circuits. In this review, we discuss the complexity of H3R isoforms with a focus on their potential roles in central nervous system (CNS) function. Comparative analysis across species highlights evolutionary conservation and divergence in H3R splicing, suggesting species-specific regulatory mechanisms. Understanding the functionality of H3R isoforms is crucial for the development of targeted therapeutics. This knowledge will inform the design of more precise pharmacological interventions, potentially enhancing therapeutic efficacy and reducing adverse effects in the treatment of neurological and psychiatric disorders.
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Affiliation(s)
| | | | | | - Henry F. Vischer
- Amsterdam Institute of Molecular and Life Sciences, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands; (M.G.); (J.F.O.); (R.L.)
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Zielinski N, Baiceanu D, Dragomir A, Heyckendorf J, Ibraim E, Köhler N, Leschczyk C, Popa C, Rachow A, Sachsenweger J, Sanchez Carballo P, Schaub D, Zeeb H, Tulu B, DiNardo AR, Lange C, Reimann M. A Transcriptomic Biomarker Predicting Linezolid-Associated Neuropathy During Treatment of Drug-Resistant Tuberculosis. Pathog Immun 2024; 9:25-42. [PMID: 38939039 PMCID: PMC11210591 DOI: 10.20411/pai.v9i2.705] [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: 04/01/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Background Neuropathic adverse events occur frequently in linezolid-containing regimens, some of which remain irreversible after drug discontinuation. Objective We aimed to identify and validate a host RNA-based biomarker that can predict linezolid-associated neuropathy before multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB) treatment initiation and to identify genes and pathways that are associated with linezolid-associated neuropathy. Methods Adult patients initiating MDR/RR-TB treatment including linezolid were prospectively enrolled in 3 independent cohorts in Germany. Clinical data and whole blood RNA for transcriptomic analysis were collected. The primary outcome was linezolid-associated optic and/or peripheral neuropathy. A random forest algorithm was used for biomarker identification. The biomarker was validated in an additional fourth cohort of patients with MDR/RR-TB from Romania. Results A total of 52 patients from the 3 identification cohorts received linezolid treatment. Of those, 24 (46.2%) developed peripheral and/or optic neuropathies during linezolid treatment. The majority (59.3%) of the episodes were of moderate (grade 2) severity. In total, the expression of 1,479 genes differed significantly at baseline of treatment. Suprabasin (SBSN) was identified as a potential biomarker to predict linezolid-associated neuropathy. In the validation cohort, 10 of 42 (23.8%) patients developed grade ≥3 neuropathies. The area under the curve for the biomarker algorithm prediction of grade ≥3 neuropathies was 0.63 (poor; 95% confidence interval: 0.42 - 0.84). Conclusions We identified and preliminarily validated a potential clinical biomarker to predict linezolid-associated neuropathies before the initiation of MDR/RR-TB therapy. Larger studies of the SBSN biomarker in more diverse populations are warranted.
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Affiliation(s)
- Nika Zielinski
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Dragos Baiceanu
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
| | - Antonela Dragomir
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
- UMF Carol Davila, Bucharest, Romania
| | - Jan Heyckendorf
- Clinic for Internal Medicine I, Leibniz Lung Clinic,
University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Kiel, Germany
| | - Elmira Ibraim
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
| | - Niklas Köhler
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Christoph Leschczyk
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Division of Cellular Microbiology, Research Center
Borstel, Borstel, Germany
| | - Cristina Popa
- Marius Nasta Institute of Pneumophtiziology (MNI),
Bucharest, Romania
- Eastern-European Study Site of DZIF in MNI,
Bucharest, Romania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical
Medicine, Medical Centre of the University of Munich (LMU), Munich,
Germany
- German Centre for Infection Research (DZIF),
Partner Site Munich, Munich, Germany
- Unit Global Health, Helmholtz Zentrum
München, German Research Centre for Environmental Health (HMGU),
Neuherberg, Germany
| | - Jens Sachsenweger
- Department of Pneumology, Asklepios Clinic
Hamburg-Harburg, Hamburg, Germany
| | - Patricia Sanchez Carballo
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Dagmar Schaub
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Hajo Zeeb
- Department of Prevention and Evaluation, Leibniz
Institute for Prevention Research and Epidemiology – BIPS, Bremen,
Germany
- Faculty of Human and Health Sciences, University
of Bremen, Bremen, Germany
| | - Begna Tulu
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
| | - Andrew R. DiNardo
- Baylor College of Medicine and Texas
Children's Hospital, Global TB Program, Houston, Texas
- Radboud University Medical Center, Internal
Medicine, Nijmegen, Netherlands
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
- Baylor College of Medicine and Texas
Children's Hospital, Global TB Program, Houston, Texas
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research
Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner
Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Respiratory Medicine and International Health,
University of Lübeck, Lübeck, Germany
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Chagas PS, Chagas HIS, Naeini SE, Bhandari B, Gouron J, Malta TM, Salles ÉL, Wang LP, Yu JC, Baban B. Network-Based Transcriptome Analysis Reveals FAM3C as a Novel Potential Biomarker for Glioblastoma. J Cell Biochem 2024:e30612. [PMID: 38923575 DOI: 10.1002/jcb.30612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
Glioblastoma (GBM) is the most common form of malignant primary brain tumor with a high mortality rate. The aim of the present study was to investigate the clinical significance of Family with Sequence Similarity 3, Member C, FAM3C, in GBM using bioinformatic-integrated analysis. First, we performed the transcriptomic integration analysis to assess the expression profile of FAM3C in GBM using several data sets (RNA-sequencing and scRNA-sequencing), which were obtained from TCGA and GEO databases. By using the STRING platform, we investigated FAM3C-coregulated genes to construct the protein-protein interaction network. Next, Metascape, Enrichr, and CIBERSORT databases were used. We found FAM3C high expression in GBM with poor survival rates. Further, we observed, via FAM3C coexpression network analysis, that FAM3C plays key roles in several hallmarks of cancer. Surprisingly, we also highlighted five FAM3C‑coregulated genes overexpressed in GBM. Specifically, we demonstrated the association between the high expression of FAM3C and the abundance of the different immune cells, which may markedly worsen GBM prognosis. For the first time, our findings suggest that FAM3C not only can be a new emerging biomarker with promising therapeutic values to GBM patients but also gave a new insight into a potential resource for future GBM studies.
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Affiliation(s)
- Pablo Shimaoka Chagas
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
| | | | - Sahar Emami Naeini
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Bidhan Bhandari
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Jules Gouron
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
| | - Tathiane M Malta
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Évila Lopes Salles
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Lei P Wang
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
- Georgia Institute of Cannabis Research, Medicinal Cannabis of Georgia LLC, Augusta, Georgia, USA
| | - Jack C Yu
- Department of Surgery, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Babak Baban
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
- Georgia Institute of Cannabis Research, Medicinal Cannabis of Georgia LLC, Augusta, Georgia, USA
- Department of Neurology, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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Shukla AK, Verma M, Bathla M, Randhawa S, Saini TC, Kumari A, Acharya A. Transferrin Immobilized Graphene Oxide Nanocomposite for Targeted Cancer Chemodynamic Therapy via Increasing Intracellular Labile Fe 2+ Concentration. ACS APPLIED BIO MATERIALS 2024; 7:3649-3659. [PMID: 38728425 DOI: 10.1021/acsabm.3c01147] [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: 05/12/2024]
Abstract
Recently, different alternative regulated cell death (RCD) pathways, viz., necroptosis, pyroptosis, ferroptosis, cuproptosis etc., have been explored as important targets for the development of cancer medications in recent years, as these can change the immunogenicity of the tumor microenvironment (TME) and will finally lead to the inhibition of cancer progression and metastasis. Here, we report the development of transferrin immobilized graphene oxide (Tfn@GOAPTES) nanocomposite as a therapeutic strategy toward cancer cell killing. The electrostatic immobilization of Tfn on the GOAPTES surface was confirmed by different spectroscopy and microscopy techniques. The Tfn immobilization was found to be ∼74 ± 4%, whereas the stability of the protein on the GO surface suggested a robust nature of the nanocomposite. The MTT assay suggested that Tfn@GOAPTES exhibited cytotoxicity toward HeLa cells via increased lipid peroxidation and DNA damage. Western blot studies resulted in decreased expression of acetylation on lysine 40 of α-tubulin and increased expression of LC3a/b for Tfn@GOAPTES treated HeLa cells, suggesting autophagy to be the main cause of the cell death mechanism. Overall, we predict that the present approach can be used as a therapeutic strategy for cancer cell killing via selective induction of a high concentration of intracellular iron.
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Affiliation(s)
- Ashish K Shukla
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohini Verma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manik Bathla
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shiwani Randhawa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Trilok Chand Saini
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Avnesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Liang H, Sedillo JC, Schrodi SJ, Ikeda A. Structural variants in linkage disequilibrium with GWAS-significant SNPs. Heliyon 2024; 10:e32053. [PMID: 38882374 PMCID: PMC11177133 DOI: 10.1016/j.heliyon.2024.e32053] [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: 01/12/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
With the recent expansion of structural variant identification in the human genome, understanding the role of these impactful variants in disease architecture is critically important. Currently, a large proportion of genome-wide-significant genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are functionally unresolved, raising the possibility that some of these SNPs are associated with disease through linkage disequilibrium with causal structural variants. Hence, understanding the linkage disequilibrium between newly discovered structural variants and statistically significant SNPs may provide a resource for further investigation into disease-associated regions in the genome. Here we present a resource cataloging structural variant-significant SNP pairs in high linkage disequilibrium. The database is composed of (i) SNPs that have exhibited genome-wide significant association with traits, primarily disease phenotypes, (ii) newly released structural variants (SVs), and (iii) linkage disequilibrium values calculated from unphased data. All data files including those detailing SV and GWAS SNP associations and results of GWAS-SNP-SV pairs are available at the SV-SNP LD Database and can be accessed at 'https://github.com/hliang-SchrodiLab/SV_SNPs. Our analysis results represent a useful fine mapping tool for interrogating SVs in linkage disequilibrium with disease-associated SNPs. We anticipate that this resource may play an important role in subsequent studies which investigate incorporating disease causing SVs into disease risk prediction models.
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Affiliation(s)
- Hao Liang
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Joni C Sedillo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
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Chen H, Du X. Increased FGF2 expression promotes immune cell infiltration and correlates with an unfavorable prognosis in thyroid cancer. Heliyon 2024; 10:e32272. [PMID: 38873667 PMCID: PMC11170142 DOI: 10.1016/j.heliyon.2024.e32272] [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: 09/22/2023] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
To delve into the expression and functions of FGF2 in patient with thyroid cancer (THCA), we conducted a systematic analysis of the association of FGF2 with immune cell infiltration, and prognosis in THCA patients. The transcription and protein levels, methylation, and biological properties of FGF2 were examined, along with its correlation with prognosis and immune cell infiltration in THCA patients using online databases UALCAN, Human Protein Atlas, Kaplan-Meier Plotter, DNMIVD, cBioPortal, GEPIA, Metascape, Linkedomics and TIMER. Clinical samples were collected for Western blot analyses. FGF2 was substantially overexpressed in the tumor group and shown correlations with age, tumor histology, nodal metastasis, and cancer stages. Moreover, higher expression of FGF2 (HR = 3.42, 95 % CI:1.57-7.44, p = 0.00099) was greatly correlated with poorer relapse-free survival in THCA patients, particularly in female patients. FGF2 methylation level was increased in the tumor group (p = 1.29E-6), and higher methylation levels of FGF2 were positively correlated with the poorer progression-free interval in THCA patients (p = 0.015). FGF2 mutations were markedly associated with shorter disease-free survival, with a mutation rate of 6 % among the total 498 THCA patients. FGF2 functions were potentially related to cell adhesion, cytokine-cytokine receptor interaction and angiogenesis. FGF2 expression showed positive correlations with the infiltration of B cells (Cor = 0.569, p = 1.04e-42), CD4+ T cells (Cor = 0.555, p = 9.43e-41), macrophages (Cor = 0.438, p = 2.94e-42), neutrophils (Cor = 0.578, p = 9.354e-45), and dendritic cells (Cor = 0.591, p = 5.00e-47). FGF2 is a potential prognostic marker in THCA patients, with its functions possibly related to cell adhesion, interaction of the cytokine-cytokine receptor, angiogenesis, and the promotion of multiple immune cell infiltration.
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Affiliation(s)
- Han Chen
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, China
| | - Xiaoyun Du
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, China
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Karakaya T, Slaufova M, Di Filippo M, Hennig P, Kündig T, Beer HD. CARD8: A Novel Inflammasome Sensor with Well-Known Anti-Inflammatory and Anti-Apoptotic Activity. Cells 2024; 13:1032. [PMID: 38920661 PMCID: PMC11202080 DOI: 10.3390/cells13121032] [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: 05/15/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Inflammasomes comprise a group of protein complexes with fundamental roles in the induction of inflammation. Upon sensing stress factors, their assembly induces the activation and release of the pro-inflammatory cytokines interleukin (IL)-1β and -18 and a lytic type of cell death, termed pyroptosis. Recently, CARD8 has joined the group of inflammasome sensors. The carboxy-terminal part of CARD8, consisting of a function-to-find-domain (FIIND) and a caspase activation and recruitment domain (CARD), resembles that of NLR family pyrin domain containing 1 (NLRP1), which is recognized as the main inflammasome sensor in human keratinocytes. The interaction with dipeptidyl peptidases 8 and 9 (DPP8/9) represents an activation checkpoint for both sensors. CARD8 and NLRP1 are activated by viral protease activity targeting their amino-terminal region. However, CARD8 also has some unique features compared to the established inflammasome sensors. Activation of CARD8 occurs independently of the inflammasome adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC), leading mainly to pyroptosis rather than the activation and secretion of pro-inflammatory cytokines. CARD8 was also shown to have anti-inflammatory and anti-apoptotic activity. It interacts with, and inhibits, several proteins involved in inflammation and cell death, such as the inflammasome sensor NLRP3, CARD-containing proteins caspase-1 and -9, nucleotide-binding oligomerization domain containing 2 (NOD2), or nuclear factor kappa B (NF-κB). Single nucleotide polymorphisms (SNPs) of CARD8, some of them occurring at high frequencies, are associated with various inflammatory diseases. The molecular mechanisms underlying the different pro- and anti-inflammatory activities of CARD8 are incompletely understood. Alternative splicing leads to the generation of multiple CARD8 protein isoforms. Although the functional properties of these isoforms are poorly characterized, there is evidence that suggests isoform-specific roles. The characterization of the functions of these isoforms, together with their cell- and disease-specific expression, might be the key to a better understanding of CARD8's different roles in inflammation and inflammatory diseases.
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Affiliation(s)
- Tugay Karakaya
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland; (T.K.); (M.S.); (M.D.F.); (P.H.); (T.K.)
| | - Marta Slaufova
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland; (T.K.); (M.S.); (M.D.F.); (P.H.); (T.K.)
| | - Michela Di Filippo
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland; (T.K.); (M.S.); (M.D.F.); (P.H.); (T.K.)
| | - Paulina Hennig
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland; (T.K.); (M.S.); (M.D.F.); (P.H.); (T.K.)
| | - Thomas Kündig
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland; (T.K.); (M.S.); (M.D.F.); (P.H.); (T.K.)
- Faculty of Medicine, University of Zurich, CH-8006 Zurich, Switzerland
| | - Hans-Dietmar Beer
- Department of Dermatology, University Hospital Zurich, CH-8952 Schlieren, Switzerland; (T.K.); (M.S.); (M.D.F.); (P.H.); (T.K.)
- Faculty of Medicine, University of Zurich, CH-8006 Zurich, Switzerland
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Yang F, Begemann A, Reichhart N, Haeckel A, Steindl K, Schellenberger E, Sturm RF, Barth M, Bassani S, Boonsawat P, Courtin T, Delobel B, Gunning B, Hardies K, Jennesson M, Legoff L, Linnankivi T, Prouteau C, Smal N, Spodenkiewicz M, Toelle SP, Van Gassen K, Van Paesschen W, Verbeek N, Ziegler A, Zweier M, Horn AHC, Sticht H, Lerche H, Weckhuysen S, Strauß O, Rauch A. Missense variants in ANO4 cause sporadic encephalopathic or familial epilepsy with evidence for a dominant-negative effect. Am J Hum Genet 2024; 111:1184-1205. [PMID: 38744284 PMCID: PMC11179416 DOI: 10.1016/j.ajhg.2024.04.014] [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: 11/17/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
Anoctamins are a family of Ca2+-activated proteins that may act as ion channels and/or phospholipid scramblases with limited understanding of function and disease association. Here, we identified five de novo and two inherited missense variants in ANO4 (alias TMEM16D) as a cause of fever-sensitive developmental and epileptic or epileptic encephalopathy (DEE/EE) and generalized epilepsy with febrile seizures plus (GEFS+) or temporal lobe epilepsy. In silico modeling of the ANO4 structure predicted that all identified variants lead to destabilization of the ANO4 structure. Four variants are localized close to the Ca2+ binding sites of ANO4, suggesting impaired protein function. Variant mapping to the protein topology suggests a preliminary genotype-phenotype correlation. Moreover, the observation of a heterozygous ANO4 deletion in a healthy individual suggests a dysfunctional protein as disease mechanism rather than haploinsufficiency. To test this hypothesis, we examined mutant ANO4 functional properties in a heterologous expression system by patch-clamp recordings, immunocytochemistry, and surface expression of annexin A5 as a measure of phosphatidylserine scramblase activity. All ANO4 variants showed severe loss of ion channel function and DEE/EE associated variants presented mild loss of surface expression due to impaired plasma membrane trafficking. Increased levels of Ca2+-independent annexin A5 at the cell surface suggested an increased apoptosis rate in DEE-mutant expressing cells, but no changes in Ca2+-dependent scramblase activity were observed. Co-transfection with ANO4 wild-type suggested a dominant-negative effect. In summary, we expand the genetic base for both encephalopathic sporadic and inherited fever-sensitive epilepsies and link germline variants in ANO4 to a hereditary disease.
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Affiliation(s)
- Fang Yang
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Anais Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Nadine Reichhart
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Akvile Haeckel
- Institute for Radiology and Children's Radiology, Charité-Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Eyk Schellenberger
- Institute for Radiology and Children's Radiology, Charité-Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Ronja Fini Sturm
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Magalie Barth
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Sissy Bassani
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Paranchai Boonsawat
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Thomas Courtin
- Sorbonne Université, INSERM, CNRS, Institut du Cerveau - Paris Brain Institute - ICM, 75013 Paris, France; Hôpital Pitié-Salpêtrière, DMU BioGe'M, AP-HP, 75013 Paris, France
| | - Bruno Delobel
- Service de Cytogénétique, GH de l'Institut Catholique de Lille, Hopital Saint Vincent de Paul, Lille, France
| | | | - Katia Hardies
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Louis Legoff
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Tarja Linnankivi
- Epilepsia Helsinki, University of Helsinki and Helsinki University Hospital, 00029 HUS Helsinki, Finland; Department of Pediatric Neurology and Pediatric Research Center, New Children's Hospital, Helsinki University Hospital and University of Helsinki, 00029 HUS Helsinki, Finland
| | - Clément Prouteau
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Noor Smal
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerp, Belgium
| | - Marta Spodenkiewicz
- Department of Genetics, La Réunion University Hospital, Saint-Pierre, France
| | - Sandra P Toelle
- Department of Pediatric Neurology, Children's University Hospital Zurich, Zurich, Switzerland
| | - Koen Van Gassen
- University Medical Center Utrecht, Department of Genetics, Utrecht, the Netherlands
| | - Wim Van Paesschen
- Laboratory for Epilepsy Research, KU Leuven, and Neurology Department, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Nienke Verbeek
- University Medical Center Utrecht, Department of Genetics, Utrecht, the Netherlands
| | - Alban Ziegler
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Sarah Weckhuysen
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium; Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, 2610 Antwerp, Belgium
| | - Olaf Strauß
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Children's University Hospital Zurich, Zurich, Switzerland.
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Sun Y, Men W, Kennerknecht I, Fang W, Zheng HF, Zhang W, Rao Y. Human genetics of face recognition: discovery of MCTP2 mutations in humans with face blindness (congenital prosopagnosia). Genetics 2024; 227:iyae047. [PMID: 38547502 DOI: 10.1093/genetics/iyae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/19/2024] [Indexed: 06/06/2024] Open
Abstract
Face recognition is important for both visual and social cognition. While prosopagnosia or face blindness has been known for seven decades and face-specific neurons for half a century, the molecular genetic mechanism is not clear. Here we report results after 17 years of research with classic genetics and modern genomics. From a large family with 18 congenital prosopagnosia (CP) members with obvious difficulties in face recognition in daily life, we uncovered a fully cosegregating private mutation in the MCTP2 gene which encodes a calcium binding transmembrane protein expressed in the brain. After screening through cohorts of 6589, we found more CPs and their families, allowing detection of more CP associated mutations in MCTP2. Face recognition differences were detected between 14 carriers with the frameshift mutation S80fs in MCTP2 and 19 noncarrying volunteers. Six families including one with 10 members showed the S80fs-CP correlation. Functional magnetic resonance imaging found association of impaired recognition of individual faces by MCTP2 mutant CPs with reduced repetition suppression to repeated facial identities in the right fusiform face area. Our results have revealed genetic predisposition of MCTP2 mutations in CP, 76 years after the initial report of prosopagnosia and 47 years after the report of the first CP. This is the first time a gene required for a higher form of visual social cognition was found in humans.
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Affiliation(s)
- Yun Sun
- Chinese Institutes for Medical Research, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Weiwei Men
- Center for MRI Research, Academy for Advanced Interdisciplinary Studies, Beijing Key Lab for Medical Physics and Engineering, Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing 100871, China
| | - Ingo Kennerknecht
- Institute of Human Genetics, Westfälische Wilhelms-Universität, Münster 48149, Germany
| | - Wan Fang
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hou-Feng Zheng
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Wenxia Zhang
- Chinese Institutes for Medical Research, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Rao
- Chinese Institutes for Medical Research, Capital Medical University, Beijing 100069, China
- Chinese Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518107, China
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46
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Möbus L, Serra A, Fratello M, Pavel A, Federico A, Greco D. A Multi-Dimensional Approach to Map Disease Relationships Challenges Classical Disease Views. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401754. [PMID: 38840452 DOI: 10.1002/advs.202401754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/05/2024] [Indexed: 06/07/2024]
Abstract
The categorization of human diseases is mainly based on the affected organ system and phenotypic characteristics. This is limiting the view to the pathological manifestations, while it neglects mechanistic relationships that are crucial to develop therapeutic strategies. This work aims to advance the understanding of diseases and their relatedness beyond traditional phenotypic views. Hence, the similarity among 502 diseases is mapped using six different data dimensions encompassing molecular, clinical, and pharmacological information retrieved from public sources. Multiple distance measures and multi-view clustering are used to assess the patterns of disease relatedness. The integration of all six dimensions into a consensus map of disease relationships reveals a divergent disease view from the International Classification of Diseases (ICD), emphasizing novel insights offered by a multi-view disease map. Disease features such as genes, pathways, and chemicals that are enriched in distinct disease groups are identified. Finally, an evaluation of the top similar diseases of three candidate diseases common in the Western population shows concordance with known epidemiological associations and reveals rare features shared between Type 2 diabetes (T2D) and Alzheimer's disease. A revision of disease relationships holds promise for facilitating the reconstruction of comorbidity patterns, repurposing drugs, and advancing drug discovery in the future.
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Affiliation(s)
- Lena Möbus
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Antonio Federico
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Tampere Institute for Advanced Study, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00790, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, 00790, Finland
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47
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Li Y, Munoz-Mayorga D, Nie Y, Kang N, Tao Y, Lagerwall J, Pernaci C, Curtin G, Coufal NG, Mertens J, Shi L, Chen X. Microglial lipid droplet accumulation in tauopathy brain is regulated by neuronal AMPK. Cell Metab 2024; 36:1351-1370.e8. [PMID: 38657612 PMCID: PMC11153007 DOI: 10.1016/j.cmet.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/25/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
The accumulation of lipid droplets (LDs) in aging and Alzheimer's disease brains is considered a pathological phenomenon with unresolved cellular and molecular mechanisms. Utilizing stimulated Raman scattering (SRS) microscopy, we observed significant in situ LD accumulation in microglia of tauopathy mouse brains. SRS imaging, combined with deuterium oxide (D2O) labeling, revealed heightened lipogenesis and impaired lipid turnover within LDs in tauopathy fly brains and human neurons derived from induced pluripotent stem cells (iPSCs). Transfer of unsaturated lipids from tauopathy iPSC neurons to microglia induced LD accumulation, oxidative stress, inflammation, and impaired phagocytosis. Neuronal AMP-activated protein kinase (AMPK) inhibits lipogenesis and promotes lipophagy in neurons, thereby reducing lipid flux to microglia. AMPK depletion in prodromal tauopathy mice increased LD accumulation, exacerbated pro-inflammatory microgliosis, and promoted neuropathology. Our findings provide direct evidence of native, aberrant LD accumulation in tauopathy brains and underscore the critical role of AMPK in regulating brain lipid homeostasis.
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Affiliation(s)
- Yajuan Li
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Daniel Munoz-Mayorga
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Yuhang Nie
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Ningxin Kang
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Yuren Tao
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Jessica Lagerwall
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Carla Pernaci
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; Sanford Consortium for Regenerative Medicine, San Diego, CA, USA
| | - Genevieve Curtin
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; Sanford Consortium for Regenerative Medicine, San Diego, CA, USA
| | - Nicole G Coufal
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; Sanford Consortium for Regenerative Medicine, San Diego, CA, USA
| | - Jerome Mertens
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Lingyan Shi
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, San Diego, CA, USA.
| | - Xu Chen
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA.
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48
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Du X, Qi Z, Jiao Y, Wu W, Huang Q, Sun X, Hu S. HK2 promotes migration and invasion of intrahepatic cholangiocarcinoma via enhancing cancer stem-like cells' resistance to anoikis. Cell Signal 2024; 118:111126. [PMID: 38453126 DOI: 10.1016/j.cellsig.2024.111126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Cancer stem-like cells (CSLCs) and anoikis resistance play crucial roles in the metastasis of cancers. However, it remains unclear whether CSLCs are related to anoikis resistance in intrahepatic cholangiocarcinoma (ICC). Here we identified a group of stemness-related anoikis genes (SRAGs) via bioinformatic analysis of public data. Accordingly, a novel anoikis-related classification was established and it divided ICC into C1 and C2 type. Different type ICC displayed distinct prognosis, molecular as well immune characteristics. Furthermore, we found one key SRAGs via several machine learning algorithms. HK2 was up-regulated in tumor-repopulating cells (TRCs) of ICC, a kind of CSLCs with a potent resistance to anoikis. Its up-regulation may be caused by the activation of MTORC1 signaling in ICC-TRCs. And inhibition of HK2 significantly increased anoikis and decreased migration as well invasion in ICC-TRCs. Our studies provide an insight into the molecular mechanism underlying the resistance of ICC-TRCs to anoikis and enhance the evidences for targeting HK2 in ICC.
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Affiliation(s)
- Xiaojing Du
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhuoran Qi
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yunjia Jiao
- Clinical Laboratory, Minhang Hospital, Fudan University, No. 170, Xinsong Road, Shanghai 201199, China
| | - Wenzhi Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Qingke Huang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xuecheng Sun
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Sunkuan Hu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China..
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Kalogeropoulos K, Moldt Haack A, Madzharova E, Di Lorenzo A, Hanna R, Schoof EM, Auf dem Keller U. CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics. Mol Cell Proteomics 2024; 23:100781. [PMID: 38703894 PMCID: PMC11192779 DOI: 10.1016/j.mcpro.2024.100781] [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: 02/21/2024] [Revised: 04/11/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024] Open
Abstract
Positional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in both sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable the generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, concomitant progress has not been observed to the same extent in data analysis and post-processing steps, arguably constituting the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide-level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate the applicability of our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0.
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Affiliation(s)
| | - Aleksander Moldt Haack
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Elizabeta Madzharova
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Antea Di Lorenzo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City Haifa, Israel
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Munro V, Kelly V, Messner CB, Kustatscher G. Cellular control of protein levels: A systems biology perspective. Proteomics 2024; 24:e2200220. [PMID: 38012370 DOI: 10.1002/pmic.202200220] [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: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
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Affiliation(s)
- Victoria Munro
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Van Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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