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Huang Y, Ma T, Wan Z, Zhong C, Wang J. AFP: Finding pathways accounting for stoichiometry along with atom group tracking in metabolic network. J Biotechnol 2024; 392:139-151. [PMID: 39009230 DOI: 10.1016/j.jbiotec.2024.07.004] [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: 08/15/2023] [Revised: 04/29/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
Abstract
Automatically finding novel pathways plays an important role in the initial designs of metabolic pathways in synthetic biology and metabolic engineering. Although path-finding methods have been successfully applied in identifying valuable synthetic pathways, few efforts have been made in fusing atom group tracking into building stoichiometry model to search metabolic pathways from arbitrary start compound via Mixed Integer Linear Programming (MILP). We propose a novel method called AFP to find metabolic pathways by incorporating atom group tracking into reaction stoichiometry via MILP. AFP tracks the movements of atom groups in the reaction stoichiometry to construct MILP model to search the pathways containing atom groups exchange in the reactions and adapts the MILP model to provide the options of searching pathways from an arbitrary or given compound to the target compound. Combining atom group tracking with reaction stoichiometry to build MILP model for pathfinding may promote the search of well-designed alternative pathways at the stoichiometric modeling level. The experimental comparisons to the known pathways show that our proposed method AFP is more effective to recover the known pathways than other existing methods and is capable of discovering biochemically feasible pathways producing the metabolites of interest.
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Affiliation(s)
- Yiran Huang
- School of Computer and Electronics and Information, Guangxi University, Nanning, China; Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, China; Key Laboratory of Parallel, Distributed and Intelligent Computing, (Guangxi University), Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, China; Guangxi Intelligent Digital Services Research Center of Engineering Technology, Guangxi University, Nanning, China.
| | - Tao Ma
- School of Computer and Electronics and Information, Guangxi University, Nanning, China
| | - Zhiyuan Wan
- School of Computer and Electronics and Information, Guangxi University, Nanning, China
| | - Cheng Zhong
- School of Computer and Electronics and Information, Guangxi University, Nanning, China; Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, China; Key Laboratory of Parallel, Distributed and Intelligent Computing, (Guangxi University), Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, China; Guangxi Intelligent Digital Services Research Center of Engineering Technology, Guangxi University, Nanning, China
| | - Jianyi Wang
- Medical College, Guangxi University, Nanning, China
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2
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Angela Kwak H, Liu L, Tredup C, Röhm S, Prinos P, Böttcher J, Schapira M. Chemical coverage of human biological pathways. Drug Discov Today 2024:104144. [PMID: 39179147 DOI: 10.1016/j.drudis.2024.104144] [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: 04/18/2024] [Revised: 08/02/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Chemical probes and chemogenomic compounds are valuable tools to link gene to phenotype, explore human biology, and uncover novel targets for precision medicine. The mission of the Target 2035 initiative is to discover chemical tools for all human proteins by the year 2035. Here, we draw a landscape of the current chemical coverage of human biological pathways. Although available chemical tools target only 3% of the human proteome, they already cover 53% of human biological pathways and represent a versatile toolkit to dissect a vast portion of human biology. Pathways targeted by existing drugs might be enriched in unknown but valid drug targets and could be prioritized in future Target 2035 efforts.
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Affiliation(s)
- Haejin Angela Kwak
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Lihua Liu
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Claudia Tredup
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sandra Röhm
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Jark Böttcher
- Boehringer Ingelheim RCV, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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3
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Marassi V, La Rocca G, Placci A, Muntiu A, Vincenzoni F, Vitali A, Desiderio C, Maraldi T, Beretti F, Russo E, Miceli V, Conaldi PG, Papait A, Romele P, Cargnoni A, Silini AR, Alviano F, Parolini O, Giordani S, Zattoni A, Reschiglian P, Roda B. Native characterization and QC profiling of human amniotic mesenchymal stromal cell vesicular fractions for secretome-based therapy. Talanta 2024; 276:126216. [PMID: 38761653 DOI: 10.1016/j.talanta.2024.126216] [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: 12/18/2023] [Revised: 04/09/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Human amniotic mesenchymal stromal cells (hAMSCs) have unique immunomodulatory properties making them attractive candidates for regenerative applications in inflammatory diseases. Most of their beneficial properties are mediated through their secretome. The bioactive factors concurring to its therapeutic activity are still unknown. Evidence suggests synergy between the two main components of the secretome, soluble factors and vesicular fractions, pivotal in shifting inflammation and promoting self-healing. Biological variability and the absence of quality control (QC) protocols hinder secretome-based therapy translation to clinical applications. Moreover, vesicular secretome contains a multitude of particles with varying size, cargos and functions whose complexity hinders full characterization and comprehension. This study achieved a significant advancement in secretome characterization by utilizing native, FFF-based separation and characterizing extracellular vesicles derived from hAMSCs. This was accomplished by obtaining dimensionally homogeneous fractions then characterized based on their protein content, potentially enabling the identification of subpopulations with diverse functionalities. This method proved to be successful as an independent technique for secretome profiling, with the potential to contribute to the standardization of a qualitative method. Additionally, it served as a preparative separation tool, streamlining populations before ELISA and LC-MS characterization. This approach facilitated the categorization of distinctive and recurring proteins, along with the identification of clusters associated with vesicle activity and functions. However, the presence of proteins unique to each fraction obtained through the FFF separation tool presents a challenge for further analysis of the protein content within these cargoes.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy
| | - Giampiero La Rocca
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
| | - Anna Placci
- Department of Chemistry G. Ciamician, University of Bologna, Italy
| | - Alexandra Muntiu
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168, Rome, Italy
| | - Federica Vincenzoni
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168, Rome, Italy
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, 00168, Rome, Italy
| | - Tullia Maraldi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Francesca Beretti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Eleonora Russo
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
| | - Vitale Miceli
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta Specializzazione), 90127, Palermo, Italy
| | - Pier Giulio Conaldi
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta Specializzazione), 90127, Palermo, Italy
| | - Andrea Papait
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy; Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Pietro Romele
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, 25124, Brescia, Italy
| | - Anna Cargnoni
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, 25124, Brescia, Italy
| | - Antonietta Rosa Silini
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, 25124, Brescia, Italy
| | - Francesco Alviano
- Department of Biomedical and Neuromotor Science, University of Bologna, Bologna, Italy
| | - Ornella Parolini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy; Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Stefano Giordani
- Department of Chemistry G. Ciamician, University of Bologna, Italy
| | - Andrea Zattoni
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy
| | - Barbara Roda
- Department of Chemistry G. Ciamician, University of Bologna, Italy; byFlow srl, Bologna, Italy.
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Mukhopadhyay U, Levantovsky S, Carusone TM, Gharbi S, Stein F, Behrends C, Bhogaraju S. A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates. SCIENCE ADVANCES 2024; 10:eadp3000. [PMID: 39121224 PMCID: PMC11313854 DOI: 10.1126/sciadv.adp3000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/03/2024] [Indexed: 08/11/2024]
Abstract
Over 600 E3 ligases in humans execute ubiquitination of specific target proteins in a spatiotemporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrich bona fide substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. We applied our method, which we named Ub-POD, to the really interesting new gene (RING) E3 ligase RAD18 and identified proliferating cell nuclear antigen and several other critical players in the DNA damage repair pathway. Furthermore, we successfully applied Ub-POD to the RING ubiquitin ligase tumor necrosis factor receptor-associated factor 6 and a U-box-type E3 ubiquitin ligase carboxyl terminus of Hsc70-interacting protein. We anticipate that our method could be widely adapted to all classes of ubiquitin ligases to identify substrates.
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Affiliation(s)
- Urbi Mukhopadhyay
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sophie Levantovsky
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Teresa Maria Carusone
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sarah Gharbi
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sagar Bhogaraju
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
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González-Buenfil R, Vieyra-Sánchez S, Quinto-Cortés CD, Oppenheimer SJ, Pomat W, Laman M, Cervantes-Hernández MC, Barberena-Jonas C, Auckland K, Allen A, Allen S, Phipps ME, Huerta-Sanchez E, Ioannidis AG, Mentzer AJ, Moreno-Estrada A. Genetic Signatures of Positive Selection in Human Populations Adapted to High Altitude in Papua New Guinea. Genome Biol Evol 2024; 16:evae161. [PMID: 39173139 PMCID: PMC11339866 DOI: 10.1093/gbe/evae161] [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: 07/09/2024] [Indexed: 08/24/2024] Open
Abstract
Papua New Guinea (PNG) hosts distinct environments mainly represented by the ecoregions of the Highlands and Lowlands that display increased altitude and a predominance of pathogens, respectively. Since its initial peopling approximately 50,000 years ago, inhabitants of these ecoregions might have differentially adapted to the environmental pressures exerted by each of them. However, the genetic basis of adaptation in populations from these areas remains understudied. Here, we investigated signals of positive selection in 62 highlanders and 43 lowlanders across 14 locations in the main island of PNG using whole-genome genotype data from the Oceanian Genome Variation Project (OGVP) and searched for signals of positive selection through population differentiation and haplotype-based selection scans. Additionally, we performed archaic ancestry estimation to detect selection signals in highlanders within introgressed regions of the genome. Among highland populations we identified candidate genes representing known biomarkers for mountain sickness (SAA4, SAA1, PRDX1, LDHA) as well as candidate genes of the Notch signaling pathway (PSEN1, NUMB, RBPJ, MAML3), a novel proposed pathway for high altitude adaptation in multiple organisms. We also identified candidate genes involved in oxidative stress, inflammation, and angiogenesis, processes inducible by hypoxia, as well as in components of the eye lens and the immune response. In contrast, candidate genes in the lowlands are mainly related to the immune response (HLA-DQB1, HLA-DQA2, TAAR6, TAAR9, TAAR8, RNASE4, RNASE6, ANG). Moreover, we find two candidate regions to be also enriched with archaic introgressed segments, suggesting that archaic admixture has played a role in the local adaptation of PNG populations.
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Affiliation(s)
- Ram González-Buenfil
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Sofía Vieyra-Sánchez
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Consuelo D Quinto-Cortés
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | | | - William Pomat
- Vector-Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Moses Laman
- Vector-Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Mayté C Cervantes-Hernández
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Carmina Barberena-Jonas
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | | | - Angela Allen
- Department of Molecular Haematology, MRC Weatherall Institute of Molecular Medicine, Headley Way, Headington, Oxford, OX3 9DS, UK
| | - Stephen Allen
- Department of Clinical Sciences,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Emilia Huerta-Sanchez
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Alexander G Ioannidis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomedical Data Science, Stanford Medical School, Stanford, CA, USA
| | | | - Andrés Moreno-Estrada
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
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6
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Sadeghipour A, Taha SR, Shariat Zadeh M, Kosari F, Babaheidarian P, Fattahi F, Abdi N, Tajik F. Expression and Clinical Significance of Ki-67, CD10, BCL6, MUM1, c-MYC, and EBV in Diffuse Large B Cell Lymphoma Patients. Appl Immunohistochem Mol Morphol 2024; 32:309-321. [PMID: 38872345 DOI: 10.1097/pai.0000000000001208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Diffuse large B cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma (NHL) in adults. Although studies regarding the association between the expression of Ki-67, CD10, BCL6, and MUM1 proteins, as well as c-MYC amplification and EBV status with clinicopathologic characteristics have rapidly progressed, their co-expression and prognostic role remain unsatisfactory. Therefore, this study aimed to investigate the association between the expression of all markers and clinicopathologic features and their prognostic value in DLBCL. Also, the co-expression of markers was investigated. METHODS The protein expression levels and prognostic significance of Ki-67, CD10, BCL6, and MUM1 were investigated with clinical follow-up in a total of 53 DLBCL specimens (including germinal center B [GCB] and activated B cell [ABC] subtypes) as well as adjacent normal samples using immunohistochemistry (IHC). Besides, the clinical significance and prognostic value of c-MYC and EBV status were also evaluated through chromogenic in situ hybridization (CISH), and their correlation with other markers was also assessed. RESULTS The results demonstrated a positive correlation between CD10 and BCL6 expression, with both markers being associated with the GCB subtype ( P< 0.001 and P =0.001, respectively). Besides, we observe a statistically significant association between MUM1 protein expression and clinicopathologic type ( P< 0.005) as well as a positive association between c-MYC and recurrence ( P =0.028). Our survival analysis showed that patients who had responded to R-CHOP treatment had better overall survival (OS) and progression-free survival (PFS) than those who did not. CONCLUSION Collectively, this study's results add these markers' value to the existing clinical understanding of DLBCL. However, further investigations are needed to explore markers' prognostic and biological roles in DLBCL patients.
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MESH Headings
- Humans
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Male
- Female
- Middle Aged
- Interferon Regulatory Factors/metabolism
- Interferon Regulatory Factors/genetics
- Proto-Oncogene Proteins c-bcl-6/metabolism
- Proto-Oncogene Proteins c-bcl-6/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Proto-Oncogene Proteins c-myc/genetics
- Neprilysin/metabolism
- Adult
- Aged
- Ki-67 Antigen/metabolism
- Herpesvirus 4, Human
- Biomarkers, Tumor/metabolism
- Prognosis
- Epstein-Barr Virus Infections
- Aged, 80 and over
- Doxorubicin/therapeutic use
- Immunohistochemistry
- Gene Expression Regulation, Neoplastic
- Vincristine/therapeutic use
- Clinical Relevance
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Affiliation(s)
- Alireza Sadeghipour
- Department of Pathology, School of Medicine, Iran University of Medical Sciences
- Oncopathology Research Center, Iran University of Medical Sciences
| | - Seyed Reza Taha
- Oncopathology Research Center, Iran University of Medical Sciences
| | | | - Farid Kosari
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Babaheidarian
- Department of Pathology, School of Medicine, Iran University of Medical Sciences
| | - Fahimeh Fattahi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Navid Abdi
- Department of Pathology, School of Medicine, Iran University of Medical Sciences
| | - Fatemeh Tajik
- Oncopathology Research Center, Iran University of Medical Sciences
- Department of Surgery, University of California, Irvine Medical Center, Orange, CA
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Arredondo Eve A, Tunc E, Mehta D, Yoo JY, Yilmaz HE, Emren SV, Akçay FA, Madak Erdogan Z. PFAS and their association with the increased risk of cardiovascular disease in postmenopausal women. Toxicol Sci 2024; 200:312-323. [PMID: 38758093 DOI: 10.1093/toxsci/kfae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Cardiovascular diseases (CVDs) are one of the major causes of death globally. In addition to traditional risk factors such as unhealthy lifestyles (smoking, obesity, sedentary) and genetics, common environmental exposures, including persistent environmental contaminants, may also influence CVD risk. Per- and polyfluoroalkyl substances (PFASs) are a class of highly fluorinated chemicals used in household consumer and industrial products known to persist in our environment for years, causing health concerns that are now linked to endocrine disruptions and related outcomes in women, including interference of the cardiovascular and reproductive systems. In postmenopausal women, higher levels of PFAS are observed than in premenopausal women due to the cessation of menstruation, which is crucial for PFAS excretion. Because of these findings, we explored the association between perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), and perfluorobutanesulfonic acid in postmenopausal women from our previously established CVD study. We used liquid chromatography with tandem mass spectrometry, supported by machine learning approaches, and the detection and quantification of serum metabolites and proteins. Here, we show that PFOS can be a good predictor of coronary artery disease, whereas PFOA can be an intermediate predictor of coronary microvascular disease. We also found that the PFAS levels in our study are significantly associated with inflammation-related proteins. Our findings may provide new insight into the potential mechanisms underlying the PFAS-induced risk of CVDs in this population. This study shows that exposure to PFOA and PFOS is associated with an increased risk of cardiovascular disease in postmenopausal women. PFOS and PFOA levels correlate with amino acids and proteins related to inflammation. These circulating biomarkers contribute to the etiology of CVD and potentially implicate a mechanistic relationship between PFAS exposure and increased risk of cardiovascular events in this population.
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Affiliation(s)
- Alicia Arredondo Eve
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Elif Tunc
- Research and Training Hospital, Katip Celebi University, Izmir, 35310, Turkey
| | - Dhruv Mehta
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jin Young Yoo
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huriye Erbak Yilmaz
- Research and Training Hospital, Katip Celebi University, Izmir, 35310, Turkey
- Izmir Biomedicine and Genome Center, Balcova, Izmir, 35340, Turkey
| | - Sadık Volkan Emren
- Research and Training Hospital, Katip Celebi University, Izmir, 35310, Turkey
| | | | - Zeynep Madak Erdogan
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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Scott MA, Harvey KM, Karisch BB, Woolums AR, Tracy RM, Russell JR, Engel CL. Integrated Blood Transcriptome and Multi-Tissue Trace Mineral Analyses of Healthy Stocker Cattle Fed Complexed or Inorganic Trace Mineral Supplement. Animals (Basel) 2024; 14:2186. [PMID: 39123712 PMCID: PMC11311009 DOI: 10.3390/ani14152186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Supplementing trace minerals is common in managing bovine respiratory disease (BRD) in post-weaned cattle; however, its influence on host immunity and metabolism in high-risk cattle remains unclear. We aimed to assess the impact of three supplementation programs on liver and serum trace element concentrations and blood gene expression. Fifty-six high-risk beef steers were randomly assigned to one of three groups over 60 days: (1) sulfate-sourced Cu, Co, Mn, and Zn (INR), (2) amino acid-complexed Cu, Mn, Co, and Zn (AAC), or (3) AAC plus trace mineral and vitamin drench (COMBO). Serum and liver biopsies for Cu, Co, Mn, and Zn at d0, d28, and d60 were analyzed from cattle free of BRD (n = 9 INR; n = 6 AAC; n = 10 COMBO). Differences and correlations of mineral concentrations were analyzed via generalized linear mixed models and Spearman's rank coefficients, respectively (p < 0.05). Whole blood RNA samples from healthy cattle (n = 4 INR; n = 4 AAC; n = 4 COMBO) at d0, d13, d28, d45, and d60 were sequenced and analyzed for differentially expressed genes (DEGs) via glmmSeq (FDR < 0.05), edgeR (FDR < 0.10), and Trendy (p < 0.10). Serum and liver Cu and Co concentrations increased over time in all groups, with higher liver Cu in COMBO (487.985 μg/g) versus AAC (392.043 μg/g) at d60 (p = 0.013). Serum and liver Cu concentrations (ρ = 0.579, p = 6.59 × 10-8) and serum and liver Co concentrations (ρ = 0.466, p = 2.80 × 10-5) were linearly correlated. Minimal gene expression differences were found between AAC versus COMBO (n = 2 DEGs) and INR versus COMBO (n = 0 DEGs) over time. AAC versus INR revealed 107 DEGs (d13-d60) with increased traits in AAC including metabolism of carbohydrates/fat-soluble vitamins, antigen presentation, ATPase activity, and B- and T-cell activation, while osteoclast differentiation and neutrophil degranulation decreased in AAC compared to INR. Our study identifies gene expression differences in high-risk cattle fed inorganic or amino acid-complexed mineral supplements, revealing adaptive immune and metabolic mechanisms that may be improved by organically sourced supplementation.
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Affiliation(s)
- Matthew A. Scott
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX 79015, USA
| | - Kelsey M. Harvey
- Prairie Research Unit, Mississippi State University, Prairie, MS 39756, USA
| | - Brandi B. Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, Mississippi State University, Starkville, MS 39762, USA
| | - Rebecca M. Tracy
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX 79015, USA
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ElGrawani W, Sun G, Kliem FP, Sennhauser S, Pierre-Ferrer S, Rosi-Andersen A, Boccalaro I, Bethge P, Heo WD, Helmchen F, Adamantidis AR, Forger DB, Robles MS, Brown SA. BDNF-TrkB signaling orchestrates the buildup process of local sleep. Cell Rep 2024; 43:114500. [PMID: 39046880 DOI: 10.1016/j.celrep.2024.114500] [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: 05/15/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Sleep debt accumulates during wakefulness, leading to increased slow wave activity (SWA) during sleep, an encephalographic marker for sleep need. The use-dependent demands of prior wakefulness increase sleep SWA locally. However, the circuitry and molecular identity of this "local sleep" remain unclear. Using pharmacology and optogenetic perturbations together with transcriptomics, we find that cortical brain-derived neurotrophic factor (BDNF) regulates SWA via the activation of tyrosine kinase B (TrkB) receptor and cAMP-response element-binding protein (CREB). We map BDNF/TrkB-induced sleep SWA to layer 5 (L5) pyramidal neurons of the cortex, independent of neuronal firing per se. Using mathematical modeling, we here propose a model of how BDNF's effects on synaptic strength can increase SWA in ways not achieved through increased firing alone. Proteomic analysis further reveals that TrkB activation enriches ubiquitin and proteasome subunits. Together, our study reveals that local SWA control is mediated by BDNF-TrkB-CREB signaling in L5 excitatory cortical neurons.
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Affiliation(s)
- Waleed ElGrawani
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland.
| | - Guanhua Sun
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA
| | - Fabian P Kliem
- Institute of Medical Psychology and Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany
| | - Simon Sennhauser
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Sara Pierre-Ferrer
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| | - Alex Rosi-Andersen
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| | - Ida Boccalaro
- Zentrum für Experimentelle Neurologie, Department of Neurology, Inselspital University Hospital Bern, Bern, Switzerland
| | - Philipp Bethge
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland; Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Won Do Heo
- Department of Biological Science, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Fritjof Helmchen
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland; Brain Research Institute, University of Zurich, Zurich, Switzerland; University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
| | - Antoine R Adamantidis
- Zentrum für Experimentelle Neurologie, Department of Neurology, Inselspital University Hospital Bern, Bern, Switzerland.
| | - Daniel B Forger
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany.
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
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10
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Arifin MZ, Leitner J, Egan D, Waidhofer-Söllner P, Kolch W, Zhernovkov V, Steinberger P. BTLA and PD-1 signals attenuate TCR-mediated transcriptomic changes. iScience 2024; 27:110253. [PMID: 39021788 PMCID: PMC11253514 DOI: 10.1016/j.isci.2024.110253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/29/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
T cell co-inhibitory immune checkpoints, such as PD-1 or BTLA, are bona fide targets in cancer therapy. We used a human T cell reporter line to measure transcriptomic changes mediated by PD-1- and BTLA-induced signaling. T cell receptor (TCR)-complex stimulation resulted in the upregulation of a large number of genes but also in repression of a similar number of genes. PD-1 and BTLA signals attenuated transcriptomic changes mediated by TCR-complex signaling: upregulated genes tended to be suppressed and the expression of a significant number of downregulated genes was higher during PD-1 or BTLA signaling. BTLA was a significantly stronger attenuator of TCR-complex-induced transcriptome changes than PD-1. A strong overlap between genes that were regulated indicated quantitative rather than qualitative differences between these receptors. In line with their function as attenuators of TCR-complex-mediated changes, we found strongly regulated genes to be prime targets of PD-1 and BTLA signaling.
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Affiliation(s)
- Muhammad Zainul Arifin
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Judith Leitner
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Donagh Egan
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Petra Waidhofer-Söllner
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vadim Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peter Steinberger
- Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
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11
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Molinari C, Solaini L, Rebuzzi F, Tedaldi G, Angeli D, Petracci E, Prascevic D, Ewald J, Rahm E, Canale M, Giovanni M, Tomezzoli A, Bencivenga M, Ambrosio MR, Marrelli D, Morgagni P, Ercolani G, Ulivi P, Saragoni L. Genomic events stratifying prognosis of early gastric cancer. Gastric Cancer 2024:10.1007/s10120-024-01536-z. [PMID: 39028418 DOI: 10.1007/s10120-024-01536-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The purpose of the study was to conduct a comprehensive genomic characterization of gene alterations, microsatellite instability (MSI), and tumor mutational burden (TMB) in submucosal-penetrating (Pen) early gastric cancers (EGCs) with varying prognoses. METHODS Samples from EGC patients undergoing surgery and with 10-year follow-up data available were collected. Tissue genomic alterations were characterized using Trusight Oncology panel (TSO500). Pathway instability (PI) scores for a selection of 218 GC-related pathways were calculated both for the present case series and EGCs from the TCGA cohort. RESULTS Higher age and tumor location in the upper-middle tract are significantly associated with an increased hazard of relapse or death from any cause (p = 0.006 and p = 0.032). Even if not reaching a statistical significance, Pen A tumors more frequently present higher TMB values, higher frequency of MSI-subtypes and an overall increase in PI scores, along with an enrichment in immune pathways. ARID1A gene was observed to be significantly more frequently mutated in Pen A tumors (p = 0.006), as well as in patients with high TMB (p = 0.027). Tumors harboring LRP1B alterations seem to have a higher hazard of relapse or death from any cause (p = 0.089), being mutated mainly in relapsed patients (p = 0.093). CONCLUSIONS We found that the most aggressive subtype Pen A is characterized by a higher frequency of ARID1A mutations and a higher genetic instability, while LRP1B alterations seem to be related to a lower disease-free survival. Further investigations are needed to provide a rationale for the use of these markers to stratify prognosis in EGC patients.
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Affiliation(s)
- Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Leonardo Solaini
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- General and Oncologic Surgery, Morgagni-Pierantoni Hospital, AUSL Romagna, Forlì, Italy.
| | - Francesca Rebuzzi
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Gianluca Tedaldi
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Davide Angeli
- Biostatistics and Clinical Trials Unit, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST), "Dino Amadori", Meldola, FC, Italy
| | - Elisabetta Petracci
- Biostatistics and Clinical Trials Unit, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST), "Dino Amadori", Meldola, FC, Italy
| | - Dusan Prascevic
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig University, Humboldtstr. 25, 04105, Leipzig, Germany
| | - Jan Ewald
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig University, Humboldtstr. 25, 04105, Leipzig, Germany
| | - Erhard Rahm
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden/Leipzig University, Humboldtstr. 25, 04105, Leipzig, Germany
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Martinelli Giovanni
- Department of Hematology and Sciences Oncology, Institute of Haematology "L. and A. Seràgnoli", S. Orsola University Hospital, Bologna, Italy
| | - Anna Tomezzoli
- Department of Pathology, University of Verona, Verona, Italy
| | | | | | | | - Paolo Morgagni
- General and Oncologic Surgery, Morgagni-Pierantoni Hospital, AUSL Romagna, Forlì, Italy
| | - Giorgio Ercolani
- General and Oncologic Surgery, Morgagni-Pierantoni Hospital, AUSL Romagna, Forlì, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Luca Saragoni
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, Italy
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12
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Silva AAR, Cardoso MR, de Oliveira DC, Godoy P, Talarico MCR, Gutiérrez JM, Rodrigues Peres RM, de Carvalho LM, Miyaguti NADS, Sarian LO, Tata A, Derchain SFM, Porcari AM. Plasma Metabolome Signatures to Predict Responsiveness to Neoadjuvant Chemotherapy in Breast Cancer. Cancers (Basel) 2024; 16:2473. [PMID: 39001535 PMCID: PMC11240312 DOI: 10.3390/cancers16132473] [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: 06/18/2024] [Revised: 06/27/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND Neoadjuvant chemotherapy (NACT) has arisen as a treatment option for breast cancer (BC). However, the response to NACT is still unpredictable and dependent on cancer subtype. Metabolomics is a tool for predicting biomarkers and chemotherapy response. We used plasma to verify metabolomic alterations in BC before NACT, relating to clinical data. METHODS Liquid chromatography coupled to mass spectrometry (LC-MS) was performed on pre-NACT plasma from patients with BC (n = 75). After data filtering, an SVM model for classification was built and validated with 75%/25% of the data, respectively. RESULTS The model composed of 19 identified metabolites effectively predicted NACT response for training/validation sets with high sensitivity (95.4%/93.3%), specificity (91.6%/100.0%), and accuracy (94.6%/94.7%). In both sets, the panel correctly classified 95% of resistant and 94% of sensitive females. Most compounds identified by the model were lipids and amino acids and revealed pathway alterations related to chemoresistance. CONCLUSION We developed a model for predicting patient response to NACT. These metabolite panels allow clinical gain by building precision medicine strategies based on tumor stratification.
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Affiliation(s)
- Alex Ap. Rosini Silva
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
| | - Marcella R. Cardoso
- Department of Obstetrics and Gynecology, Division of Gynecologic and Breast Oncology, Faculty of Medical Sciences, University of Campinas (UNICAMP—Universidade Estadual de Campinas), Campinas 13083881, São Paulo, Brazil
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Danilo Cardoso de Oliveira
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
| | - Pedro Godoy
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
| | - Maria Cecília R. Talarico
- Department of Obstetrics and Gynecology, Division of Gynecologic and Breast Oncology, Faculty of Medical Sciences, University of Campinas (UNICAMP—Universidade Estadual de Campinas), Campinas 13083881, São Paulo, Brazil
| | - Junier Marrero Gutiérrez
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
| | - Raquel M. Rodrigues Peres
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
| | - Lucas M. de Carvalho
- Post Graduate Program in Health Sciences, São Francisco University, Bragança Paulista 12916900, São Paulo, Brazil
| | - Natália Angelo da Silva Miyaguti
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
| | - Luis O. Sarian
- Department of Obstetrics and Gynecology, Division of Gynecologic and Breast Oncology, Faculty of Medical Sciences, University of Campinas (UNICAMP—Universidade Estadual de Campinas), Campinas 13083881, São Paulo, Brazil
| | - Alessandra Tata
- Laboratory of Experimental Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale Fiume 78, 36100 Vicenza, Italy;
| | - Sophie F. M. Derchain
- Department of Obstetrics and Gynecology, Division of Gynecologic and Breast Oncology, Faculty of Medical Sciences, University of Campinas (UNICAMP—Universidade Estadual de Campinas), Campinas 13083881, São Paulo, Brazil
| | - Andreia M. Porcari
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Av. São Francisco de Assis, 218, Sala 211, Prédio 5, Bragança Paulista 12916900, São Paulo, Brazil; (A.A.R.S.); (D.C.d.O.)
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13
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Reyaz E, Tandon R, Beg MA, Dey R, Puri N, Salotra P, Nakhasi HL, Selvapandiyan A. Proteome profile of Leishmania donovani Centrin1 -/- parasite-infected human macrophage cell line and its implications in determining possible mechanisms of protective immunity. Microbes Infect 2024; 26:105340. [PMID: 38663721 DOI: 10.1016/j.micinf.2024.105340] [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: 10/23/2023] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Our developed cell division-specific 'centrin' gene deleted Leishmania donovani (LdCen1-/-) the causative parasite of the fatal visceral-leishmaniasis (VL), exhibits a selective growth arrest at the intracellular stage and is anticipated as a live attenuated vaccine candidate against VL. LdCen1-/- immunization in animals has shown increased IFN-γ secreting CD4+ and CD8+ T cells along with protection conferred by a protective proinflammatory immune response. A label-free proteomics approach has been employed to understand the physiology of infection and predict disease interceptors during Leishmania-host interactions. Proteomic modulation after infection of human macrophage cell lines suggested elevated annexin A6, implying involvement in various biological processes such as membrane repair, transport, actin dynamics, cell proliferation, survival, differentiation, and inflammation, thereby potentiating its immunological protective capacity. Additionally, S100A8 and S100A9 proteins, known for maintaining homeostatic balance in regulating the inflammatory response, have been upregulated after infection. The inhibitory clade of serpins, known to inhibit cysteine proteases (CPs), was upregulated in host cells after 48 h of infection. This is reflected in the diminished expression of CPs in the parasites during infection. Such proteome analysis confirms LdCen1-/- efficacy as a vaccine candidate and predicts potential markers in future vaccine development strategies against infectious diseases.
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Affiliation(s)
- Enam Reyaz
- JH-Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Rati Tandon
- JH-Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Mirza Adil Beg
- JH-Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Ranadhir Dey
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Niti Puri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India
| | - Hira L Nakhasi
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD 20993, USA
| | - A Selvapandiyan
- JH-Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India.
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14
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Trastulla L, Dolgalev G, Moser S, Jiménez-Barrón LT, Andlauer TFM, von Scheidt M, Budde M, Heilbronner U, Papiol S, Teumer A, Homuth G, Völzke H, Dörr M, Falkai P, Schulze TG, Gagneur J, Iorio F, Müller-Myhsok B, Schunkert H, Ziller MJ. Distinct genetic liability profiles define clinically relevant patient strata across common diseases. Nat Commun 2024; 15:5534. [PMID: 38951512 PMCID: PMC11217418 DOI: 10.1038/s41467-024-49338-2] [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: 02/20/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Stratified medicine holds great promise to tailor treatment to the needs of individual patients. While genetics holds great potential to aid patient stratification, it remains a major challenge to operationalize complex genetic risk factor profiles to deconstruct clinical heterogeneity. Contemporary approaches to this problem rely on polygenic risk scores (PRS), which provide only limited clinical utility and lack a clear biological foundation. To overcome these limitations, we develop the CASTom-iGEx approach to stratify individuals based on the aggregated impact of their genetic risk factor profiles on tissue specific gene expression levels. The paradigmatic application of this approach to coronary artery disease or schizophrenia patient cohorts identified diverse strata or biotypes. These biotypes are characterized by distinct endophenotype profiles as well as clinical parameters and are fundamentally distinct from PRS based groupings. In stark contrast to the latter, the CASTom-iGEx strategy discovers biologically meaningful and clinically actionable patient subgroups, where complex genetic liabilities are not randomly distributed across individuals but rather converge onto distinct disease relevant biological processes. These results support the notion of different patient biotypes characterized by partially distinct pathomechanisms. Thus, the universally applicable approach presented here has the potential to constitute an important component of future personalized medicine paradigms.
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Affiliation(s)
- Lucia Trastulla
- Max Planck Institute of Psychiatry, Munich, Germany
- Technische Universität München Medical Graduate Center Experimental Medicine, Munich, Germany
- Human Technopole, Milan, Italy
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Georgii Dolgalev
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Sylvain Moser
- Max Planck Institute of Psychiatry, Munich, Germany
- Technische Universität München Medical Graduate Center Experimental Medicine, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - Laura T Jiménez-Barrón
- Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany
| | - Till F M Andlauer
- Max Planck Institute of Psychiatry, Munich, Germany
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Moritz von Scheidt
- Klinik für Herz-und Kreislauferkrankungen, Deutsches Herzzentrum München, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Monika Budde
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, 80336, Germany
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, 80336, Germany
| | - Sergi Papiol
- Max Planck Institute of Psychiatry, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, 80336, Germany
| | - Alexander Teumer
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Institute of Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Peter Falkai
- Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, 80336, Germany
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, 80336, Germany
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Heribert Schunkert
- Klinik für Herz-und Kreislauferkrankungen, Deutsches Herzzentrum München, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Michael J Ziller
- Max Planck Institute of Psychiatry, Munich, Germany.
- Department of Psychiatry, University of Münster, Münster, Germany.
- Center for Soft Nanoscience, University of Münster, Münster, Germany.
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15
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Kamathewatta KI, Condello AK, Kulappu Arachchige SN, Young ND, Shil PK, Noormohammadi AH, Tivendale KA, Wawegama NK, Browning GF. Characterisation of the tracheal transcriptional response of chickens to chronic infection with Mycoplasma synoviae. Vet Microbiol 2024; 294:110119. [PMID: 38772075 DOI: 10.1016/j.vetmic.2024.110119] [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: 03/05/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
Mycoplasma synoviae causes infectious synovitis and respiratory tract infections in chickens and is responsible for significant economic losses in the poultry industry. Effective attachment and colonisation of the trachea is critical for the persistence of the organism and progression of the disease it causes. The respiratory tract infection is usually sub-clinical, but concurrent infection with infectious bronchitis virus (IBV) is known to enhance the pathogenicity of M. synoviae. This study aimed to explore differentially expressed genes in the tracheal mucosa, and their functional categories, during chronic infection with M. synoviae, using a M. synoviae-IBV infection model. The transcriptional profiles of the trachea were assessed 2 weeks after infection using RNA sequencing. In chickens infected with M. synoviae or IBV, only 1 or 8 genes were differentially expressed compared to uninfected chickens, respectively. In contrast, the M. synoviae-IBV infected chickens had 621 upregulated and 206 downregulated genes compared to uninfected chickens. Upregulated genes and their functional categories were suggestive of uncontrolled lymphoid cell proliferation and an ongoing pro-inflammatory response. Genes associated with anti-inflammatory effects, pathogen removal, apoptosis, regulation of the immune response, airway homoeostasis, cell adhesion and tissue regeneration were downregulated. Overall, transcriptional changes in the trachea, 2 weeks after infection with M. synoviae and IBV, indicate immune dysregulation, robust inflammation and a lack of cytotoxic damage during chronic infection. This model provides insights into the pathogenesis of chronic infection with M. synoviae.
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Affiliation(s)
- Kanishka I Kamathewatta
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Anna Kanci Condello
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Sathya N Kulappu Arachchige
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Pollob K Shil
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, Australia
| | - Kelly A Tivendale
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia.
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16
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Lister KC, Wong C, Uttam S, Parisien M, Stecum P, Brown N, Cai W, Hooshmandi M, Gu N, Amiri M, Beaudry F, Jafarnejad SM, Tavares-Ferreira D, Inturi NN, Mazhar K, Zhao HT, Fitzsimmons B, Gkogkas CG, Sonenberg N, Price TJ, Diatchenko L, Atlasi Y, Mogil JS, Khoutorsky A. Translational control in the spinal cord regulates gene expression and pain hypersensitivity in the chronic phase of neuropathic pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600539. [PMID: 38979173 PMCID: PMC11230214 DOI: 10.1101/2024.06.24.600539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sensitization of spinal nociceptive circuits plays a crucial role in neuropathic pain. This sensitization depends on new gene expression that is primarily regulated via transcriptional and translational control mechanisms. The relative roles of these mechanisms in regulating gene expression in the clinically relevant chronic phase of neuropathic pain are not well understood. Here, we show that changes in gene expression in the spinal cord during the chronic phase of neuropathic pain are substantially regulated at the translational level. Downregulating spinal translation at the chronic phase alleviated pain hypersensitivity. Cell-type-specific profiling revealed that spinal inhibitory neurons exhibited greater changes in translation after peripheral nerve injury compared to excitatory neurons. Notably, increasing translation selectively in all inhibitory neurons or parvalbumin-positive (PV+) interneurons, but not excitatory neurons, promoted mechanical pain hypersensitivity. Furthermore, increasing translation in PV+ neurons decreased their intrinsic excitability and spiking activity, whereas reducing translation in spinal PV+ neurons prevented the nerve injury-induced decrease in excitability. Thus, translational control mechanisms in the spinal cord, particularly in inhibitory neurons, play a role in mediating neuropathic pain hypersensitivity.
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Affiliation(s)
- Kevin C. Lister
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Calvin Wong
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Sonali Uttam
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Marc Parisien
- Department of Anesthesia, McGill University, Montreal, QC, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Patricia Stecum
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Nicole Brown
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Weihua Cai
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Mehdi Hooshmandi
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Ning Gu
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Mehdi Amiri
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Francis Beaudry
- Département de biomédecine vétérinaire, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Centre de recherche sur le cerveau et l’apprentissage (CIRCA), Université de Montréal, Montréal, Québec, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, BT9 7AE, UK
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, 75080
| | - Nikhil Nageshwar Inturi
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, 75080
| | - Khadijah Mazhar
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, 75080
| | | | | | - Christos G. Gkogkas
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Theodore J. Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, 75080
| | - Luda Diatchenko
- Department of Anesthesia, McGill University, Montreal, QC, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Yaser Atlasi
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, BT9 7AE, UK
| | - Jeffrey S. Mogil
- Department of Anesthesia, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
- Department of Psychology, Faculty of Science, McGill University, Montreal, QC, Canada
| | - Arkady Khoutorsky
- Department of Anesthesia, McGill University, Montreal, QC, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
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17
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Jang J, Park HJ, Seong W, Kim J, Kim C. Vimentin-mediated buffering of internal integrin β1 pool increases survival of cells from anoikis. BMC Biol 2024; 22:139. [PMID: 38915055 PMCID: PMC11197373 DOI: 10.1186/s12915-024-01942-w] [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: 02/10/2024] [Accepted: 06/18/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND The intermediate filament protein vimentin is widely recognized as a molecular marker of epithelial-to-mesenchymal transition. Although vimentin expression is strongly associated with cancer metastatic potential, the exact role of vimentin in cancer metastasis and the underlying mechanism of its pro-metastatic functions remain unclear. RESULTS This study revealed that vimentin can enhance integrin β1 surface expression and induce integrin-dependent clustering of cells, shielding them against anoikis cell death. The increased integrin β1 surface expression in suspended cells was caused by vimentin-mediated protection of the internal integrin β1 pool against lysosomal degradation. Additionally, cell detachment was found to induce vimentin Ser38 phosphorylation, allowing the translocation of internal integrin β1 to the plasma membrane. Furthermore, the use of an inhibitor of p21-activated kinase PAK1, one of the kinases responsible for vimentin Ser38 phosphorylation, significantly reduced cancer metastasis in animal models. CONCLUSIONS These findings suggest that vimentin can act as an integrin buffer, storing internalized integrin β1 and releasing it when needed. Overall, this study provides insights regarding the strong correlation between vimentin expression and cancer metastasis and a basis for blocking metastasis using this novel therapeutic mechanism.
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Affiliation(s)
- Jiyoung Jang
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun Jung Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Wonyoung Seong
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Jiyoon Kim
- Donnelly Centre, University of Toronto, ON, Toronto, M5S 3E1, Canada
| | - Chungho Kim
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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18
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Huang CY, Jiang N, Shen M, Lai GG, Tan AC, Jain A, Saw SP, Ang MK, Ng QS, Lim DW, Kanesvaran R, Tan EH, Tan WL, Ong BH, Chua KL, Anantham D, Takano AM, Lim KH, Tam WL, Sim NL, Skanderup AJ, Tan DS, Rozen SG. Oncogene-Driven Non-Small Cell Lung Cancers in Patients with a History of Smoking Lack Smoking-Induced Mutations. Cancer Res 2024; 84:2009-2020. [PMID: 38587551 DOI: 10.1158/0008-5472.can-23-2551] [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: 09/01/2023] [Revised: 12/29/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Non-small cell lung cancers (NSCLC) in nonsmokers are mostly driven by mutations in the oncogenes EGFR, ERBB2, and MET and fusions involving ALK and RET. In addition to occurring in nonsmokers, alterations in these "nonsmoking-related oncogenes" (NSRO) also occur in smokers. To better understand the clonal architecture and genomic landscape of NSRO-driven tumors in smokers compared with typical-smoking NSCLCs, we investigated genomic and transcriptomic alterations in 173 tumor sectors from 48 NSCLC patients. NSRO-driven NSCLCs in smokers and nonsmokers had similar genomic landscapes. Surprisingly, even in patients with prominent smoking histories, the mutational signature caused by tobacco smoking was essentially absent in NSRO-driven NSCLCs, which was confirmed in two large NSCLC data sets from other geographic regions. However, NSRO-driven NSCLCs in smokers had higher transcriptomic activities related to the regulation of the cell cycle. These findings suggest that, whereas the genomic landscape is similar between NSRO-driven NSCLC in smokers and nonsmokers, smoking still affects the tumor phenotype independently of genomic alterations. SIGNIFICANCE Non-small cell lung cancers driven by nonsmoking-related oncogenes do not harbor genomic scars caused by smoking regardless of smoking history, indicating that the impact of smoking on these tumors is mainly nongenomic.
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Affiliation(s)
- Chen-Yang Huang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Nanhai Jiang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Meixin Shen
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Gillianne G Lai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Stephanie P Saw
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mei Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Darren W Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Eng Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Boon-Hean Ong
- Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore, Singapore
| | - Kevin L Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Devanand Anantham
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Angela M Takano
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ngak Leng Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anders J Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel S Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
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19
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Boucau J, Naidoo T, Liu Y, Dasgupta S, Jain N, Castillo JR, Jacobson NE, Nargan K, Cimini BA, Eliceiri KW, Steyn AJ, Barczak AK. A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597479. [PMID: 38895338 PMCID: PMC11185692 DOI: 10.1101/2024.06.04.597479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Post-TB lung disease (PTLD) causes a significant burden of global disease. Fibrosis is a central component of many clinical features of PTLD. To date, we have a limited understanding of the mechanisms of TB-associated fibrosis and how these mechanisms are similar to or dissimilar from other fibrotic lung pathologies. We have adapted a mouse model of TB infection to facilitate the mechanistic study of TB-associated lung fibrosis. We find that the morphologies of fibrosis that develop in the mouse model are similar to the morphologies of fibrosis observed in human tissue samples. Using Second Harmonic Generation (SHG) microscopy, we are able to quantify a major component of fibrosis, fibrillar collagen, over time and with treatment. Inflammatory macrophage subpopulations persist during treatment; matrix remodeling enzymes and inflammatory gene signatures remain elevated. Our mouse model suggests that there is a therapeutic window during which adjunctive therapies could change matrix remodeling or inflammatory drivers of tissue pathology to improve functional outcomes after treatment for TB infection.
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Affiliation(s)
- Julie Boucau
- The Ragon Institute of Mass General Brigham, MIT, and Harvard, Cambridge, MA, USA
| | - Threnesan Naidoo
- Africa Health Research Institute (AHRI), University of Kwazulu-Natal, Durban, South Africa
- Departments of Forensic & Legal Medicine and Laboratory Medicine & Pathology, Walter Sisulu University, Mthatha, Eastern Cape, South Africa
| | - Yuming Liu
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Neha Jain
- The Ragon Institute of Mass General Brigham, MIT, and Harvard, Cambridge, MA, USA
| | | | - Nicholas E. Jacobson
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Kievershen Nargan
- Africa Health Research Institute (AHRI), University of Kwazulu-Natal, Durban, South Africa
| | | | - Kevin W. Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Medical Physics, University of Wisconsin, Madison, WI, USA
| | - Adrie J.C. Steyn
- Africa Health Research Institute (AHRI), University of Kwazulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amy K. Barczak
- The Ragon Institute of Mass General Brigham, MIT, and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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20
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Nauta S, Greven J, Hofman M, Mohren R, Meesters DM, Möckel D, Lammers T, Hildebrand F, Siegel TP, Cuypers E, Heeren RM, Poeze M. Mass Spectrometry Reveals Molecular Effects of Citrulline Supplementation during Bone Fracture Healing in a Rat Model. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1184-1196. [PMID: 38679918 PMCID: PMC11157653 DOI: 10.1021/jasms.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
Bone fracture healing is a complex process in which specific molecular knowledge is still lacking. The citrulline-arginine-nitric oxide metabolism is one of the involved pathways, and its enrichment via citrulline supplementation can enhance fracture healing. This study investigated the molecular effects of citrulline supplementation during the different fracture healing phases in a rat model. Microcomputed tomography (μCT) was applied for the analysis of the fracture callus formation. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid-chromatography tandem mass spectrometry (LC-MS/MS) were used for lipid and protein analyses, respectively. μCT analysis showed no significant differences in the fracture callus volume and volume fraction between the citrulline supplementation and control group. The observed lipid profiles for the citrulline supplementation and control group were distinct for the different fracture healing stages. The main contributing lipid classes were phosphatidylcholines (PCs) and lysophosphatidylcholines (LPCs). The changing effect of citrulline supplementation throughout fracture healing was indicated by changes in the differentially expressed proteins between the groups. Pathway analysis showed an enhancement of fracture healing in the citrulline supplementation group in comparison to the control group via improved angiogenesis and earlier formation of the soft and hard callus. This study showed the molecular effects on lipids, proteins, and pathways associated with citrulline supplementation during bone fracture healing, even though no effect was visible with μCT.
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Affiliation(s)
- Sylvia Nauta
- Division
of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging
(M4i) Institute, Maastricht University, 6229ER Maastricht, The Netherlands
- Division
of Traumasurgery, Department of Surgery, Maastricht University Medical Center, 6229HX Maastricht, The Netherlands
| | - Johannes Greven
- Department
of Orthopedics, Trauma and Reconstructive Surgery, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Martijn Hofman
- Center
of Musculoskeletal Surgery, Bonifatius Hospital
Lingen, 49808 Lingen, Germany
| | - Ronny Mohren
- Division
of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging
(M4i) Institute, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Dennis M. Meesters
- Department
of Genetics & Cell Biology, Maastricht
University, 6229ER Maastricht, The Netherlands
- NUTRIM, School
for Nutrition and Translational Research in Metabolism, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Diana Möckel
- Department
of Nanomedicine and Theranostics, Institute for Experimental Molecular
Imaging, RWTH Aachen University Clinic, 52074 Aachen, Germany
| | - Twan Lammers
- Department
of Nanomedicine and Theranostics, Institute for Experimental Molecular
Imaging, RWTH Aachen University Clinic, 52074 Aachen, Germany
| | - Frank Hildebrand
- Department
of Orthopedics, Trauma and Reconstructive Surgery, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Tiffany Porta Siegel
- Division
of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging
(M4i) Institute, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Eva Cuypers
- Division
of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging
(M4i) Institute, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Ron M.A. Heeren
- Division
of Imaging Mass Spectrometry, Maastricht MultiModal Molecular Imaging
(M4i) Institute, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Martijn Poeze
- Division
of Traumasurgery, Department of Surgery, Maastricht University Medical Center, 6229HX Maastricht, The Netherlands
- NUTRIM, School
for Nutrition and Translational Research in Metabolism, Maastricht University, 6229ER Maastricht, The Netherlands
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21
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Almeida MC, Eger SJ, He C, Audouard M, Nikitina A, Glasauer SMK, Han D, Mejía-Cupajita B, Acosta-Uribe J, Villalba-Moreno ND, Littau JL, Elcheikhali M, Rivera EK, Carrettiero DC, Villegas-Lanau CA, Sepulveda-Falla D, Lopera F, Kosik KS. Single-nucleus RNA sequencing demonstrates an autosomal dominant Alzheimer's disease profile and possible mechanisms of disease protection. Neuron 2024; 112:1778-1794.e7. [PMID: 38417436 PMCID: PMC11156559 DOI: 10.1016/j.neuron.2024.02.009] [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: 05/16/2023] [Revised: 01/07/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024]
Abstract
Highly penetrant autosomal dominant Alzheimer's disease (ADAD) comprises a distinct disease entity as compared to the far more prevalent form of AD in which common variants collectively contribute to risk. The downstream pathways that distinguish these AD forms in specific cell types have not been deeply explored. We compared single-nucleus transcriptomes among a set of 27 cases divided among PSEN1-E280A ADAD carriers, sporadic AD, and controls. Autophagy genes and chaperones clearly defined the PSEN1-E280A cases compared to sporadic AD. Spatial transcriptomics validated the activation of chaperone-mediated autophagy genes in PSEN1-E280A. The PSEN1-E280A case in which much of the brain was spared neurofibrillary pathology and harbored a homozygous APOE3-Christchurch variant revealed possible explanations for protection from AD pathology including overexpression of LRP1 in astrocytes, increased expression of FKBP1B, and decreased PSEN1 expression in neurons. The unique cellular responses in ADAD and sporadic AD require consideration when designing clinical trials.
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Affiliation(s)
- Maria Camila Almeida
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Center for Natural and Humans Sciences, Federal University of ABC, Sao Bernardo do Campo, SP 09608020, Brazil
| | - Sarah J Eger
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Caroline He
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Morgane Audouard
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Arina Nikitina
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stella M K Glasauer
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Dasol Han
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Barbara Mejía-Cupajita
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia
| | - Nelson David Villalba-Moreno
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessica Lisa Littau
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Megan Elcheikhali
- Department of Statistics and Applied Probability, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Erica Keane Rivera
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Daniel Carneiro Carrettiero
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Center for Natural and Humans Sciences, Federal University of ABC, Sao Bernardo do Campo, SP 09608020, Brazil
| | | | - Diego Sepulveda-Falla
- Molecular Neuropathology of Alzheimer's Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia, School of Medicine, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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22
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Duran P, Yang BA, Plaster E, Eiken M, Loebel C, Aguilar CA. Tracking of Nascent Matrix Deposition during Muscle Stem Cell Activation across Lifespan Using Engineered Hydrogels. Adv Biol (Weinh) 2024; 8:e2400091. [PMID: 38616175 DOI: 10.1002/adbi.202400091] [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: 02/18/2024] [Revised: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Adult stem cells occupy a niche that contributes to their function, but how stem cells rebuild their microenvironment after injury remains an open-ended question. Herein, biomaterial-based systems and metabolic labeling are utilized to evaluate how skeletal muscle stem cells deposit extracellular matrix. Muscle stem cells and committed myoblasts are observed to generate less nascent matrix than muscle resident fibro-adipogenic progenitors. When cultured on substrates that matched the stiffness of physiological uninjured and injured muscles, muscle stem cells increased nascent matrix deposition with activation kinetics. Reducing the ability to deposit nascent matrix by an inhibitor of vesicle trafficking (Exo-1) attenuated muscle stem cell function and mimicked impairments observed from muscle stem cells isolated from old muscles. Old muscle stem cells are observed to deposit less nascent matrix than young muscle stem cells, which is rescued with therapeutic supplementation of insulin-like growth factors. These results highlight the role of nascent matrix production with muscle stem cell activation.
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Affiliation(s)
- Pamela Duran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleanor Plaster
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madeline Eiken
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science & Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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23
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Lu YC, Tseng LW, Wu CE, Yang CW, Yang TH, Chen HY. Can Chinese herbal medicine offer feasible solutions for newly diagnosed esophageal cancer patients with malnutrition? a multi-institutional real-world study. Front Pharmacol 2024; 15:1364318. [PMID: 38855746 PMCID: PMC11157104 DOI: 10.3389/fphar.2024.1364318] [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: 01/02/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Background Esophageal cancer (EC) is a major cause of cancer-related mortality in Taiwan and globally. Patients with EC are highly prone to malnutrition, which adversely affects their prognosis. While Chinese herbal medicine (CHM) is commonly used alongside conventional anti-cancer treatments, its long-term impact on EC patients with malnutrition remains unclear. Methods This study utilized a multi-center cohort from the Chang Gung Research Database, focusing on the long-term outcomes of CHM in EC patients with malnutrition between 1 January 2001, and 31 December 2018. Patients were monitored for up to 5 years or until death. Overall survival (OS) rates were calculated using the Kaplan-Meier method. Overlap weighting and landmark analysis were employed to address confounding and immortal time biases. Additionally, the study analyzed prescription data using a CHM network to identify key CHMs for EC with malnutrition, and potential molecular pathways were investigated using the Reactome database. Results EC patients with malnutrition who used CHM had a higher 5-year OS compared with nonusers (22.5% vs. 9% without overlap weighting; 24.3% vs. 13.3% with overlap weighting; log-rank test: p = 0.006 and 0.016, respectively). The median OS of CHM users was significantly longer than that of nonusers (19.8 vs. 12.9 months, respectively). Hazard ratio (HR) analysis showed a 31% reduction in all-cause mortality risk for CHM users compared with nonusers (HR: 0.69, 95% confidence interval: 0.50-0.94, p = 0.019). We also examined 665 prescriptions involving 306 CHM, with Hedyotis diffusa Willd. exhibiting the highest frequency of use. A CHM network was created to determine the primary CHMs and their combinations. The identified CHMs were associated with the regulation of immune and metabolic pathways, particularly in areas related to immune modulation, anti-cancer cachexia, promotion of digestion, and anti-tumor activity. Conclusion The results of this study suggest a correlation between CHM use and improved clinical outcomes in EC patients with malnutrition. The analysis identified core CHMs and combinations of formulations that play a crucial role in immunomodulation and metabolic regulation. These findings lay the groundwork for more extensive research on the use of CHM for the management of malnutrition in patients with EC.
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Affiliation(s)
- Yi-Chin Lu
- Division of Chinese Internal Medicine, Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Liang-Wei Tseng
- Division of Chinese Acupuncture and Traumatology, Center of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chiao-En Wu
- Division of Haematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ching-Wei Yang
- Division of Chinese Internal Medicine, Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tsung-Hsien Yang
- Division of Chinese Internal Medicine, Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsing-Yu Chen
- Division of Chinese Internal Medicine, Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Bampali M, Kouvela A, Kesesidis N, Kassela K, Dovrolis N, Karakasiliotis I. West Nile Virus Subgenomic RNAs Modulate Gene Expression in a Neuronal Cell Line. Viruses 2024; 16:812. [PMID: 38793693 PMCID: PMC11125720 DOI: 10.3390/v16050812] [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: 02/19/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are small non-coding products of the incomplete degradation of viral genomic RNA. They accumulate during flaviviral infection and have been associated with many functional roles inside the host cell. Studies so far have demonstrated that sfRNA plays a crucial role in determining West Nile virus (WNV) pathogenicity. However, its modulatory role on neuronal homeostasis has not been studied in depth. In this study, we investigated the mechanism of sfRNA biosynthesis and its importance for WNV replication in neuronal cells. We found that sfRNA1 is functionally redundant for both replication and translation of WNV. However, the concurrent absence of sfRNA1 and sfRNA2 species is detrimental for the survival of the virus. Differential expression analysis on RNA-seq data from WT and ΔsfRNA replicon cell lines revealed transcriptional changes induced by sfRNA and identified a number of putative targets. Overall, it was shown that sfRNA contributes to the viral evasion by suppressing the interferon-mediated antiviral response. An additional differential expression analysis among replicon and control Neuro2A cells also clarified the transcriptional changes that support WNV replication in neuronal cells. Increased levels of translation and oxidative phosphorylation, post-translational modification processes, and activated DNA repair pathways were observed in replicon cell lines, while developmental processes such as axonal growth were deficient.
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Affiliation(s)
| | | | | | | | | | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.B.); (A.K.); (N.K.); (K.K.); (N.D.)
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25
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Moll M, Hecker J, Platig J, Zhang J, Ghosh AJ, Pratte KA, Wang RS, Hill D, Konigsberg IR, Chiles JW, Hersh CP, Castaldi PJ, Glass K, Dy JG, Sin DD, Tal-Singer R, Mouded M, Rennard SI, Anderson GP, Kinney GL, Bowler RP, Curtis JL, McDonald ML, Silverman EK, Hobbs BD, Cho MH. Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.20.24307621. [PMID: 38826461 PMCID: PMC11142287 DOI: 10.1101/2024.05.20.24307621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Rationale Genetic variants and gene expression predict risk of chronic obstructive pulmonary disease (COPD), but their effect on COPD heterogeneity is unclear. Objectives Define high-risk COPD subtypes using both genetics (polygenic risk score, PRS) and blood gene expression (transcriptional risk score, TRS) and assess differences in clinical and molecular characteristics. Methods We defined high-risk groups based on PRS and TRS quantiles by maximizing differences in protein biomarkers in a COPDGene training set and identified these groups in COPDGene and ECLIPSE test sets. We tested multivariable associations of subgroups with clinical outcomes and compared protein-protein interaction networks and drug repurposing analyses between high-risk groups. Measurements and Main Results We examined two high-risk omics-defined groups in non-overlapping test sets (n=1,133 NHW COPDGene, n=299 African American (AA) COPDGene, n=468 ECLIPSE). We defined "High activity" (low PRS/high TRS) and "severe risk" (high PRS/high TRS) subgroups. Participants in both subgroups had lower body-mass index (BMI), lower lung function, and alterations in metabolic, growth, and immune signaling processes compared to a low-risk (low PRS, low TRS) reference subgroup. "High activity" but not "severe risk" participants had greater prospective FEV 1 decline (COPDGene: -51 mL/year; ECLIPSE: - 40 mL/year) and their proteomic profiles were enriched in gene sets perturbed by treatment with 5-lipoxygenase inhibitors and angiotensin-converting enzyme (ACE) inhibitors. Conclusions Concomitant use of polygenic and transcriptional risk scores identified clinical and molecular heterogeneity amongst high-risk individuals. Proteomic and drug repurposing analysis identified subtype-specific enrichment for therapies and suggest prior drug repurposing failures may be explained by patient selection.
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Amran A, Pigatto L, Farley J, Godini R, Pocock R, Gopal S. The matrisome landscape controlling in vivo germ cell fates. Nat Commun 2024; 15:4200. [PMID: 38760342 PMCID: PMC11101451 DOI: 10.1038/s41467-024-48283-4] [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: 08/17/2023] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
The developmental fate of cells is regulated by intrinsic factors and the extracellular environment. The extracellular matrix (matrisome) delivers chemical and mechanical cues that can modify cellular development. However, comprehensive understanding of how matrisome factors control cells in vivo is lacking. Here we show that specific matrisome factors act individually and collectively to control germ cell development. Surveying development of undifferentiated germline stem cells through to mature oocytes in the Caenorhabditis elegans germ line enabled holistic functional analysis of 443 conserved matrisome-coding genes. Using high-content imaging, 3D reconstruction, and cell behavior analysis, we identify 321 matrisome genes that impact germ cell development, the majority of which (>80%) are undescribed. Our analysis identifies key matrisome networks acting autonomously and non-autonomously to coordinate germ cell behavior. Further, our results demonstrate that germ cell development requires continual remodeling of the matrisome landscape. Together, this study provides a comprehensive platform for deciphering how extracellular signaling controls cellular development and anticipate this will establish new opportunities for manipulating cell fates.
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Affiliation(s)
- Aqilah Amran
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund Cancer Center, Lund University, Lund, Sweden
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Lara Pigatto
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund Cancer Center, Lund University, Lund, Sweden
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Johanna Farley
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Lund Cancer Center, Lund University, Lund, Sweden
| | - Rasoul Godini
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia.
| | - Sandeep Gopal
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
- Lund Cancer Center, Lund University, Lund, Sweden.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute. Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia.
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Fitzpatrick AM, Huang M, Mohammad AF, Stephenson ST, Kamaleswaran R, Grunwell JR. Dysfunctional neutrophil type 1 interferon responses in preschool children with recurrent wheezing and IL-4-mediated aeroallergen sensitization. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100229. [PMID: 38510797 PMCID: PMC10950716 DOI: 10.1016/j.jacig.2024.100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/25/2023] [Accepted: 12/24/2023] [Indexed: 03/22/2024]
Abstract
Background The innate mechanisms associated with viral exacerbations in preschool children with recurrent wheezing are not understood. Objective We sought to assess differential gene expression in blood neutrophils from preschool children with recurrent wheezing, stratified by aeroallergen sensitization, at baseline and after exposure to polyinosinic:polycytidylic acid (poly(I:C)) and also to examine whether poly(I:C)-stimulated blood neutrophils influenced airway epithelial gene expression. Methods Blood neutrophils were purified and cultured overnight with poly(I:C) and underwent next-generation sequencing with Reactome pathway analysis. Primary human small airway epithelial cells were treated with poly(I:C)-treated neutrophil culture supernatants and were analyzed for type 1 interferon gene expression with a targeted array. Symptoms and exacerbations were assessed in participants over 12 months. Results A total of 436 genes were differently expressed in neutrophils from children with versus without aeroallergen sensitization at baseline, with significant downregulation of type 1 interferons. These type 1 interferons were significantly upregulated in sensitized children after poly(I:C) stimulation. Confirmatory experiments demonstrated similar upregulation of type 1 interferons in IL-4-treated neutrophils stimulated with poly(I:C). Poly(I:C)-treated neutrophil supernatants from children with aeroallergen sensitization also induced a type 1 interferon response in epithelial cells. Children with aeroallergen sensitization also had higher symptom scores during exacerbations, and these symptom differences persisted for 3 days after prednisolone treatment. Conclusions Type 1 interferon responses are dysregulated in preschool children with aeroallergen sensitization, which is in turn associated with exacerbation severity. Given the importance of type 1 interferon signaling in viral resolution, additional studies of neutrophil type 1 interferon responses are needed in this population.
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Affiliation(s)
- Anne M. Fitzpatrick
- Department of Pediatrics, Emory University, Atlanta, Ga
- Division of Pulmonary Medicine, Children’s Healthcare of Atlanta, Atlanta, Ga
| | - Min Huang
- Department of Biomedical Informatics, Emory University, Atlanta, Ga
| | | | | | | | - Jocelyn R. Grunwell
- Department of Pediatrics, Emory University, Atlanta, Ga
- Division of Critical Care Medicine, Children’s Healthcare of Atlanta, Atlanta, Ga
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Ciesla J, Huang KL, Wagner EJ, Munger J. A UL26-PIAS1 complex antagonizes anti-viral gene expression during Human Cytomegalovirus infection. PLoS Pathog 2024; 20:e1012058. [PMID: 38768227 PMCID: PMC11142722 DOI: 10.1371/journal.ppat.1012058] [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: 05/31/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Viral disruption of innate immune signaling is a critical determinant of productive infection. The Human Cytomegalovirus (HCMV) UL26 protein prevents anti-viral gene expression during infection, yet the mechanisms involved are unclear. We used TurboID-driven proximity proteomics to identify putative UL26 interacting proteins during infection to address this issue. We find that UL26 forms a complex with several immuno-regulatory proteins, including several STAT family members and various PIAS proteins, a family of E3 SUMO ligases. Our results indicate that UL26 prevents STAT phosphorylation during infection and antagonizes transcriptional activation induced by either interferon α (IFNA) or tumor necrosis factor α (TNFα). Additionally, we find that the inactivation of PIAS1 sensitizes cells to inflammatory stimulation, resulting in an anti-viral transcriptional environment similar to ΔUL26 infection. Further, PIAS1 is important for HCMV cell-to-cell spread, which depends on the presence of UL26, suggesting that the UL26-PIAS1 interaction is vital for modulating intrinsic anti-viral defense.
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Affiliation(s)
- Jessica Ciesla
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Kai-Lieh Huang
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
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Aragón-Herrera A, Feijóo-Bandín S, Vázquez-Abuín X, Anido-Varela L, Moraña-Fernández S, Bravo SB, Tarazón E, Roselló-Lletí E, Portolés M, García-Seara J, Seijas J, Rodríguez-Penas D, Bani D, Gualillo O, González-Juanatey JR, Lago F. Human recombinant relaxin-2 (serelaxin) regulates the proteome, lipidome, lipid metabolism and inflammatory profile of rat visceral adipose tissue. Biochem Pharmacol 2024; 223:116157. [PMID: 38518995 DOI: 10.1016/j.bcp.2024.116157] [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: 01/14/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Recombinant human relaxin-2 (serelaxin) has been widely proven as a novel drug with myriad effects at different cardiovascular levels, which support its potential therapeutic efficacy in several cardiovascular diseases (CVD). Considering these effects, together with the influence of relaxin-2 on adipocyte physiology and adipokine secretion, and the connection between visceral adipose tissue (VAT) dysfunction and the development of CVD, we could hypothesize that relaxin-2 may regulate VAT metabolism. Our objective was to evaluate the impact of a 2-week serelaxin treatment on the proteome and lipidome of VAT from Sprague-Dawley rats. We found that serelaxin increased 1 polyunsaturated fatty acid and 6 lysophosphatidylcholines and decreased 4 triglycerides in VAT employing ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) based platforms, and that regulates 47 phosphoproteins using SWATH/MS analysis. Through RT-PCR, we found that serelaxin treatment also caused an effect on VAT lipolysis through an increase in the mRNA expression of hormone-sensitive lipase (HSL) and a decrease in the expression of adipose triglyceride lipase (ATGL), together with a reduction in the VAT expression of the fatty acid transporter cluster of differentiation 36 (Cd36). Serelaxin also caused an anti-inflammatory effect in VAT by the decrease in the mRNA expression of tumor necrosis factor α (TNFα), interleukin-1β (IL-1β), chemerin, and its receptor. In conclusion, our results highlight the regulatory role of serelaxin in the VAT proteome and lipidome, lipolytic function, and inflammatory profile, suggesting the implication of several mechanisms supporting the potential benefit of serelaxin for the prevention of obesity and metabolic disorders.
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Affiliation(s)
- Alana Aragón-Herrera
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain.
| | - Sandra Feijóo-Bandín
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Xocas Vázquez-Abuín
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura Anido-Varela
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Sandra Moraña-Fernández
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Cardiology Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Susana B Bravo
- Proteomics Unit, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Estefanía Tarazón
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain; Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital, Valencia, Spain
| | - Esther Roselló-Lletí
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain; Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital, Valencia, Spain
| | - Manuel Portolés
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain; Cardiocirculatory Unit, Health Research Institute of La Fe University Hospital, Valencia, Spain
| | - Javier García-Seara
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain; Arrhytmia Unit, Cardiology Department, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Department of Psychiatry, Radiology, Public Health, Nursing and Medicine, IDIS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - José Seijas
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain; Cardiology Department Clinical Trial Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Diego Rodríguez-Penas
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Cardiology Department Clinical Trial Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniele Bani
- Research Unit of Histology & Embryology, Department of Experimental & Clinical Medicine, University of Florence, Florence, Italy
| | - Oreste Gualillo
- Laboratory of Neuroendocrine Interactions in Rheumatology and Inflammatory Diseases, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - José Ramón González-Juanatey
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain; Department of Psychiatry, Radiology, Public Health, Nursing and Medicine, IDIS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Cardiology Department, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisca Lago
- Cellular and Molecular Cardiology Research Unit, IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
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D'Antona S, Porro D, Gallivanone F, Bertoli G. Characterization of cell cycle, inflammation, and oxidative stress signaling role in non-communicable diseases: Insights into genetic variants, microRNAs and pathways. Comput Biol Med 2024; 174:108346. [PMID: 38581999 DOI: 10.1016/j.compbiomed.2024.108346] [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: 10/09/2023] [Revised: 02/16/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Non-Communicable Diseases (NCDs) significantly impact global health, contributing to over 70% of premature deaths, as reported by the World Health Organization (WHO). These diseases have complex and multifactorial origins, involving genetic, epigenetic, environmental and lifestyle factors. While Genome-Wide Association Study (GWAS) is widely recognized as a valuable tool for identifying variants associated with complex phenotypes; the multifactorial nature of NCDs necessitates a more comprehensive exploration, encompassing not only the genetic but also the epigenetic aspect. For this purpose, we employed a bioinformatics-multiomics approach to examine the genetic and epigenetic characteristics of NCDs (i.e. colorectal cancer, coronary atherosclerosis, squamous cell lung cancer, psoriasis, type 2 diabetes, and multiple sclerosis), aiming to identify novel biomarkers for diagnosis and prognosis. Leveraging GWAS summary statistics, we pinpointed Single Nucleotide Polymorphisms (SNPs) independently associated with each NCD. Subsequently, we identified genes linked to cell cycle, inflammation and oxidative stress mechanisms, revealing shared genes across multiple diseases, suggesting common functional pathways. From an epigenetic perspective, we identified microRNAs (miRNAs) with regulatory functions targeting these genes of interest. Our findings underscore critical genetic pathways implicated in these diseases. In colorectal cancer, the dysregulation of the "Cytokine Signaling in Immune System" pathway, involving LAMA5 and SMAD7, regulated by Hsa-miR-21-5p, Hsa-miR-103a-3p, and Hsa-miR-195-5p, emerged as pivotal. In coronary atherosclerosis, the pathway associated with "binding of TCF/LEF:CTNNB1 to target gene promoters" displayed noteworthy implications, with the MYC factor controlled by Hsa-miR-16-5p as a potential regulatory factor. Squamous cell lung carcinoma analysis revealed significant pathways such as "PTK6 promotes HIF1A stabilization," regulated by Hsa-let-7b-5p. In psoriasis, the "Endosomal/Vacuolar pathway," involving HLA-C and Hsa-miR-148a-3p and Hsa-miR-148b-3p, was identified as crucial. Type 2 Diabetes implicated the "Regulation of TP53 Expression" pathway, controlled by Hsa-miR-106a-5p and Hsa-miR-106b-5p. In conclusion, our study elucidates the genetic framework and molecular mechanisms underlying NCDs, offering crucial insights into potential genetic/epigenetic biomarkers for diagnosis and prognosis. The specificity of pathways and related miRNAs in different pathologies highlights promising candidates for further clinical validation, with the potential to advance personalized treatments and alleviate the global burden of NCDs.
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Affiliation(s)
- Salvatore D'Antona
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Danilo Porro
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Francesca Gallivanone
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Gloria Bertoli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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KAWARA TAKETO, INOUE KOJI, SHIOZAWA SHUNICHI, OSAWA KAYO, KOMAI KOICHIRO. Genetic Rare Variants Affecting Multiple Pathways in Japanese Patients with Palindromic Rheumatism. THE KOBE JOURNAL OF MEDICAL SCIENCES 2024; 70:E26-E38. [PMID: 38719338 PMCID: PMC11086632 DOI: 10.24546/0100489391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/14/2024] [Indexed: 05/12/2024]
Abstract
Palindromic rheumatism (PR) is a type of cryptogenic paroxysmal arthritis. Several genes may be involved in PR pathogenesis; however, conducting comprehensive case-control genetic studies for PR poses challenges owing to its rarity as a disease. Moreover, case-control studies may overlook rare variants that occur infrequently but play a significant role in pathogenesis. This study aimed to identify disease-related genes in Japanese patients with PR using whole-genome sequencing (WGS) and rare-variant analysis. Genomic DNA was obtained from two familial cases and one sporadic case, and it was subjected to WGS. WGS data of 104 healthy individuals obtained from a public database were used as controls. We performed data analysis for rare variants on detected variants using SKAT-O, KBAC, and SKAT, and subsequently defined significant genes. Significant genes combined with variants shared between the cases were defined as disease-related genes. We also performed pathway analysis for disease-related genes using Reactome. We identified 2,695,244 variants shared between cases; after excluding polymorphisms and noise, 74,640 variants were detected. We identified 540 disease-related genes, including 1,893 variants. Furthermore, we identified 32 significant pathways. Our results indicate that the detected genes and pathways in this study may be involved in PR pathogenesis.
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Affiliation(s)
- TAKETO KAWARA
- Division of Medical Biophysics, Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - KOJI INOUE
- Shichikawa Arthritis Research Center, Osaka Rehabilitation Hospital, Hannan, Japan
| | | | - KAYO OSAWA
- Department of Medical Technology, Kobe Tokiwa University, Kobe, Japan
| | - KOICHIRO KOMAI
- Division of Medical Biophysics, Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
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Zhang N, Li J, Dong Z, Hu Y, Zhong Z, Gong Q, Kuang W. The digestion and dietary carbohydrate pathway contains 100% gene mutations enrichment among 117 patients with major depressive disorder. Front Psychiatry 2024; 15:1362612. [PMID: 38742130 PMCID: PMC11089147 DOI: 10.3389/fpsyt.2024.1362612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction Major depressive disorder (MDD) is partially inheritable while its mechanism is still uncertain. Methods This cross-sectional study focused on gene pathways as a whole rather than polymorphisms of single genes. Deep sequencing and gene enrichment analysis based on pathways in Reactome database were obtained to reveal gene mutations. Results A total of 117 patients with MDD and 78 healthy controls were enrolled. The Digestion and Dietary Carbohydrate pathway (Carbohydrate pathway) was determined to contain 100% mutations in patients with MDD and 0 mutation in matched healthy controls. Discussion Findings revealed in the current study enable a better understanding of gene pathways mutations status in MDD patients, indicating a possible genetic mechanism of MDD development and a potential diagnostic or therapeutic target.
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Affiliation(s)
- Ni Zhang
- Department of Psychiatry, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Li
- Department of Psychiatry, West China Hospital, Sichuan University, Chengdu, China
| | - Zaiquan Dong
- Department of Psychiatry, West China Hospital, Sichuan University, Chengdu, China
| | - Yongbo Hu
- Department of Psychiatry, West China Hospital, Sichuan University, Chengdu, China
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Zhihui Zhong
- Laboratory of Non-human Primate Disease Modeling Research, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Weihong Kuang
- Department of Psychiatry, West China Hospital, Sichuan University, Chengdu, China
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Lépine M, Robert MC, Sleno L. Discovery and Verification of Sjögren's Syndrome Protein Biomarkers in Tears by Targeted LC-MRM. J Proteome Res 2024. [PMID: 38682820 DOI: 10.1021/acs.jproteome.4c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Sjögren's syndrome (SS) is an autoimmune rheumatic disorder characterized by exocrine gland dysfunction, mainly from the lacrimal and salivary glands. The disease causes severe aqueous dry eye syndrome (DED) and is associated with high rates of complications, including corneal ulceration, scaring, and perforation. Systemic complications may occur as well as a higher risk of developing lymphoma. Diagnosis of SS-DED is often delayed and difficult to establish. With the aim of discovering biomarkers to help discriminate SS-DED patients, a combination of untargeted and targeted LC-MS/MS analyses were performed on tear samples collected on Schirmer strips and subjected to tryptic digestion. Following the analysis of three cohorts and the development of two targeted LC-sMRM methods for the verification of putative biomarkers found in the first cohort of samples, 64 proteins could be linked to Sjögren's syndrome, in the hopes of helping to confirm diagnoses as well as potentially stratifying the severity of disease in these patients. Proteins that were increased in SS-DED showed activation of the immune system and alterations in homeostasis. Several proteases and protease inhibitors were found to be significantly changing in SS-DED, as well as a consistent decrease in specific proteins known to be secreted by the lacrimal gland.
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Affiliation(s)
- Maggy Lépine
- University of Quebec in Montreal (UQAM), Chemistry Department, PO Box 8888, Downtown Station, Montreal, Quebec H3C 3P8, Canada
- CERMO-FC, Centre d'Excellence de Recherche sur les Maladies Orphelines-Fondation Courtois, 141 Avenue du President Kennedy, Montreal, Quebec H2X 3Y7, Canada
| | - Marie-Claude Robert
- Centre de Recherche du Centre Hospitalier Universitaire de (CR-CHUM), Ophthalmology Department, 900 Saint Denis Street, Montreal, Quebec H2X 0A9, Canada
- CERMO-FC, Centre d'Excellence de Recherche sur les Maladies Orphelines-Fondation Courtois, 141 Avenue du President Kennedy, Montreal, Quebec H2X 3Y7, Canada
| | - Lekha Sleno
- University of Quebec in Montreal (UQAM), Chemistry Department, PO Box 8888, Downtown Station, Montreal, Quebec H3C 3P8, Canada
- CERMO-FC, Centre d'Excellence de Recherche sur les Maladies Orphelines-Fondation Courtois, 141 Avenue du President Kennedy, Montreal, Quebec H2X 3Y7, Canada
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Sengupta A, Singh SK, Kumar R. Support Vector Machine-Based Prediction Models for Drug Repurposing and Designing Novel Drugs for Colorectal Cancer. ACS OMEGA 2024; 9:18584-18592. [PMID: 38680332 PMCID: PMC11044175 DOI: 10.1021/acsomega.4c01195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Colorectal cancer (CRC) has witnessed a concerning increase in incidence and poses a significant therapeutic challenge due to its poor prognosis. There is a pressing demand to identify novel drug therapies to combat CRC. In this study, we addressed this need by utilizing the pharmacological profiles of anticancer drugs from the Genomics of Drug Sensitivity in Cancer (GDSC) database and developed QSAR models using the Support Vector Machine (SVM) algorithm for prediction of alternative and promiscuous anticancer compounds for CRC treatment. Our QSAR models demonstrated their robustness by achieving a high correlation of determination (R2) after 10-fold cross-validation. For 12 CRC cell lines, R2 ranged from 0.609 to 0.827. The highest performance was achieved for SW1417 and GP5d cell lines with R2 values of 0.827 and 0.786, respectively. Further, we listed the most common chemical descriptors in the drug profiles of the CRC cell lines and we also further reported the correlation of these descriptors with drug activity. The KRFP314 fingerprint was the predominantly occurring descriptor, with the KRFPC314 fingerprint following closely in prevalence within the drug profiles of the CRC cell lines. Beyond predictive modeling, we also confirmed the applicability of our developed QSAR models via in silico methods by conducting descriptor-drug analyses and recapitulating drug-to-oncogene relationships. We also identified two potential anti-CRC FDA-approved drugs, viomycin and diamorphine, using QSAR models. To ensure the easy accessibility and utility of our research findings, we have incorporated these models into a user-friendly prediction Web server named "ColoRecPred", available at https://project.iith.ac.in/cgntlab/colorecpred. We anticipate that this Web server can be used for screening of chemical libraries to identify potential anti-CRC drugs.
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Affiliation(s)
- Avik Sengupta
- Department
of Biotechnology, Indian Institute of Technology
Hyderabad, Kandi, Telangana 502284, India
| | - Saurabh Kumar Singh
- Department
of Chemistry, Indian Institute of Technology
Hyderabad, Kandi, Telangana 502284, India
| | - Rahul Kumar
- Department
of Biotechnology, Indian Institute of Technology
Hyderabad, Kandi, Telangana 502284, India
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Erdogan C, Suer I, Kaya M, Ozturk S, Aydin N, Kurt Z. Bioinformatics analysis of the potentially functional circRNA-miRNA-mRNA network in breast cancer. PLoS One 2024; 19:e0301995. [PMID: 38635539 PMCID: PMC11025867 DOI: 10.1371/journal.pone.0301995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
Breast cancer (BC) is the most common cancer among women with high morbidity and mortality. Therefore, new research is still needed for biomarker detection. GSE101124 and GSE182471 datasets were obtained from the Gene Expression Omnibus (GEO) database to evaluate differentially expressed circular RNAs (circRNAs). The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases were used to identify the significantly dysregulated microRNAs (miRNAs) and genes considering the Prediction Analysis of Microarray classification (PAM50). The circRNA-miRNA-mRNA relationship was investigated using the Cancer-Specific CircRNA, miRDB, miRTarBase, and miRWalk databases. The circRNA-miRNA-mRNA regulatory network was annotated using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. The protein-protein interaction network was constructed by the STRING database and visualized by the Cytoscape tool. Then, raw miRNA data and genes were filtered using some selection criteria according to a specific expression level in PAM50 subgroups. A bottleneck method was utilized to obtain highly interacted hub genes using cytoHubba Cytoscape plugin. The Disease-Free Survival and Overall Survival analysis were performed for these hub genes, which are detected within the miRNA and circRNA axis in our study. We identified three circRNAs, three miRNAs, and eighteen candidate target genes that may play an important role in BC. In addition, it has been determined that these molecules can be useful in the classification of BC, especially in determining the basal-like breast cancer (BLBC) subtype. We conclude that hsa_circ_0000515/miR-486-5p/SDC1 axis may be an important biomarker candidate in distinguishing patients in the BLBC subgroup of BC.
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Affiliation(s)
- Cihat Erdogan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ilknur Suer
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Murat Kaya
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sukru Ozturk
- Department of Internal Medicine, Division of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Nizamettin Aydin
- Department of Computer Engineering, Faculty of Computer and Informatics, Istanbul Technical University, Istanbul, Turkey
| | - Zeyneb Kurt
- Information School, The University of Sheffield, Sheffield, United Kingdom
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Mehra R, Patra V, Dhillan R, Sharma A, Kashyap S, Rastogi G, Gupta L, Singh R, Chopra C, Sharma V. Replication study identified EFEMP1 association with varicose vein predisposition among Indians. Eur J Med Res 2024; 29:232. [PMID: 38609985 PMCID: PMC11015598 DOI: 10.1186/s40001-024-01786-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Varicose vein is a chronic condition that affects the lower extremities of the human body. Several factors have been implicated in the development of this disease, viz age, gender, weight, height and prolonged standing. Recently, genome-wide studies have identified genetic biomarkers that are associated with varicose veins in different ethnic groups. Such genetic studies are lacking in South Asians specifically in Indians where the prevalence of varicose veins is high, and it is important to replicate these variants in the stated population. The study aimed to replicate the association of genetic variants associated with varicose veins in this target population, which were found to be associated with the other ethnic groups. METHODOLOGY The studied cohort is of the Indian population comprising unrelated 104 varicose veins cases and 448 non-varicose vein controls. The samples were genotyped using the Illumina Global Screening Array. Using the genomic data from UK BioBank and 23andMe studied cohorts; eight genetic variants were selected to replicate in our dataset. The allelic association was performed to identify the effective allele and risk was estimated using odds ratio and p-value as level of significance. Multifactor Dimensionality Reduction was used to estimate the cumulative effect of variants in Indians. RESULT Variant rs3791679 of EFEMP1 was found to be associated with varicose veins in Indians. After observing the association of the EFEMP1 with varicose veins, we further ensued to identify all genetic variants within EFEMP1 to uncover the additional variants associated with this trait. Interestingly, we identified six new variants of EFEMP1 gene that have shown association. Moreover, the cumulative effect of all associated variations was estimated and the risk was 2.7 times higher in cases than controls whereas independently their effect ranges from 0.37-1.58. CONCLUSION This study identifies EFEMP1 as a potential gene related to the risk of varicose veins in Indians. It also highlights that evaluating the maximum number of variants of a gene rather than focusing solely on replicating single variations offers a more comprehensive and nuanced understanding of the genetic factors contributing to a complex trait like varicose veins.
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Affiliation(s)
- Rohit Mehra
- Department of Vascular and Endovascular Surgery, Command Hospital (Southern Command), Pune, India.
| | - Vikram Patra
- Department of Vascular and Endovascular Surgery, Command Hospital (Northern Command), Udhampur, India
| | - Rishi Dhillan
- Department of Vascular and Endovascular Surgery, Army Hospital (Research and Referral), Delhi, India
| | - Anuka Sharma
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India
| | - Sonal Kashyap
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Garima Rastogi
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India
| | - Love Gupta
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Varun Sharma
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India.
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Ke CH, Wu HY, Wang YS, Huang WH, Lin CS. Tumors Established in a Defective Immune Environment Reprogram the Oncogenic Signaling Pathways to Escalate Tumor Antigenicity. Biomedicines 2024; 12:846. [PMID: 38672200 PMCID: PMC11047836 DOI: 10.3390/biomedicines12040846] [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: 03/20/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Tumors developed in immunocompromised hosts are more immunogenic. However, few studies have addressed the potential mechanisms underlying the high immunogenicity of tumors found in a suppressed immune system. Therefore, we aimed to elucidate the impacts of the immune system on tumor behaviors and immunogenicity sculpting. A murine colorectal adenocarcinoma cell line, CT26wt, was administrated into immunocompetent (BALB/c) and immunocompromised (NOD.SCID) mice, respectively. On day 11, the CT26 cells slowly progressed in the NOD.SCID mice compared to the BALB/c mice. We then performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) and analyzed the differentially expressed proteins (DEPs). The DEPs participated in numerous oncogenic pathways, PI3K/AKT/mTOR cell signaling, and the silencing of several tumor suppressors, such as PTEN and RBL1, during tumorigenesis. On day 34, the CT26/SCID tumors inversely became malignant counterparts; then the CT26/SCID tumors were harvested and re-inoculated into immunocompetent mice (CT26/SCID-Re tumors) to determine the immunogenicity. The CT26/SCID-Re tumor growth rate significantly decreased. Furthermore, increased infiltrations of dendritic cells and tumor-infiltrating T lymphocytes were found in the CT26/SCID-Re tumors. These findings suggest that immunogenic tumors might express multiple tumor rejection antigens, unlike wild-type tumors, and attract more immune cells, therefore decreasing the growth rate. Collectively, our study first revealed that in immunodeficient hosts, tumor suppressors were silenced and oncogenic signaling pathways were changed during the initial phase of tumor development. With tumor progression, the tumor antigens were overexpressed, exhibiting elevated immunogenicity. This study offers a hint on the mechanisms of tumorigenesis and provides a niche for investigating the interaction between host immunity and cancer development.
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Affiliation(s)
- Chiao-Hsu Ke
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (C.-H.K.); (Y.-S.W.)
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei 10617, Taiwan;
| | - Yu-Shan Wang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (C.-H.K.); (Y.-S.W.)
- Uni-Pharma Co., Ltd., Taipei 11494, Taiwan
| | - Wei-Hsiang Huang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan;
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan; (C.-H.K.); (Y.-S.W.)
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38
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Sowislok A, Busch A, Kaschani F, Kaiser M, Jäger M. Differences in the Synovial Fluid Proteome of Septic and Aseptic Implant Failure. Antibiotics (Basel) 2024; 13:346. [PMID: 38667022 PMCID: PMC11047638 DOI: 10.3390/antibiotics13040346] [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: 03/07/2024] [Revised: 03/25/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024] Open
Abstract
Implant loosening is a severe complication after total joint replacement. Here, differential diagnosis between septic and aseptic cases is crucial for further surgical treatment, but low-grade periprosthetic joint infections (PJIs) in particular remain a challenge. In this study, we analyzed the synovial fluid proteome of 21 patients undergoing revision surgery for septic (eight cases) or aseptic (thirteen cases) implant failure using LC-MS/MS to identify potential new biomarkers as future diagnostic tools. Staphylococci were found in four cases, Streptococci in two cases, Serratia marcescens and Cutibacterium acnes in one case. Proteomic analysis of the synovial fluid resulted in the identification of 515 different proteins based on at least two peptides. A statistical comparison revealed 37 differentially abundant proteins (p < 0.05), of which 17 proteins (46%) showed a higher abundance in the septic group. The proteins with the highest fold change included the known marker proteins c-reactive protein (7.57-fold) and the calprotectin components protein S100-A8 (4.41-fold) and protein S100-A9 (3.1-fold). However, the protein with the highest fold change was leucine-rich alpha-2-glycoprotein 1 (LRG1) (9.07-fold), a currently discussed new biomarker for inflammatory diseases. Elevated LRG1 levels could facilitate the diagnosis of PJI in the future, but their significance needs to be further investigated.
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Affiliation(s)
- Andrea Sowislok
- Chair of Orthopedics and Trauma Surgery, University of Duisburg-Essen, 45147 Essen, Germany;
| | - André Busch
- Department of Orthopedics, Trauma and Reconstructive Surgery, Katholisches Klinikum Essen Philippus, 45355 Essen, Germany;
| | - Farnusch Kaschani
- Analytics Core Facility Essen (ACE), ZMB, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany;
| | - Markus Kaiser
- Chemical Biology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany;
| | - Marcus Jäger
- Chair of Orthopedics and Trauma Surgery, University of Duisburg-Essen, 45147 Essen, Germany;
- Department of Orthopedics, Trauma and Reconstructive Surgery, Katholisches Klinikum Essen Philippus, 45355 Essen, Germany;
- Department of Orthopedics, Trauma and Reconstructive Surgery, St. Marien Hospital Mülheim a. d. Ruhr, 45468 Mülheim, Germany
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Carvalho EM, Ding EA, Saha A, Weldy A, Zushin PJH, Stahl A, Aghi MK, Kumar S. Viscoelastic high-molecular-weight hyaluronic acid hydrogels support rapid glioblastoma cell invasion with leader-follower dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588167. [PMID: 38617333 PMCID: PMC11014578 DOI: 10.1101/2024.04.04.588167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Hyaluronic acid (HA), the primary component of brain extracellular matrix, is increasingly used to model neuropathological processes, including glioblastoma (GBM) tumor invasion. While elastic hydrogels based on crosslinked low-molecular-weight (LMW) HA are widely exploited for this purpose and have proven valuable for discovery and screening, brain tissue is both viscoelastic and rich in high-MW (HMW) HA, and it remains unclear how these differences influence invasion. To address this question, hydrogels comprised of either HMW (1.5 MDa) or LMW (60 kDa) HA are introduced, characterized, and applied in GBM invasion studies. Unlike LMW HA hydrogels, HMW HA hydrogels relax stresses quickly, to a similar extent as brain tissue, and to a greater extent than many conventional HA-based scaffolds. GBM cells implanted within HMW HA hydrogels invade much more rapidly than in their LMW HA counterparts and exhibit distinct leader-follower dynamics. Leader cells adopt dendritic morphologies, similar to invasive GBM cells observed in vivo. Transcriptomic, pharmacologic, and imaging studies suggest that leader cells exploit hyaluronidase, an enzyme strongly enriched in human GBMs, to prime a path for followers. This study offers new insight into how HA viscoelastic properties drive invasion and argues for the use of highly stress-relaxing materials to model GBM.
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Affiliation(s)
- Emily M Carvalho
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Erika A Ding
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Atul Saha
- Department of Neurosurgery, University of California, San Francisco, CA 94158, USA
| | - Anna Weldy
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Peter-James H Zushin
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley 94720, USA
| | - Andreas Stahl
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley 94720, USA
| | - Manish K Aghi
- Department of Neurosurgery, University of California, San Francisco, CA 94158, USA
| | - Sanjay Kumar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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Kamathewatta KI, Kulappu Arachchige SN, Young ND, Condello AK, Wawegama NK, Browning GF. Transcriptomic analysis of the effects of tylosin on the protective immunity provided by the Mycoplasma gallisepticum vaccine Vaxsafe MG ts-304. Vet Microbiol 2024; 291:110029. [PMID: 38364466 DOI: 10.1016/j.vetmic.2024.110029] [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: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
The antimicrobial tylosin is commonly used to control mycoplasma infections, sometimes in combination with vaccination. However, the efficacy of a live mycoplasma vaccine, when combined with subsequent antimicrobial treatment, against the effects of subsequent infection with a virulent strain is unknown. This study employed differential gene expression analysis to evaluate the effects of tylosin on the protection provided by the live attenuated Vaxsafe MG ts-304 vaccine, which has been shown to be safe and to provide long-term protective immunity against infection with Mycoplasma gallisepticum. The transcriptional profiles of the tracheal mucosa revealed significantly enhanced inflammation, immune cell proliferation and adaptive immune responses in unvaccinated, untreated birds and in unvaccinated birds treated with tylosin 2 weeks after infection with virulent M. gallisepticum. These responses, indicative of the typical immune dysregulation caused by infection with M. gallisepticum, were less severe in the unvaccinated, tylosin-treated birds than in the unvaccinated, untreated birds. This was attributable to the effect of residual levels of tylosin in the tracheal mucosa on replication of virulent M. gallisepticum. These responses were not detected in vaccinated, tylosin-treated birds or in vaccinated, untreated birds after infection. The tracheal mucosal transcriptional profiles of these birds resembled those of unvaccinated, untreated, uninfected birds, suggesting a rapid and protective secondary immune response and effective vaccination. Overall, these results show that, although tylosin treatment reduced the duration of immunity, the initial protective immunity induced by Vaxsafe MG ts-304 lasted for at least 22 weeks after vaccination, even after the administration of tylosin for 16 weeks following vaccination.
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Affiliation(s)
- Kanishka I Kamathewatta
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Sathya N Kulappu Arachchige
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anna Kanci Condello
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia.
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Mueller FB, Yang H, Li C, Dadhania DM, Xiang JZ, Salvatore S, Seshan SV, Sharma VK, Suthanthiran M, Muthukumar T. RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell-mediated Rejection. Transplantation 2024; 108:911-922. [PMID: 38291584 PMCID: PMC10963156 DOI: 10.1097/tp.0000000000004896] [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] [Indexed: 02/01/2024]
Abstract
BACKGROUND Delineation of T-cell genes, gene sets, pathways, and T-cell subtypes associated with acute T cell-mediated rejection (TCMR) may improve its management. METHODS We performed bulk RNA-sequencing of 34 kidney allograft biopsies (16 Banff TCMR and 18 no rejection [NR] biopsies) from 34 adult recipients of human kidneys. Computational analysis was performed to determine the differential intragraft expression of T-cell genes at the level of single-gene, gene set, and pathways. RESULTS T-cell signaling pathway gene sets for plenary T-cell activation were overrepresented in TCMR biopsies compared with NR biopsies. Heightened expression of T-cell signaling genes was validated using external TCMR biopsies. Pro- and anti-inflammatory immune gene sets were enriched, and metabolism gene sets were depleted in TCMR biopsies compared with NR biopsies. Gene signatures of regulatory T cells, Th1 cells, Th2 cells, Th17 cells, T follicular helper cells, CD4 tissue-resident memory T cells, and CD8 tissue-resident memory T cells were enriched in TCMR biopsies compared with NR biopsies. T-cell exhaustion and anergy were also molecular attributes of TCMR. Gene sets associated with antigen processing and presentation, and leukocyte transendothelial migration were overexpressed in TCMR biopsies compared with NR biopsies. Cellular deconvolution of graft infiltrating cells by gene expression patterns identified CD8 T cell to be the most abundant T-cell subtype infiltrating the allograft during TCMR. CONCLUSIONS Our delineation of intragraft T-cell gene expression patterns, in addition to yielding new biological insights, may help prioritize T-cell genes and T-cell subtypes for therapeutic targeting.
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Affiliation(s)
- Franco B. Mueller
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Hua Yang
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Darshana M. Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Transplantation Medicine, NewYork Presbyterian Hospital-Weill Cornell Medical College, New York, NY
| | - Jenny Z. Xiang
- Genomics Resources Core Facility, Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY
| | - Steven Salvatore
- Division of Renal Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Surya V. Seshan
- Division of Renal Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Vijay K. Sharma
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Transplantation Medicine, NewYork Presbyterian Hospital-Weill Cornell Medical College, New York, NY
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, NY
- Department of Transplantation Medicine, NewYork Presbyterian Hospital-Weill Cornell Medical College, New York, NY
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Shah ET, Molloy C, Gough M, Kryza T, Samuel SG, Tucker A, Bhatia M, Ferguson G, Heyman R, Vora S, Monkman J, Bolderson E, Kulasinghe A, He Y, Gabrielli B, Hooper JD, Richard DJ, O'Byrne KJ, Adams MN. Inhibition of Aurora B kinase (AURKB) enhances the effectiveness of 5-fluorouracil chemotherapy against colorectal cancer cells. Br J Cancer 2024; 130:1196-1205. [PMID: 38287178 PMCID: PMC10991355 DOI: 10.1038/s41416-024-02584-z] [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: 05/16/2023] [Revised: 12/18/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND 5-Fluorouracil (5-FU) remains a core component of systemic therapy for colorectal cancer (CRC). However, response rates remain low, and development of therapy resistance is a primary issue. Combinatorial strategies employing a second agent to augment the therapeutic effect of chemotherapy is predicted to reduce the incidence of treatment resistance and increase the durability of response to therapy. METHODS Here, we employed quantitative proteomics approaches to identify novel druggable proteins and molecular pathways that are deregulated in response to 5-FU, which might serve as targets to improve sensitivity to chemotherapy. Drug combinations were evaluated using 2D and 3D CRC cell line models and an ex vivo culture model of a patient-derived tumour. RESULTS Quantitative proteomics identified upregulation of the mitosis-associated protein Aurora B (AURKB), within a network of upregulated proteins, in response to a 24 h 5-FU treatment. In CRC cell lines, AURKB inhibition with the dihydrogen phosphate prodrug AZD1152, markedly improved the potency of 5-FU in 2D and 3D in vitro CRC models. Sequential treatment with 5-FU then AZD1152 also enhanced the response of a patient-derived CRC cells to 5-FU in ex vivo cultures. CONCLUSIONS AURKB inhibition may be a rational approach to augment the effectiveness of 5-FU chemotherapy in CRC.
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Affiliation(s)
- Esha T Shah
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Christopher Molloy
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Madeline Gough
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Thomas Kryza
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Selwin G Samuel
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Amos Tucker
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Maneet Bhatia
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Genevieve Ferguson
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Rebecca Heyman
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Shivam Vora
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - James Monkman
- Frazer Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Emma Bolderson
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Yaowu He
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Brian Gabrielli
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - John D Hooper
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Derek J Richard
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
| | - Kenneth J O'Byrne
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia
- Cancer Services, Princess Alexandra Hospital, Ipswich Road, Woolloongabba, QLD, 4102, Australia
| | - Mark N Adams
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
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Han Y, Barasa P, Zeger L, Salomonsson SB, Zanotti F, Egli M, Zavan B, Trentini M, Florin G, Vaerneus A, Aldskogius H, Fredriksson R, Kozlova EN. Effects of microgravity on neural crest stem cells. Front Neurosci 2024; 18:1379076. [PMID: 38660221 PMCID: PMC11041629 DOI: 10.3389/fnins.2024.1379076] [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: 01/30/2024] [Accepted: 03/15/2024] [Indexed: 04/26/2024] Open
Abstract
Exposure to microgravity (μg) results in a range of systemic changes in the organism, but may also have beneficial cellular effects. In a previous study we detected increased proliferation capacity and upregulation of genes related to proliferation and survival in boundary cap neural crest stem cells (BC) after MASER14 sounding rocket flight compared to ground-based controls. However, whether these changes were due to μg or hypergravity was not clarified. In the current MASER15 experiment BCs were exposed simultaneously to μg and 1 g conditions provided by an onboard centrifuge. BCs exposed to μg displayed a markedly increased proliferation capacity compared to 1 g on board controls, and genetic analysis of BCs harvested 5 h after flight revealed an upregulation, specifically in μg-exposed BCs, of Zfp462 transcription factor, a key regulator of cell pluripotency and neuronal fate. This was associated with alterations in exosome microRNA content between μg and 1 g exposed MASER15 specimens. Since the specimens from MASER14 were obtained for analysis with 1 week's delay, we examined whether gene expression and exosome content were different compared to the current MASER15 experiments, in which specimens were harvested 5 h after flight. The overall pattern of gene expression was different and Zfp462 expression was down-regulated in MASER14 BC μg compared to directly harvested specimens (MASER15). MicroRNA exosome content was markedly altered in medium harvested with delay compared to directly collected samples. In conclusion, our analysis indicates that even short exposure to μg alters gene expression, leading to increased BC capacity for proliferation and survival, lasting for a long time after μg exposure. With delayed harvest of specimens, a situation which may occur due to special post-flight circumstances, the exosome microRNA content is modified compared to fast specimen harvest, and the direct effects from μg exposure may be partially attenuated, whereas other effects can last for a long time after return to ground conditions.
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Affiliation(s)
- Yilin Han
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Povilas Barasa
- Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Lukas Zeger
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sara B. Salomonsson
- Department of Pharmaceutical Bioscience, Uppsala University, Uppsala, Sweden
| | - Federica Zanotti
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Marcel Egli
- Space Biology Group, School of Engineering and Architecture, Institute of Medical Engineering, Lucerne University of Applied Sciences and Arts, Hergiswil, Switzerland
- National Center for Biomedical Research in Space, Innovation Cluster Space and Aviation, University of Zurich, Zurich, Switzerland
| | - Barbara Zavan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Martina Trentini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | | | | | - Håkan Aldskogius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Bioscience, Uppsala University, Uppsala, Sweden
| | - Elena N. Kozlova
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Okumura T, Raja Xavier JP, Pasternak J, Yang Z, Hang C, Nosirov B, Singh Y, Admard J, Brucker SY, Kommoss S, Takeda S, Staebler A, Lang F, Salker MS. Rel Family Transcription Factor NFAT5 Upregulates COX2 via HIF-1α Activity in Ishikawa and HEC1a Cells. Int J Mol Sci 2024; 25:3666. [PMID: 38612478 PMCID: PMC11012216 DOI: 10.3390/ijms25073666] [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: 08/01/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Nuclear factor of activated T cells 5 (NFAT5) and cyclooxygenase 2 (COX2; PTGS2) both participate in diverse pathologies including cancer progression. However, the biological role of the NFAT5-COX2 signaling pathway in human endometrial cancer has remained elusive. The present study explored whether NFAT5 is expressed in endometrial tumors and if NFAT5 participates in cancer progression. To gain insights into the underlying mechanisms, NFAT5 protein abundance in endometrial cancer tissue was visualized by immunohistochemistry and endometrial cancer cells (Ishikawa and HEC1a) were transfected with NFAT5 or with an empty plasmid. As a result, NFAT5 expression is more abundant in high-grade than in low-grade endometrial cancer tissue. RNA sequencing analysis of NFAT5 overexpression in Ishikawa cells upregulated 37 genes and downregulated 20 genes. Genes affected included cyclooxygenase 2 and hypoxia inducible factor 1α (HIF1A). NFAT5 transfection and/or treatment with HIF-1α stabilizer exerted a strong stimulating effect on HIF-1α promoter activity as well as COX2 expression level and prostaglandin E2 receptor (PGE2) levels. Our findings suggest that activation of NFAT5-HIF-1α-COX2 axis could promote endometrial cancer progression.
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Affiliation(s)
- Toshiyuki Okumura
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan;
| | - Janet P. Raja Xavier
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Jana Pasternak
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Zhiqi Yang
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Cao Hang
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Bakhtiyor Nosirov
- Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Yogesh Singh
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Sara Y. Brucker
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Stefan Kommoss
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo 113-8421, Japan;
| | - Annette Staebler
- Institute of Pathology, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Florian Lang
- Institute of Physiology, Eberhard Karls University, D-72074 Tübingen, Germany;
| | - Madhuri S. Salker
- Department of Women’s Health, Tübingen University Hospital, D-72076 Tübingen, Germany; (T.O.); (J.P.R.X.); (J.P.); (C.H.); (Y.S.); (S.Y.B.); (S.K.)
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Raposo de Magalhães C, Sandoval K, Kagan F, McCormack G, Schrama D, Carrilho R, Farinha AP, Cerqueira M, Rodrigues PM. Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration. PLoS One 2024; 19:e0300472. [PMID: 38517901 PMCID: PMC10959376 DOI: 10.1371/journal.pone.0300472] [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: 07/28/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.
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Affiliation(s)
- Cláudia Raposo de Magalhães
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Grace McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | - Denise Schrama
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Raquel Carrilho
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Paula Farinha
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Escola Superior Agrária de Santarém, Santarém, Portugal
| | - Marco Cerqueira
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Pedro M. Rodrigues
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
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Kobiela A, Hewelt-Belka W, Frąckowiak JE, Kordulewska N, Hovhannisyan L, Bogucka A, Etherington R, Piróg A, Dapic I, Gabrielsson S, Brown SJ, Ogg GS, Gutowska-Owsiak D. Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency. Front Immunol 2024; 15:1369238. [PMID: 38585273 PMCID: PMC10995404 DOI: 10.3389/fimmu.2024.1369238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction Exosome-enriched small extracellular vesicles (sEVs) are nanosized organelles known to participate in long distance communication between cells, including in the skin. Atopic dermatitis (AD) is a chronic inflammatory skin disease for which filaggrin (FLG) gene mutations are the strongest genetic risk factor. Filaggrin insufficiency affects multiple cellular function, but it is unclear if sEV-mediated cellular communication originating from the affected keratinocytes is also altered, and if this influences peptide and lipid antigen presentation to T cells in the skin. Methods Available mRNA and protein expression datasets from filaggrin-insufficient keratinocytes (shFLG), organotypic models and AD skin were used for gene ontology analysis with FunRich tool. sEVs secreted by shFLG and control shC cells were isolated from conditioned media by differential centrifugation. Mass spectrometry was carried out for lipidomic and proteomic profiling of the cells and sEVs. T cell responses to protein, peptide, CD1a lipid antigens, as well as phospholipase A2-digested or intact sEVs were measured by ELISpot and ELISA. Results Data analysis revealed extensive remodeling of the sEV compartment in filaggrin insufficient keratinocytes, 3D models and the AD skin. Lipidomic profiles of shFLGsEV showed a reduction in the long chain (LCFAs) and polyunsaturated fatty acids (PUFAs; permissive CD1a ligands) and increased content of the bulky headgroup sphingolipids (non-permissive ligands). This resulted in a reduction of CD1a-mediated interferon-γ T cell responses to the lipids liberated from shFLG-generated sEVs in comparison to those induced by sEVs from control cells, and an increase in interleukin 13 secretion. The altered sEV lipidome reflected a generalized alteration in the cellular lipidome in filaggrin-insufficient cells and the skin of AD patients, resulting from a downregulation of key enzymes implicated in fatty acid elongation and desaturation, i.e., enzymes of the ACSL, ELOVL and FADS family. Discussion We determined that sEVs constitute a source of antigens suitable for CD1a-mediated presentation to T cells. Lipids enclosed within the sEVs secreted on the background of filaggrin insufficiency contribute to allergic inflammation by reducing type 1 responses and inducing a type 2 bias from CD1a-restricted T cells, thus likely perpetuating allergic inflammation in the skin.
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Affiliation(s)
- Adrian Kobiela
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Weronika Hewelt-Belka
- Department of Analytical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Joanna E. Frąckowiak
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Natalia Kordulewska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Lilit Hovhannisyan
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Bogucka
- The Mass Spectrometry Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Rachel Etherington
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Artur Piróg
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Susanne Gabrielsson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Sara J. Brown
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Graham S. Ogg
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Danuta Gutowska-Owsiak
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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Casanova NG, De Armond RL, Sammani S, Sun X, Sun B, Kempf C, Bime C, Garcia JGN, Parthasarathy S. Circadian disruption dysregulates lung gene expression associated with inflammatory lung injury. Front Immunol 2024; 15:1348181. [PMID: 38558813 PMCID: PMC10979643 DOI: 10.3389/fimmu.2024.1348181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 04/04/2024] Open
Abstract
Rationale Circadian systems drive the expression of multiple genes in nearly all cells and coordinate cellular-, tissue-, and system-level processes that are critical to innate immunity regulation. Objective We examined the effects of circadian rhythm disorganization, produced by light shift exposure, on innate immunity-mediated inflammatory lung responses including vascular permeability and gene expression in a C57BL/6J murine model of inflammatory lung injury. Methods A total of 32 C57BL/6J mice were assigned to circadian phase shifting (CPS) with intratracheal phosphate-buffered saline (PBS), CPS with intratracheal lipopolysaccharide (LPS), control (normal lighting) condition with intratracheal PBS, and control condition with intratracheal LPS. Bronchoalveolar lavage (BAL) protein, cell counts, tissue immunostaining, and differentially expressed genes (DEGs) were measured in lung tissues at 2 and 10 weeks. Measurements and results In mice exposed to both CPS and intratracheal LPS, both BAL protein and cell counts were increased at both 2 and 10 weeks compared to mice exposed to LPS alone. Multiple DEGs were identified in CPS-LPS-exposed lung tissues compared to LPS alone and were involved in transcriptional pathways associated with circadian rhythm disruption, regulation of lung permeability, inflammation with Rap1 signaling, and regulation of actin cytoskeleton. The most dysregulated pathways included myosin light chain kinase, MAP kinase, profilin 2, fibroblast growth factor receptor, integrin b4, and p21-activated kinase. Conclusion Circadian rhythm disruption results in exacerbated immune response and dysregulated expression of cytoskeletal genes involved in the regulation of epithelial and vascular barrier integrity-the mechanistic underpinnings of acute lung injury. Further studies need to explore circadian disorganization as a druggable target.
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Affiliation(s)
- Nancy G. Casanova
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, FL, United States
| | - Richard L. De Armond
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
- University of Arizona Health Science – Center for Sleep and Circadian Sciences, University of Arizona, Tucson, AZ, United States
| | - Saad Sammani
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Xiaoguang Sun
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Belinda Sun
- Department of Pathology, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Carrie Kempf
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, FL, United States
| | - Christian Bime
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Joe G. N. Garcia
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, FL, United States
| | - Sairam Parthasarathy
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
- University of Arizona Health Science – Center for Sleep and Circadian Sciences, University of Arizona, Tucson, AZ, United States
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Chen PC, Tsai TP, Liao YC, Liao YC, Cheng HW, Weng YH, Lin CM, Kao CY, Tai CC, Ruan JW. Intestinal dual-specificity phosphatase 6 regulates the cold-induced gut microbiota remodeling to promote white adipose browning. NPJ Biofilms Microbiomes 2024; 10:22. [PMID: 38480743 PMCID: PMC10937957 DOI: 10.1038/s41522-024-00495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Gut microbiota rearrangement induced by cold temperature is crucial for browning in murine white adipose tissue. This study provides evidence that DUSP6, a host factor, plays a critical role in regulating cold-induced gut microbiota rearrangement. When exposed to cold, the downregulation of intestinal DUSP6 increased the capacity of gut microbiota to produce ursodeoxycholic acid (UDCA). The DUSP6-UDCA axis is essential for driving Lachnospiraceae expansion in the cold microbiota. In mice experiencing cold-room temperature (CR) transitions, prolonged DUSP6 inhibition via the DUSP6 inhibitor (E/Z)-BCI maintained increased cecal UDCA levels and cold-like microbiota networks. By analyzing DUSP6-regulated microbiota dynamics in cold-exposed mice, we identified Marvinbryantia as a genus whose abundance increased in response to cold exposure. When inoculated with human-origin Marvinbryantia formatexigens, germ-free recipient mice exhibited significantly enhanced browning phenotypes in white adipose tissue. Moreover, M. formatexigens secreted the methylated amino acid Nε-methyl-L-lysine, an enriched cecal metabolite in Dusp6 knockout mice that reduces adiposity and ameliorates nonalcoholic steatohepatitis in mice. Our work revealed that host-microbiota coadaptation to cold environments is essential for regulating the browning-promoting gut microbiome.
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Affiliation(s)
- Pei-Chen Chen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tzu-Pei Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yi-Chu Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Hung-Wei Cheng
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Yi-Hsiu Weng
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chiao-Mei Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Cheng-Yuan Kao
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | | | - Jhen-Wei Ruan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
- Research Center for Medical Laboratory Biotechnology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
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Lin WY. Searching for gene-gene interactions through variance quantitative trait loci of 29 continuous Taiwan Biobank phenotypes. Front Genet 2024; 15:1357238. [PMID: 38516378 PMCID: PMC10956579 DOI: 10.3389/fgene.2024.1357238] [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: 12/17/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction: After the era of genome-wide association studies (GWAS), thousands of genetic variants have been identified to exhibit main effects on human phenotypes. The next critical issue would be to explore the interplay between genes, the so-called "gene-gene interactions" (GxG) or epistasis. An exhaustive search for all single-nucleotide polymorphism (SNP) pairs is not recommended because this will induce a harsh penalty of multiple testing. Limiting the search of epistasis on SNPs reported by previous GWAS may miss essential interactions between SNPs without significant marginal effects. Moreover, most methods are computationally intensive and can be challenging to implement genome-wide. Methods: I here searched for GxG through variance quantitative trait loci (vQTLs) of 29 continuous Taiwan Biobank (TWB) phenotypes. A discovery cohort of 86,536 and a replication cohort of 25,460 TWB individuals were analyzed, respectively. Results: A total of 18 nearly independent vQTLs with linkage disequilibrium measure r 2 < 0.01 were identified and replicated from nine phenotypes. 15 significant GxG were found with p-values <1.1E-5 (in the discovery cohort) and false discovery rates <2% (in the replication cohort). Among these 15 GxG, 11 were detected for blood traits including red blood cells, hemoglobin, and hematocrit; 2 for total bilirubin; 1 for fasting glucose; and 1 for total cholesterol (TCHO). All GxG were observed for gene pairs on the same chromosome, except for the APOA5 (chromosome 11)-TOMM40 (chromosome 19) interaction for TCHO. Discussion: This study provided a computationally feasible way to search for GxG genome-wide and applied this approach to 29 phenotypes.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei, Taiwan
- Master of Public Health Degree Program, College of Public Health, National Taiwan University, Taipei, Taiwan
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van Heugten MH, Blijdorp CJ, Arjune S, van Willigenburg H, Bezstarosti K, Demmers JA, Musterd-Bhaggoe U, Meijer E, Gansevoort RT, Zietse R, Hayat S, Kramann R, Müller RU, Salih M, Hoorn EJ. Matrix Metalloproteinase-7 in Urinary Extracellular Vesicles Identifies Rapid Disease Progression in Autosomal Dominant Polycystic Kidney Disease. J Am Soc Nephrol 2024; 35:321-334. [PMID: 38073039 PMCID: PMC10914202 DOI: 10.1681/asn.0000000000000277] [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: 05/17/2023] [Accepted: 11/12/2023] [Indexed: 03/02/2024] Open
Abstract
SIGNIFICANCE STATEMENT There is an unmet need for biomarkers of disease progression in autosomal dominant polycystic kidney disease (ADPKD). This study investigated urinary extracellular vesicles (uEVs) as a source of such biomarkers. Proteomic analysis of uEVs identified matrix metalloproteinase 7 (MMP-7) as a biomarker predictive of rapid disease progression. In validation studies, MMP-7 was predictive in uEVs but not in whole urine, possibly because uEVs are primarily secreted by tubular epithelial cells. Indeed, single-nucleus RNA sequencing showed that MMP-7 was especially increased in proximal tubule and thick ascending limb cells, which were further characterized by a profibrotic phenotype. Together, these data suggest that MMP-7 is a biologically plausible and promising uEV biomarker for rapid disease progression in ADPKD. BACKGROUND In ADPKD, there is an unmet need for early markers of rapid disease progression to facilitate counseling and selection for kidney-protective therapy. Our aim was to identify markers for rapid disease progression in uEVs. METHODS Six paired case-control groups ( n =10-59/group) of cases with rapid disease progression and controls with stable disease were formed from two independent ADPKD cohorts, with matching by age, sex, total kidney volume, and genetic variant. Candidate uEV biomarkers were identified by mass spectrometry and further analyzed using immunoblotting and an ELISA. Single-nucleus RNA sequencing of healthy and ADPKD tissue was used to identify the cellular origin of the uEV biomarker. RESULTS In the discovery proteomics experiments, the protein abundance of MMP-7 was significantly higher in uEVs of patients with rapid disease progression compared with stable disease. In the validation groups, a significant >2-fold increase in uEV-MMP-7 in patients with rapid disease progression was confirmed using immunoblotting. By contrast, no significant difference in MMP-7 was found in whole urine using ELISA. Compared with healthy kidney tissue, ADPKD tissue had significantly higher MMP-7 expression in proximal tubule and thick ascending limb cells with a profibrotic phenotype. CONCLUSIONS Among patients with ADPKD, rapid disease progressors have higher uEV-associated MMP-7. Our findings also suggest that MMP-7 is a biologically plausible biomarker for more rapid disease progression.
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Affiliation(s)
- Martijn H. van Heugten
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Charles J. Blijdorp
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sita Arjune
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Hester van Willigenburg
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Usha Musterd-Bhaggoe
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Esther Meijer
- Department of Internal Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Ron T. Gansevoort
- Department of Internal Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Zietse
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sikander Hayat
- Medical Faculty, Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Rafael Kramann
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Medical Faculty, Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Mahdi Salih
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ewout J. Hoorn
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
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