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Wang H, Parker D. Improved humanized mouse model of Staphylococcus aureus infection. Mucosal Immunol 2025:S1933-0219(25)00048-0. [PMID: 40354999 DOI: 10.1016/j.mucimm.2025.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2025] [Revised: 05/05/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025]
Abstract
Staphylococcus aureus is a significant cause of pulmonary infections, but existing mouse models fail to recapitulate human-specific responses. In this study, we developed a novel mouse model of S. aureus infection using humanized mice implanted with autologous fetal lung tissue. We show that these human lung implants support S. aureus survival and dissemination. Immunological profiling revealed extensive immune cell death after infection and an absence of chemokine induction. Transcriptomic profiling of the human lung implants revealed significant changes in gene expression, including NF-κB and JAK/STAT signaling. We identified upregulation of Cyp24a1, suggesting a role for vitamin D metabolism in host defense, but it had a mild effect on dissemination. Examination of the bacterial response to the host environment, found downregulation of virulence factors and metabolic genes, and upregulation of stress response pathways. The importance of the heat shock response in bacterial survival was shown as hrcA-deficient S. aureus exhibited reduced tissue colonization. These findings underscore the utility of this humanized lung model for studying S. aureus pathogenesis and bacterial adaptation to the human pulmonary environment.
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Affiliation(s)
- Hui Wang
- Humanized Mouse Core Facility, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ, USA.
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2
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Shao X, Zhao N, Li Y, Wang H, Xu X, Wang S. Quality Evaluation of Qingwei Huanglian Pills Based on Fingerprint and Quantitative Analysis of Multi-Index Components Combined with Chemical Pattern Recognition Analysis. J Chromatogr Sci 2025; 63:bmaf018. [PMID: 40167512 DOI: 10.1093/chromsci/bmaf018] [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: 02/27/2025] [Indexed: 04/02/2025]
Abstract
Qingwei Huanglian Pills (QHPs) is one of the most commonly used traditional Chinese medicine preparations for the treatment of mouth and tongue sores, but the existing quality evaluation standards have certain shortcomings and deficiencies. An effective and scientific quality evaluation method plays a vital role in medication safety. In this study, fingerprint and quantitative analysis of multi-index components combined with chemical pattern recognition analysis was used to comprehensively evaluate the quality of QHPs. The fingerprints of 15 batches of QHPs were generated and evaluated for similarity, with 10 characteristic peaks identified. Clustering hierarchical cluster analysis (HCA), principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were employed to cluster and rank the 15 batches, while simultaneously identifying the components responsible for differences between batches. The HPLC fingerprints of QHPs, along with the content determination of 10 components, were established. Twenty-eight common peaks were identified, and 10 components were specified. The similarity between the 15 batches of samples ranged from 0.983 to 0.999. Cluster analysis and comprehensive score ranking of 15 batches of samples were performed by HCA and PCA, respectively, and 13 chemical markers affecting batch differences were screened by OPLS-DA. The method established here can serve as a reference for the quality evaluation and product quality control of QHPs.
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Affiliation(s)
- Xiaowei Shao
- Binzhou Inspection and Testing Center, Bincheng, Binzhou 256600, China
| | - Nan Zhao
- Pharmacy Department of Binzhou Hospital of Traditional Chinese Medicine, Bincheng, Binzhou 256600, China
| | - Yuping Li
- Binzhou Inspection and Testing Center, Bincheng, Binzhou 256600, China
| | - Hongming Wang
- Binzhou Inspection and Testing Center, Bincheng, Binzhou 256600, China
| | - Xueli Xu
- Binzhou Inspection and Testing Center, Bincheng, Binzhou 256600, China
| | - Shuyue Wang
- Pharmacy Department of Binzhou Hospital of Traditional Chinese Medicine, Bincheng, Binzhou 256600, China
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3
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Pizzini L, Valle F, Osella M, Caselle M. Topic modeling analysis of the Allen Human Brain Atlas. Sci Rep 2025; 15:6928. [PMID: 40011617 PMCID: PMC11865453 DOI: 10.1038/s41598-025-91079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Accepted: 02/18/2025] [Indexed: 02/28/2025] Open
Abstract
The human brain is a complex interconnected structure controlling all elementary and high-level cognitive tasks. It is composed of many regions that exhibit specific distributions of cell types and distinct patterns of functional connections. This complexity is rooted in differential transcription. The constituent cell types of different brain regions express distinctive combinations of genes as they develop and mature, ultimately shaping their functional state in adulthood. How precisely the genetic information of anatomical structures is connected to their underlying biological functions remains an open question in modern neuroscience. A major challenge is the identification of "universal patterns", which do not depend on the particular individual, but are instead basic structural properties shared by all brains. Despite the vast amount of gene expression data available at both the bulk and single-cell levels, this task remains challenging, mainly due to the lack of suitable data mining tools. In this paper, we propose an approach to address this issue based on a hierarchical version of Stochastic Block Modeling. Thanks to its specific choice of priors, the method is particularly effective in identifying these universal features. We use as a laboratory to test our algorithm a dataset obtained from six independent human brains from the Allen Human Brain Atlas. We show that the proposed method is indeed able to identify universal patterns much better than more traditional algorithms such as Latent Dirichlet Allocation or Weighted Correlation Network Analysis. The probabilistic association between genes and samples that we find well represents the known anatomical and functional brain organization. Moreover, leveraging the peculiar "fuzzy" structure of the gene sets obtained with our method, we identify examples of transcriptional and post-transcriptional pathways associated with specific brain regions, highlighting the potential of our approach.
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Affiliation(s)
- Letizia Pizzini
- Department of Physics and INFN, University of Turin, via P.Giuria 1, 10125, Turin, Italy.
| | - Filippo Valle
- Department of Physics and INFN, University of Turin, via P.Giuria 1, 10125, Turin, Italy
| | - Matteo Osella
- Department of Physics and INFN, University of Turin, via P.Giuria 1, 10125, Turin, Italy
| | - Michele Caselle
- Department of Physics and INFN, University of Turin, via P.Giuria 1, 10125, Turin, Italy
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4
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Soucy AM, Brune JE, Jayaraman A, Shenoy AT, Korkmaz FT, Etesami NS, Hiller BE, Martin IM, Goltry WN, Ha CT, Crossland NA, Campbell JD, Beach TG, Traber KE, Jones MR, Quinton LJ, Bosmann M, Frevert CW, Mizgerd JP. Transcriptomic responses of lung mesenchymal cells during pneumonia. JCI Insight 2025; 10:e177084. [PMID: 39998887 PMCID: PMC11981624 DOI: 10.1172/jci.insight.177084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/18/2025] [Indexed: 02/27/2025] Open
Abstract
The role of mesenchymal cells during respiratory infection is not well defined, including whether, which, and how the different types of mesenchymal cells respond. We collected all mesenchymal cells from lung single-cell suspensions of mice that were naive (after receiving only saline vehicle), pneumonic (after intratracheal instillation of pneumococcus 24 hours previously), or resolved from infection (after nonlethal pneumococcal infections 6 weeks previously) and performed single-cell RNA sequencing. Cells clustered into 5 well-separated groups based on their transcriptomes: matrix fibroblasts, myofibroblasts, pericytes, smooth muscle cells, and mesothelial cells. Fibroblasts were the most abundant and could be further segregated into Pdgfra+Npnt+Ces1d+Col13a1+ alveolar fibroblasts and Cd9+Pi16+Sca1+Col14a1+ adventitial fibroblasts. The cells from naive and resolved groups overlapped in dimension reduction plots, suggesting the mesenchymal cells returned to baseline transcriptomes after resolution. During pneumonia, all mesenchymal cells responded with altered transcriptomes, revealing a core response that had been conserved across cell types as well as distinct mesenchymal cell type-specific responses. The different subsets of fibroblasts induced similar gene sets, but the alveolar fibroblasts responded more strongly than the adventitial fibroblasts. These data demonstrated diverse and specialized immune activities of lung mesenchymal cells during pneumonia.
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Affiliation(s)
- Alicia M. Soucy
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jourdan E. Brune
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Center for Lung Biology, University of Washington, Seattle, Washington, USA
| | - Archana Jayaraman
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Anukul T. Shenoy
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Filiz T. Korkmaz
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Neelou S. Etesami
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Bradley E. Hiller
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Ian M.C. Martin
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Wesley N. Goltry
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Catherine T. Ha
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Nicholas A. Crossland
- National Emerging Infectious Diseases Laboratory, Boston University, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine
- Department of Virology, Immunology, & Microbiology; and
| | - Joshua D. Campbell
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Thomas G. Beach
- Banner Sun Health Research Institute Brain and Body Donation Program, Sun City, Arizona, USA
| | - Katrina E. Traber
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Matthew R. Jones
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Lee J. Quinton
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Markus Bosmann
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Charles W. Frevert
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Center for Lung Biology, University of Washington, Seattle, Washington, USA
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington, USA
| | - Joseph P. Mizgerd
- Pulmonary Center, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Virology, Immunology, & Microbiology; and
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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5
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Yang CY, Chang TC, Lee YT, Shih TY, Li CW, Cheng CM. Exploring the Interplay Between Cervicovaginal Microbiome, HPV Infection, and Cervical Intraepithelial Neoplasia in Taiwanese Women. J Med Virol 2025; 97:e70190. [PMID: 39868896 DOI: 10.1002/jmv.70190] [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: 08/01/2024] [Revised: 01/09/2025] [Accepted: 01/13/2025] [Indexed: 01/28/2025]
Abstract
This study examined the relationship between the vaginal microbiome, HPV infection, and cervical intraepithelial neoplasia (CIN) in 173 women. Subjects were grouped by HPV status and cervical lesion severity, ranging from HPV-negative to CIN Grade 2 or higher. Using VALENCIA classification, the study identified different community state types (CSTs) of vaginal microbiota, with CST IV subtypes (Staphylococcus dominated) showing high diversity and increased pathogenic bacteria. Results showed a higher microbial diversity in women with CIN compared to HPV-negative women, with specific microbial profiles like Enterococcus faecalis and Staphylococcus aureus correlating with HPV infection severity. LEfSe and STAMP analyses revealed that particular bacterial species, such as Fannyhessea vaginae and Sneathia vaginalis, could serve as biomarkers for HPV and CIN status. Furthermore, Streptococcus and Staphylococcus were associated with HPV genotypes α7 and α9, respectively. These findings highlight how the composition of vaginal microbiota may influence HPV persistence and CIN progression, emphasizing the need for further research into microbial dysbiosis as a potential target for cervical cancer prevention and management.
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Affiliation(s)
| | - Ting-Chang Chang
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou branch, Taoyuan, Taiwan
| | - Yi-Tzu Lee
- Department of Emergency Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ting-Ying Shih
- Department of Research and Development, AllBio Life Incorporation, Taichung, Taiwan
| | - Chang-Wei Li
- Department of Research and Development, AllBio Life Incorporation, Taichung, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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6
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Sampson J, Ju HM, Zhang N, Yeoh S, Choi J, Bayliss R. Targeting ERBB3 and AKT to overcome adaptive resistance in EML4-ALK-driven non-small cell lung cancer. Cell Death Dis 2024; 15:912. [PMID: 39695132 DOI: 10.1038/s41419-024-07272-7] [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: 03/10/2024] [Revised: 11/22/2024] [Accepted: 11/29/2024] [Indexed: 12/20/2024]
Abstract
The fusion event between EML4 and ALK drives a significant oncogenic activity in 5% of non-small cell lung cancer (NSCLC). Even though potent ALK-tyrosine kinase inhibitors (ALK-TKIs) are successfully used for the treatment of EML4-ALK-positive NSCLC patients, a subset of those patients eventually acquire resistance during their therapy. Here, we investigate the kinase responses in EML4-ALK V1 and V3-harbouring NSCLC cancer cells after acute inhibition with ALK TKI, lorlatinib (LOR). Using phosphopeptide chip array and upstream kinase prediction analysis, we identified a group of phosphorylated tyrosine peptides including ERBB and AKT proteins that are upregulated upon ALK-TKI treatment in EML4-ALK-positive NSCLC cell lines. Dual inhibition of ALK and ERBB receptors or AKT disrupts RAS/MAPK and AKT/PI3K signalling pathways, and enhances apoptosis in EML4-ALK + NSCLC cancer cells. Heregulin, an ERBB3 ligand, differentially modulates the sensitivity of EML4-ALK cell lines to ALK inhibitors. We found that EML4-ALK cells made resistant to LOR are sensitive to inhibition of ERBB and AKT. These findings emphasize the important roles of AKT and ERBB3 to regulate signalling after acute LOR treatment, identifying them as potential targets that may be beneficial to prevent adaptive resistance to EML4-ALK-targeted therapies in NSCLC.
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MESH Headings
- Humans
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/metabolism
- Receptor, ErbB-3/metabolism
- Receptor, ErbB-3/genetics
- Oncogene Proteins, Fusion/metabolism
- Oncogene Proteins, Fusion/genetics
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/drug therapy
- Lung Neoplasms/metabolism
- Proto-Oncogene Proteins c-akt/metabolism
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Lactams/pharmacology
- Protein Kinase Inhibitors/pharmacology
- Aminopyridines/pharmacology
- Signal Transduction/drug effects
- Pyrazoles/pharmacology
- Neuregulin-1/metabolism
- Neuregulin-1/genetics
- Lactams, Macrocyclic/pharmacology
- Anaplastic Lymphoma Kinase/genetics
- Anaplastic Lymphoma Kinase/metabolism
- Anaplastic Lymphoma Kinase/antagonists & inhibitors
- Apoptosis/drug effects
- ErbB Receptors/metabolism
- ErbB Receptors/genetics
- ErbB Receptors/antagonists & inhibitors
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Affiliation(s)
- Josephina Sampson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Hyun-Min Ju
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 138-736, Korea
| | - Nan Zhang
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sharon Yeoh
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 138-736, Korea.
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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7
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Wang X, Wang Y, Bai B, Shaha A, Bao W, He L, Wang T, Kitange GJ, Kang N. PKMζ, a Brain-specific PKCζ Isoform, is Required for Glycolysis and Myofibroblastic Activation of Hepatic Stellate Cells. Cell Mol Gastroenterol Hepatol 2024; 19:101429. [PMID: 39542399 PMCID: PMC11750446 DOI: 10.1016/j.jcmgh.2024.101429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 11/05/2024] [Accepted: 11/07/2024] [Indexed: 11/17/2024]
Abstract
BACKGROUND & AIMS Transforming growth factor (TGF)β1 induces plasma membrane (PM) accumulation of glucose transporter 1 (Glut1) required for glycolysis of hepatic stellate cells (HSCs) and HSC activation. This study aimed to understand how Glut1 is anchored/docked onto the PM of HSCs. METHODS HSC expression of protein kinase M zeta isoform (PKMζ) was detected by reverse transcription polymerase chain reaction (RT-PCR), Western blotting, and immunofluorescence. PKMζ level was manipulated by short hairpin RNA (shRNA) or overexpression; HSC activation was assessed by cell expression of activation markers; PM Glut1, glucose uptake, and glycolysis of HSCs were analyzed by biotinylation, 2-NBDG-based assay, and Seahorse Glycolysis Stress Test. Phospho-mutants of vasodilator-stimulated phosphorylated protein (VASP) were created by site-directed mutagenesis. TGFβ transcriptome was obtained by RNA sequencing. Single-cell RNA sequencing datasets and immunofluorescence were leveraged to analyze PKMζ expression in cancer-associated fibroblasts (CAFs) of colorectal liver metastases. Function of HSC PKMζ was determined by tumor/HSC co-implantation study. RESULTS Primary human and murine HSCs express PKMζ, but not full-length PKCζ. PKMζ knockdown suppresses, whereas PKMζ overexpression potentiates PM accumulation of Glut1, glycolysis, and HSC activation induced by TGFβ1. Mechanistically, PKMζ binds to and induces VASP phosphorylation at serines 157 and 239 facilitating anchoring/docking of Glut1 onto the PM of HSCs. PKMζ expression is increased in the CAFs of murine and patient colorectal liver metastases compared with quiescent HSCs. Targeting PKMζ suppresses transcriptome, CAF activation of HSCs, and colorectal tumor growth in mice. CONCLUSIONS Because HSCs are also a major contributor of liver fibrosis, our data highlight PKMζ and VASP as targets to inhibit metabolic reprogramming, HSC activation, liver fibrosis, and the pro-metastatic microenvironment of the liver.
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Affiliation(s)
- Xianghu Wang
- Tumor Microenvironment and Metastasis, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Yuanguo Wang
- Tumor Microenvironment and Metastasis, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Bing Bai
- Tumor Microenvironment and Metastasis, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Aurpita Shaha
- Tumor Microenvironment and Metastasis, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Wenming Bao
- Tumor Microenvironment and Metastasis, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Lianping He
- School of Medicine, Taizhou University, Taizhou, Zhejiang, P. R. China
| | - Tian Wang
- School of Public Health, Anhui University of Science and Technology, Huainan, Anhui, P. R. China
| | - Gaspar J Kitange
- Cancer Therapy Resistance and Drug Target Discovery, The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Ningling Kang
- Tumor Microenvironment and Metastasis, The Hormel Institute, University of Minnesota, Austin, Minnesota.
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8
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Onyango CO, Anyona SB, Hurwitz I, Raballah E, Wasena SA, Osata SW, Seidenberg P, McMahon BH, Lambert CG, Schneider KA, Ouma C, Cheng Q, Perkins DJ. Transcriptomic and Proteomic Insights into Host Immune Responses in Pediatric Severe Malarial Anemia: Dysregulation in HSP60-70-TLR2/4 Signaling and Altered Glutamine Metabolism. Pathogens 2024; 13:867. [PMID: 39452740 PMCID: PMC11510049 DOI: 10.3390/pathogens13100867] [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: 08/06/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/26/2024] Open
Abstract
Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.
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Affiliation(s)
- Clinton O. Onyango
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno 40100, Kenya; (C.O.O.); (S.A.W.); (S.W.O.); (C.O.)
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
| | - Samuel B. Anyona
- Kenya Global Health Programs, University of New Mexico, Kisumu and Siaya 40100, Kenya; (S.B.A.); (E.R.)
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno 40100, Kenya
| | - Ivy Hurwitz
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
| | - Evans Raballah
- Kenya Global Health Programs, University of New Mexico, Kisumu and Siaya 40100, Kenya; (S.B.A.); (E.R.)
- Department of Medical Laboratory Sciences, School of Public Health Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega 50100, Kenya
| | - Sharely A. Wasena
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno 40100, Kenya; (C.O.O.); (S.A.W.); (S.W.O.); (C.O.)
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
| | - Shamim W. Osata
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno 40100, Kenya; (C.O.O.); (S.A.W.); (S.W.O.); (C.O.)
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
| | - Philip Seidenberg
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
- Department of Emergency Medicine, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Benjamin H. McMahon
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Theoretical Division, Los Alamos, NM 87545, USA
| | - Christophe G. Lambert
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
- Department of Internal Medicine, Division of Translational Informatics, University of New Mexico, Albuquerque, NM 87131, USA
| | - Kristan A. Schneider
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
- Department of Internal Medicine, Division of Translational Informatics, University of New Mexico, Albuquerque, NM 87131, USA
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno 40100, Kenya; (C.O.O.); (S.A.W.); (S.W.O.); (C.O.)
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
| | - Qiuying Cheng
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
- Kenya Global Health Programs, University of New Mexico, Kisumu and Siaya 40100, Kenya; (S.B.A.); (E.R.)
| | - Douglas J. Perkins
- Center for Global Health, Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (I.H.); (P.S.); (B.H.M.); (K.A.S.)
- Kenya Global Health Programs, University of New Mexico, Kisumu and Siaya 40100, Kenya; (S.B.A.); (E.R.)
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9
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Schultz DF, Davies BA, Payne JA, Martin CP, Minard AY, Childs BG, Zhang C, Jeganathan KB, Sturmlechner I, White TA, de Bruin A, Harkema L, Chen H, Davies MA, Jachim S, LeBrasseur NK, Piper RC, Li H, Baker DJ, van Deursen J, Billadeau DD, Katzmann DJ. Loss of HD-PTP function results in lipodystrophy, defective cellular signaling and altered lipid homeostasis. J Cell Sci 2024; 137:jcs262032. [PMID: 39155850 PMCID: PMC11449442 DOI: 10.1242/jcs.262032] [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: 02/17/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024] Open
Abstract
His domain protein tyrosine phosphatase (HD-PTP; also known as PTPN23) facilitates function of the endosomal sorting complexes required for transport (ESCRTs) during multivesicular body (MVB) formation. To uncover its role in physiological homeostasis, embryonic lethality caused by a complete lack of HD-PTP was bypassed through generation of hypomorphic mice expressing reduced protein, resulting in animals that are viable into adulthood. These mice exhibited marked lipodystrophy and decreased receptor-mediated signaling within white adipose tissue (WAT), involving multiple prominent pathways including RAS/MAPK, phosphoinositide 3-kinase (PI3K)/AKT and receptor tyrosine kinases (RTKs), such as EGFR. EGFR signaling was dissected in vitro to assess the nature of defective signaling, revealing decreased trans-autophosphorylation and downstream effector activation, despite normal EGF binding. This corresponds to decreased plasma membrane cholesterol and increased lysosomal cholesterol, likely resulting from defective endosomal maturation necessary for cholesterol trafficking and homeostasis. The ESCRT components Vps4 and Hrs have previously been implicated in cholesterol homeostasis; thus, these findings expand knowledge on which ESCRT subunits are involved in cholesterol homeostasis and highlight a non-canonical role for HD-PTP in signal regulation and adipose tissue homeostasis.
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Affiliation(s)
- Destiny F Schultz
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
- Immunology Graduate Program, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Brian A Davies
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Johanna A Payne
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Cole P Martin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Annabel Y Minard
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, USA
| | - Bennett G Childs
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Karthik B Jeganathan
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Ines Sturmlechner
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Thomas A White
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Alain de Bruin
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
| | - Liesbeth Harkema
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
| | - Huiqin Chen
- Department of Biostatistics, Division of Quantitative Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sarah Jachim
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nathan K LeBrasseur
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Darren J Baker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Jan van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
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Dias C, Mo A, Cai C, Sun L, Cabral K, Brownstein CA, Rockowitz S, Walsh CA. Cell-type-specific effects of autism-associated 15q duplication syndrome in the human brain. Am J Hum Genet 2024; 111:1544-1558. [PMID: 39079538 PMCID: PMC11339625 DOI: 10.1016/j.ajhg.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/11/2024] Open
Abstract
Recurrent copy-number variation represents one of the most well-established genetic drivers in neurodevelopmental disorders, including autism spectrum disorder. Duplication of 15q11-q13 (dup15q) is a well-described neurodevelopmental syndrome that increases the risk of autism more than 40-fold. However, the effects of this duplication on gene expression and chromatin accessibility in specific cell types in the human brain remain unknown. To identify the cell-type-specific transcriptional and epigenetic effects of dup15q in the human frontal cortex, we conducted single-nucleus RNA sequencing and multi-omic sequencing on dup15q-affected individuals (n = 6) as well as individuals with non-dup15q autism (n = 7) and neurotypical control individuals (n = 7). Cell-type-specific differential expression analysis identified significantly regulated genes, critical biological pathways, and differentially accessible genomic regions. Although there was overall increased gene expression across the duplicated genomic region, cellular identity represented an important factor mediating gene-expression changes. As compared to other cell types, neuronal subtypes showed greater upregulation of gene expression across a critical region within the duplication. Genes that fell within the duplicated region and had high baseline expression in control individuals showed only modest changes in dup15q, regardless of cell type. Of note, dup15q and autism had largely distinct signatures of chromatin accessibility but shared the majority of transcriptional regulatory motifs, suggesting convergent biological pathways. However, the transcriptional binding-factor motifs implicated in each condition implicated distinct biological mechanisms: neuronal JUN and FOS networks in autism vs. an inflammatory transcriptional network in dup15q microglia. This work provides a cell-type-specific analysis of how dup15q changes gene expression and chromatin accessibility in the human brain, and it finds evidence of marked cell-type-specific effects of this genetic driver. These findings have implications for guiding therapeutic development in dup15q syndrome, as well as understanding the functional effects of copy-number variants more broadly in neurodevelopmental disorders.
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Affiliation(s)
- Caroline Dias
- Division of Developmental Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Alisa Mo
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chunhui Cai
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kristen Cabral
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
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11
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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; 23:2219-2229. [PMID: 38682820 DOI: 10.1021/acs.jproteome.4c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
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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12
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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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13
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Bertolo A, Valido E, Stoyanov J. Optimized bacterial community characterization through full-length 16S rRNA gene sequencing utilizing MinION nanopore technology. BMC Microbiol 2024; 24:58. [PMID: 38365589 PMCID: PMC10870487 DOI: 10.1186/s12866-024-03208-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/28/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Accurate identification of bacterial communities is crucial for research applications, diagnostics, and clinical interventions. Although 16S ribosomal RNA (rRNA) gene sequencing is a widely employed technique for bacterial taxonomic classification, it often results in misclassified or unclassified bacterial taxa. This study sought to refine the full-length 16S rRNA gene sequencing protocol using the MinION sequencer, focusing on the V1-V9 regions. Our methodological enquiry examined several factors, including the number of PCR amplification cycles, choice of primers and Taq polymerase, and specific sequence databases and workflows employed. We used a microbial standard comprising eight bacterial strains (five gram-positive and three gram-negative) in known proportions as a validation control. RESULTS Based on the MinION protocol, we employed the microbial standard as the DNA template for the 16S rRNA gene amplicon sequencing procedure. Our analysis showed that an elevated number of PCR amplification cycles introduced PCR bias, and the selection of Taq polymerase and primer sets significantly affected the subsequent analysis. Bacterial identification at genus level demonstrated Pearson correlation coefficients ranging from 0.73 to 0.79 when assessed using BugSeq, Kraken-Silva and EPI2ME-16S workflows. Notably, the EPI2ME-16S workflow exhibited the highest Pearson correlation with the microbial standard, minimised misclassification, and increased alignment accuracy. At the species taxonomic level, the BugSeq workflow was superior, with a Pearson correlation coefficient of 0.92. CONCLUSIONS These findings emphasise the importance of careful selection of PCR settings and a well-structured analytical framework for 16S rRNA full-length gene sequencing. The results showed a robust correlation between the predicted and observed bacterial abundances at both the genus and species taxonomic levels, making these findings applicable across diverse research contexts and with clinical utility for reliable pathogen identification.
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Affiliation(s)
- Alessandro Bertolo
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland
- Department of Orthopaedic Surgery, University of Bern, Bern Inselspital, Bern, Switzerland
| | - Ezra Valido
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland
| | - Jivko Stoyanov
- SCI Population Biobanking & Translational Research Group, Swiss Paraplegic Research, Nottwil, Switzerland.
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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14
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Feng F, Duan Q, Jiang X, Kao X, Zhang D. DendroX: multi-level multi-cluster selection in dendrograms. BMC Genomics 2024; 25:134. [PMID: 38308243 PMCID: PMC10835886 DOI: 10.1186/s12864-024-10048-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Cluster heatmaps are widely used in biology and other fields to uncover clustering patterns in data matrices. Most cluster heatmap packages provide utility functions to divide the dendrograms at a certain level to obtain clusters, but it is often difficult to locate the appropriate cut in the dendrogram to obtain the clusters seen in the heatmap or computed by a statistical method. Multiple cuts are required if the clusters locate at different levels in the dendrogram. RESULTS We developed DendroX, a web app that provides interactive visualization of a dendrogram where users can divide the dendrogram at any level and in any number of clusters and pass the labels of the identified clusters for functional analysis. Helper functions are provided to extract linkage matrices from cluster heatmap objects in R or Python to serve as input to the app. A graphic user interface was also developed to help prepare input files for DendroX from data matrices stored in delimited text files. The app is scalable and has been tested on dendrograms with tens of thousands of leaf nodes. As a case study, we clustered the gene expression signatures of 297 bioactive chemical compounds in the LINCS L1000 dataset and visualized them in DendroX. Seventeen biologically meaningful clusters were identified based on the structure of the dendrogram and the expression patterns in the heatmap. We found that one of the clusters consisting of mostly naturally occurring compounds is not previously reported and has its members sharing broad anticancer, anti-inflammatory and antioxidant activities. CONCLUSIONS DendroX solves the problem of matching visually and computationally determined clusters in a cluster heatmap and helps users navigate among different parts of a dendrogram. The identification of a cluster of naturally occurring compounds with shared bioactivities implicates a convergence of biological effects through divergent mechanisms.
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Affiliation(s)
- Feiling Feng
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Qiaonan Duan
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Xiaoqing Jiang
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xiaoming Kao
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
| | - Dadong Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China.
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15
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Ratanasereeprasert N, Hsu LF, Wang SK, Jane Yao CC. Orthodontically induced changes to the genetic profile in periodontal ligament tissue and cytokine release in gingival crevicular fluid - A pilot investigation. J Dent Sci 2024; 19:387-396. [PMID: 38303827 PMCID: PMC10829649 DOI: 10.1016/j.jds.2023.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 07/31/2023] [Indexed: 02/03/2024] Open
Abstract
Background/purpose It has been known that genetic factors influence orthodontic tooth movement, however, scientific research on humans is lacking. Therefore, this study aimed to investigate dynamic changes to the genetic profile in human periodontal ligament (PDL) tissue and cytokine release in gingival crevicular fluid (GCF) during the first 28 days of orthodontic treatment. Materials and methods Fifteen teeth from three patients were recruited. Full-mouth fixed appliances with extraction of four premolars and one maxillary third molar was planned for orthodontic treatment. GCF collection and tooth extraction were performed following force application for 0, 1, 3, 7, and 28 days. GCF was analyzed using multiplex immunoassay for 27 cytokines. PDL tissue was collected after extraction and submitted for RNA exome-sequencing using Illumina sequencing platform. Further analysis of differentially expressed genes (DEGs), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and heatmaps were conducted. Results GCF cytokine levels varied among three patients; some patients exhibited a peak cytokine level on Day 0 whereas others did so on Days 1-3. In RNA exome sequencing data, GO and KEGG analyses showed that genes associated with sensory receptors were upregulated on Day 1, genes involved in bone remodeling were upregulated on Days 3 and 28, and genes related to osteoclast differentiation were upregulated on Day 7. Conclusion RNA sequencing data demonstrate that the specific types of genes are expressed at different time points, whereas the data on cytokine changes show a large variation in concentration levels and dynamic change patterns among the patients.
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Affiliation(s)
| | - Li-Fang Hsu
- Department of Dentistry, National Taiwan University Hospital, Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Shih-Kai Wang
- Department of Dentistry, School of Dentistry, National Taiwan University, Department of Pediatric Dentistry, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Chung-Chen Jane Yao
- Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
- Division of Orthodontics and Dentofacial Orthopedics, Dental Department, National Taiwan University Hospital, Taipei, Taiwan
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16
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Jain D, Schmidt W. Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH. Mol Cell Proteomics 2024; 23:100685. [PMID: 38000714 PMCID: PMC10837763 DOI: 10.1016/j.mcpro.2023.100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Environment pH (pHe) is a key parameter dictating a surfeit of conditions critical to plant survival and fitness. To elucidate the mechanisms that recalibrate cytoplasmic and apoplastic pH homeostasis, we conducted a comprehensive proteomic/phosphoproteomic inventory of plants subjected to transient exposure to acidic or alkaline pH, an approach that covered the majority of protein-coding genes of the reference plant Arabidopsis thaliana. Our survey revealed a large set-of so far undocumented pHe-dependent phospho-sites, indicative of extensive post-translational regulation of proteins involved in the acclimation to pHe. Changes in pHe altered both electrogenic H+ pumping via P-type ATPases and H+/anion co-transport processes, putatively leading to altered net trans-plasma membrane translocation of H+ ions. In pH 7.5 plants, the transport (but not the assimilation) of nitrogen via NRT2-type nitrate and AMT1-type ammonium transporters was induced, conceivably to increase the cytosolic H+ concentration. Exposure to both acidic and alkaline pH resulted in a marked repression of primary root elongation. No such cessation was observed in nrt2.1 mutants. Alkaline pH decreased the number of root hairs in the wild type but not in nrt2.1 plants, supporting a role of NRT2.1 in developmental signaling. Sequestration of iron into the vacuole via alterations in protein abundance of the vacuolar iron transporter VTL5 was inversely regulated in response to high and low pHe, presumptively in anticipation of associated changes in iron availability. A pH-dependent phospho-switch was also observed for the ABC transporter PDR7, suggesting changes in activity and, possibly, substrate specificity. Unexpectedly, the effect of pHe was not restricted to roots and provoked pronounced changes in the shoot proteome. In both roots and shoots, the plant-specific TPLATE complex components AtEH1 and AtEH2-essential for clathrin-mediated endocytosis-were differentially phosphorylated at multiple sites in response to pHe, indicating that the endocytic cargo protein trafficking is orchestrated by pHe.
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Affiliation(s)
- Dharmesh Jain
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichun, Taiwan; Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan.
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17
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Cui W, Fiore N, Figueroa F, Rubilar C, Pizarro L, Pinto M, Pérez S, Beltrán MF, Carreras C, Pimentel P, Zamorano A. Transcriptome Analysis of Sweet Cherry ( Prunus avium L.) Cultivar 'Lapins' upon Infection of Pseudomonas syringae pv. syringae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3718. [PMID: 37960074 PMCID: PMC10647540 DOI: 10.3390/plants12213718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Bacterial canker caused by Pseudomonas syringae pv. syringae (Pss) is responsible for substantial loss to the production of sweet cherry in Chile. To date, the molecular mechanisms of the Pss-sweet cherry interaction and the disease-related genes in the plant are poorly understood. In order to gain insight into these aspects, a transcriptomic analysis of the sweet cherry cultivar 'Lapins' for differentially expressed genes (DEGs) in response to Pss inoculation was conducted. Three Pss strains, A1M3, A1M197, and 11116_b1, were inoculated in young twigs, and RNA was extracted from tissue samples at the inoculation site and distal sections. RNA sequencing and transcriptomic expression analysis revealed that the three strains induced different patterns of responses in local and distal tissues. In the local tissues, A1M3 triggered a much more extensive response than the other two strains, enriching DEGs especially involved in photosynthesis. In the distal tissues, the three strains triggered a comparable extent of responses, among which 11116_b1 induced a group of DEGs involved in defense responses. Furthermore, tissues from various inoculations exhibited an enrichment of DEGs related to carbohydrate metabolism, terpene metabolism, and cell wall biogenesis. This study opened doors to future research on the Pss-sweet cherry interaction, immunity responses, and disease control.
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Affiliation(s)
- Weier Cui
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Nicola Fiore
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Franco Figueroa
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Carlos Rubilar
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Lorena Pizarro
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Manuel Pinto
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Universidad de O’Higgins, San Fernando 3070000, Chile; (F.F.); (C.R.); (L.P.); (M.P.)
| | - Set Pérez
- Laboratorio de Patología Vegetal, Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile;
| | - María Francisca Beltrán
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Claudia Carreras
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
| | - Paula Pimentel
- Laboratorio de Fisiología del Estrés, Centro de Estudios Avanzados en Fruticultura (CEAF), Camino Las Parcelas, 882, Rengo 2940000, Chile;
| | - Alan Zamorano
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile; (W.C.); (N.F.); (M.F.B.); (C.C.)
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18
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Martins ÁM, Lopes TM, Diniz F, Pires J, Osório H, Pinto F, Freitas D, Reis CA. Differential Protein and Glycan Packaging into Extracellular Vesicles in Response to 3D Gastric Cancer Cellular Organization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300588. [PMID: 37340602 PMCID: PMC10460857 DOI: 10.1002/advs.202300588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/26/2023] [Indexed: 06/22/2023]
Abstract
Alterations of the glycosylation machinery are common events in cancer, leading to the synthesis of aberrant glycan structures by tumor cells. Extracellular vesicles (EVs) play a modulatory role in cancer communication and progression, and interestingly, several tumor-associated glycans have already been identified in cancer EVs. Nevertheless, the impact of 3D tumor architecture in the selective packaging of cellular glycans into EVs has never been addressed. In this work, the capacity of gastric cancer cell lines with differential glycosylation is evaluated in producing and releasing EVs when cultured under conventional 2D monolayer or in 3D culture conditions. Furthermore, the proteomic content is identified and specific glycans are studied in the EVs produced by these cells, upon differential spatial organization. Here, it is observed that although the proteome of the analyzed EVs is mostly conserved, an EV differential packaging of specific proteins and glycans is found. In addition, protein-protein interaction and pathway analysis reveal individual signatures on the EVs released by 2D- and 3D-cultured cells, suggesting distinct biological functions. These protein signatures also show a correlation with clinical data. Overall, this data highlight the importance of tumor cellular architecture when assessing the cancer-EV cargo and its biological role.
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Affiliation(s)
- Álvaro M. Martins
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)University of PortoR. Jorge de Viterbo FerreiraPorto4050-313Portugal
| | - Tânia M. Lopes
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
| | - Francisca Diniz
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)University of PortoR. Jorge de Viterbo FerreiraPorto4050-313Portugal
| | - José Pires
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Faculty of Medicine of the University of PortoAlameda Prof. Hernâni MonteiroPorto4200-319Portugal
| | - Hugo Osório
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Faculty of Medicine of the University of PortoAlameda Prof. Hernâni MonteiroPorto4200-319Portugal
| | - Filipe Pinto
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
| | - Daniela Freitas
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
| | - Celso A. Reis
- i3S‐Institute for Research and Innovation in HealthUniversity of PortoRua Alfredo Allen 208Porto4200-135Portugal
- IPATIMUP‐Institute of Molecular Pathology and ImmunologyUniversity of PortoRua Júlio Amaral de Carvalho 45Porto4200-135Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)University of PortoR. Jorge de Viterbo FerreiraPorto4050-313Portugal
- Faculty of Medicine of the University of PortoAlameda Prof. Hernâni MonteiroPorto4200-319Portugal
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19
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Pirone A, Ciregia F, Lazzarini G, Miragliotta V, Ronci M, Zuccarini M, Zallocco L, Beghelli D, Mazzoni MR, Lucacchini A, Giusti L. Proteomic Profiling Reveals Specific Molecular Hallmarks of the Pig Claustrum. Mol Neurobiol 2023; 60:4336-4358. [PMID: 37095366 PMCID: PMC10293365 DOI: 10.1007/s12035-023-03347-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
The present study, employing a comparative proteomic approach, analyzes the protein profile of pig claustrum (CLA), putamen (PU), and insula (IN). Pig brain is an interesting model whose key translational features are its similarities with cortical and subcortical structures of human brain. A greater difference in protein spot expression was observed in CLA vs PU as compared to CLA vs IN. The deregulated proteins identified in CLA resulted to be deeply implicated in neurodegenerative (i.e., sirtuin 2, protein disulfide-isomerase 3, transketolase) and psychiatric (i.e., copine 3 and myelin basic protein) disorders in humans. Metascape analysis of differentially expressed proteins in CLA vs PU comparison suggested activation of the α-synuclein pathway and L1 recycling pathway corroborating the involvement of these anatomical structures in neurodegenerative diseases. The expression of calcium/calmodulin-dependent protein kinase and dihydropyrimidinase like 2, which are linked to these pathways, was validated using western blot analysis. Moreover, the protein data set of CLA vs PU comparison was analyzed by Ingenuity Pathways Analysis to obtain a prediction of most significant canonical pathways, upstream regulators, human diseases, and biological functions. Interestingly, inhibition of presenilin 1 (PSEN1) upstream regulator and activation of endocannabinoid neuronal synapse pathway were observed. In conclusion, this is the first study presenting an extensive proteomic analysis of pig CLA in comparison with adjacent areas, IN and PUT. These results reinforce the common origin of CLA and IN and suggest an interesting involvement of CLA in endocannabinoid circuitry, neurodegenerative, and psychiatric disorders in humans.
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Affiliation(s)
- Andrea Pirone
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy.
| | - Federica Ciregia
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giulia Lazzarini
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | | | - Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences, University G. D'Annunzio of Chieti-Pescara, Chieti, Italy
- Interuniversitary Consortium for Engineering and Medicine, COIIM, Campobasso, Italy
| | - Mariachiara Zuccarini
- Department of Medical, Oral and Biotechnological Sciences, University G. D'Annunzio of Chieti-Pescara, Chieti, Italy
| | - Lorenzo Zallocco
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Daniela Beghelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Laura Giusti
- School of Pharmacy, University of Camerino, Camerino, Italy
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20
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Alkim C, Farias D, Fredonnet J, Serrano-Bataille H, Herviou P, Picot M, Slama N, Dejean S, Morin N, Enjalbert B, François JM. Toxic effect and inability of L-homoserine to be a nitrogen source for growth of Escherichia coli resolved by a combination of in vivo evolution engineering and omics analyses. Front Microbiol 2022; 13:1051425. [PMID: 36583047 PMCID: PMC9792984 DOI: 10.3389/fmicb.2022.1051425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
L-homoserine is a pivotal intermediate in the carbon and nitrogen metabolism of E. coli. However, this non-canonical amino acid cannot be used as a nitrogen source for growth. Furthermore, growth of this bacterium in a synthetic media is potently inhibited by L-homoserine. To understand this dual effect, an adapted laboratory evolution (ALE) was applied, which allowed the isolation of a strain able to grow with L-homoserine as the nitrogen source and was, at the same time, desensitized to growth inhibition by this amino acid. Sequencing of this evolved strain identified only four genomic modifications, including a 49 bp truncation starting from the stop codon of thrL. This mutation resulted in a modified thrL locus carrying a thrL* allele encoding a polypeptide 9 amino acids longer than the thrL encoded leader peptide. Remarkably, the replacement of thrL with thrL* in the original strain MG1655 alleviated L-homoserine inhibition to the same extent as strain 4E, but did not allow growth with this amino acid as a nitrogen source. The loss of L-homoserine toxic effect could be explained by the rapid conversion of L-homoserine into threonine via the thrL*-dependent transcriptional activation of the threonine operon thrABC. On the other hand, the growth of E. coli on a mineral medium with L-homoserine required an activation of the threonine degradation pathway II and glycine cleavage system, resulting in the release of ammonium ions that were likely recaptured by NAD(P)-dependent glutamate dehydrogenase. To infer about the direct molecular targets of L-homoserine toxicity, a transcriptomic analysis of wild-type MG1655 in the presence of 10 mM L-homoserine was performed, which notably identified a potent repression of locomotion-motility-chemotaxis process and of branched-chain amino acids synthesis. Since the magnitude of these effects was lower in a ΔthrL mutant, concomitant with a twofold lower sensitivity of this mutant to L-homoserine, it could be argued that growth inhibition by L-homoserine is due to the repression of these biological processes. In addition, L-homoserine induced a strong upregulation of genes in the sulfate reductive assimilation pathway, including those encoding its transport. How this non-canonical amino acid triggers these transcriptomic changes is discussed.
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Affiliation(s)
- Ceren Alkim
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France,Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Daniele Farias
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Julie Fredonnet
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | | | - Pauline Herviou
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Marc Picot
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Nawel Slama
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | | | - Nicolas Morin
- Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France
| | - Brice Enjalbert
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean M. François
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France,Toulouse White Biotechnology Center (TWB), UMS-INSA-INRA-CNRS, Toulouse, France,*Correspondence: Jean M. François,
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21
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Diwa RR, Elvira MV, Deocaris CC, Fukuyama M, Belo LP. Transport of toxic metals in the bottom sediments and health risk assessment of Corbicula fluminea (Asiatic clam) collected from Laguna de Bay, Philippines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156522. [PMID: 35679944 DOI: 10.1016/j.scitotenv.2022.156522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Laguna de Bay, the 3rd largest lake in Southeast Asia, is the most significant source of freshwater fish in the Philippines. With decades of unregulated discharge of industrial, domestic, and agricultural wastewaters into the lake, this study investigates the apportionment of heavy metals from the bottom sediments and its impact on the toxicity of Corbicula fluminea (Asiatic clam), a popular food item in the markets. The sediment samples from the western part of the lake contained higher Cd, Cu, Pb, and Zn and lower As and Cr concentrations compared to the eastern part. There were positive correlations for As, Cr, Cu, Pb, and Zn and negative correlations for Cd and Ni concentrations noted between sediments and C. fluminea. Human health risk associated with the consumption of C. fluminea collected from Laguna de Bay was attributed to the following heavy metals: Cu > As > Zn > Cd > Pb > Cr > Ni. Interestingly, the observed trend in toxicities of the shellfish was consistent with the transport phenomenon of heavy metals facilitated by the counterclockwise direction of the bottom current. This study strongly suggests the re-evaluation of the waste management plan in the industrial zones and policies regulating the sale of the shellfish harvest.
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Affiliation(s)
- Reymar R Diwa
- Atomic Research Division, Philippine Nuclear Research Institute, Department of Science & Technology, Diliman, Quezon City 1101, Philippines; Research and Development Center, Rizal Technological University, Mandaluyong City 1550, Philippines
| | - Marlon V Elvira
- College of Forestry and Environmental Science, Caraga State University, Butuan City 8600, Philippines
| | - Custer C Deocaris
- Atomic Research Division, Philippine Nuclear Research Institute, Department of Science & Technology, Diliman, Quezon City 1101, Philippines; Technological Institute of the Philippines, Cubao, Aurora Blvd., Quezon City, Philippines; BAN Toxics, Barangay Central, Quezon City 1100, Philippines
| | - Mayuko Fukuyama
- Graduate School of Engineering Science, Akita University, Akita Prefecture 010-8502, Japan
| | - Lawrence P Belo
- BAN Toxics, Barangay Central, Quezon City 1100, Philippines; Department of Chemical Engineering, De La Salle University, Manila 1004, Philippines.
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22
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Ke CH, Wang YS, Chiang HC, Wu HY, Liu WJ, Huang CC, Huang YC, Lin CS. Xenograft cancer vaccines prepared from immunodeficient mice increase tumor antigen diversity and host T cell efficiency against colorectal cancers. Cancer Lett 2022; 526:66-75. [PMID: 34808284 DOI: 10.1016/j.canlet.2021.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
Autologous cancer vaccines (ACVs) are a desirable approach for personalized medicine, but the efficiency of ACVs remains unsatisfactory due to their low immunogenicity. This study developed a platform that can enhance the immunogenicity of ACVs by transplanting the tumors into immunodeficient mice. The CT26 cell line was inoculated into severe combined immunodeficient mice (SCID) for vaccine preparation where escalates tumor development, subsequently diversifying the tumor antigenic topology. CT26/SCID cancer vaccines significantly inhibited tumor growth, increased the amount of tumor infiltrating lymphocytes, and triggered Th-1 predominant immune responses. Tumor antigenic profiles of CT26/SCID cells were further analyzed by liquid chromatography-tandem mass spectrometry. Compared to CT26 parental cells, a total of 428 differentially expressed proteins (DEPs) were detected. These DEPs revealed that CT26/SCID cells overexpressed several novel therapeutic targets, including KNG1, apoA-I and, β2-GPI, which can trigger cytotoxic T cells towards Th-1 predominant immune responses and directly suppress proliferation in tumors. CT26/SCID cancer vaccines can be easily manufactured, while traits of triggering stronger antigen-specific Th-1 immune activity against tumors, are retained. Results of this study provide an effective proof-of-concept of an ACV for personalized cancer immunotherapy.
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Affiliation(s)
- Chiao-Hsu Ke
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd., 106319, Taipei, Taiwan
| | - Yu-Shan Wang
- Lab. 2612, Rekiin Biotech Inc., 114737, Taipei, Taiwan
| | | | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, 106319, Taipei, Taiwan
| | - Wang-Jing Liu
- Department of Earth and Life Science, University of Taipei, 1 Ai-Guo West Road, Taipei, 100234, Taipei, Taiwan
| | | | - Yi-Chun Huang
- Lab. 2612, Rekiin Biotech Inc., 114737, Taipei, Taiwan
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd., 106319, Taipei, Taiwan.
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23
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Martins LJ, Szaniawski MA, Williams ESCP, Coiras M, Hanley TM, Planelles V. HIV-1 Accessory Proteins Impart a Modest Interferon Response and Upregulate Cell Cycle-Related Genes in Macrophages. Pathogens 2022; 11:163. [PMID: 35215107 PMCID: PMC8878269 DOI: 10.3390/pathogens11020163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/18/2021] [Accepted: 01/23/2022] [Indexed: 12/10/2022] Open
Abstract
HIV-1 infection of myeloid cells is associated with the induction of an IFN response. How HIV-1 manipulates and subverts the IFN response is of key interest for the design of therapeutics to improve immune function and mitigate immune dysregulation in people living with HIV. HIV-1 accessory genes function to improve viral fitness by altering host pathways in ways that enable transmission to occur without interference from the immune response. We previously described changes in transcriptomes from HIV-1 infected and from IFN-stimulated macrophages and noted that transcription of IFN-regulated genes and genes related to cell cycle processes were upregulated during HIV-1 infection. In the present study, we sought to define the roles of individual viral accessory genes in upregulation of IFN-regulated and cell cycle-related genes using RNA sequencing. We observed that Vif induces a set of genes involved in mitotic processes and that these genes are potently downregulated upon stimulation with type-I and -II IFNs. Vpr also upregulated cell cycle-related genes and was largely responsible for inducing an attenuated IFN response. We note that the induced IFN response most closely resembled a type-III IFN response. Vpu and Nef-regulated smaller sets of genes whose transcriptomic signatures upon infection related to cytokine and chemokine processes. This work provides more insight regarding processes that are manipulated by HIV-1 accessory proteins at the transcriptional level.
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Affiliation(s)
- Laura J. Martins
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
| | - Matthew A. Szaniawski
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA;
| | - Elizabeth S. C. P. Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
| | - Mayte Coiras
- AIDS Immunopathology Unit, National Center of Microbiology (CNM) Instituto de Salud Carlos III (ISDIII), 28222 Madrid, Spain;
| | - Timothy M. Hanley
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
- Division of Hematopathology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; (L.J.M.); (E.S.C.P.W.)
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24
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Roles of Close Homologues SigB and SigD in Heat and High Light Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803. Life (Basel) 2022; 12:life12020162. [PMID: 35207450 PMCID: PMC8875361 DOI: 10.3390/life12020162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that the sigB and sigD genes are both induced in high light and heat stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (containing SigD as the only functional group 2 σ factor), and ΔsigCDE (SigB as the only functional group 2 σ factor) strains in standard, high light, and high temperature conditions revealed that the SigB and SigD factors regulate different sets of genes and SigB and SigD regulons are highly dependent on stress conditions. The SigB regulon is bigger than the SigD regulon at high temperature, whereas, in high light, the SigD regulon is bigger than the SigB regulon. Furthermore, our results show that favoring the SigB or SigD factor by deleting other group 2 σ factors does not lead to superior acclimation to high light or high temperature, indicating that all group 2 σ factors play roles in the acclimation processes.
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25
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Gu Z, Hübschmann D. Make Interactive Complex Heatmaps in R. Bioinformatics 2021; 38:1460-1462. [PMID: 34864868 PMCID: PMC8826183 DOI: 10.1093/bioinformatics/btab806] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/29/2021] [Accepted: 11/27/2021] [Indexed: 01/05/2023] Open
Abstract
SUMMARY Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In this work, we introduce a new R package InteractiveComplexHeatmap that brings interactivity to the widely used ComplexHeatmap package. InteractiveComplexHeatmap is designed with an easy-to-use interface where static complex heatmaps can be directly exported to an interactive Shiny web application only with one additional line of code. InteractiveComplexHeatmap also provides flexible functionalities for integrating interactive heatmap widgets to build more complex and customized Shiny web applications. AVAILABILITY AND IMPLEMENTATION The InteractiveComplexHeatmap package and documentations are freely available from the Bioconductor project: https://bioconductor.org/packages/InteractiveComplexHeatmap/. A complete and printer-friendly version of the documentation can also be found in Supplementary File S1. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zuguang Gu
- Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), Im Neuen-heimer Feld 280, 69120 Heidelberg, Germany,To whom correspondence should be addressed. or
| | - Daniel Hübschmann
- Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), Im Neuen-heimer Feld 280, 69120 Heidelberg, Germany,Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany,German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany,Department of Pediatric Immunology, Hematology and Oncology, University Hospital Heidel-berg, 69120 Heidelberg, Germany,To whom correspondence should be addressed. or
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26
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Webb JL, Moe SM, Bolstad AK, McNeill EM. Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive. PLoS One 2021; 16:e0255085. [PMID: 34379632 PMCID: PMC8357136 DOI: 10.1371/journal.pone.0255085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, learning, and memory. Previous sequencing studies have demonstrated that aging alters gene expression in the PFC, however the extent to which these changes are conserved across species and are meaningful in neurodegeneration is unknown. Identifying conserved, age-related genetic and morphological changes in the brain allows application of the wealth of tools available to study underlying mechanisms in model organisms such as Drosophila melanogaster. RNA sequencing data from human PFC and fly heads were analyzed to determine conserved transcriptome signatures of age. Our analysis revealed that expression of 50 conserved genes can accurately determine age in Drosophila (R2 = 0.85) and humans (R2 = 0.46). These transcriptome signatures were also able to classify Drosophila into three age groups with a mean accuracy of 88% and classify human samples with a mean accuracy of 69%. Overall, this work identifies 50 highly conserved aging-associated genetic changes in the brain that can be further studied in model organisms and demonstrates a novel approach to uncovering genetic changes conserved across species from multi-study public databases.
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Affiliation(s)
- Joe L. Webb
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
| | - Simon M. Moe
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
| | - Andrew K. Bolstad
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States of America
| | - Elizabeth M. McNeill
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, United States of America
- Neuroscience Interdepartmental Graduate program, Iowa State University, Ames, IA, United States of America
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27
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He Y, Zhang R, Quan Z, He B, Xu Y, Chen Z, Ren Y, Liu X. Synthesis, Characterization, and Specific Localization of Mitochondrial-Targeted Antioxidant Peptide SS31 Probe. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9915699. [PMID: 34056004 PMCID: PMC8142804 DOI: 10.1155/2021/9915699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/07/2021] [Indexed: 11/23/2022]
Abstract
The aim of this study is to investigate the targeting efficiency of FITC-SS31 to mitochondria in both normal and H2O2-induced oxidative damaged 661W cells, characterizing the properties of FITC-SS31 in the biological assays. The purity and molecular weight of FITC-SS31 were identified using HPLC and MS. MTT and LDH assays were used to evaluate the cytotoxicity and cell permeability. The binding ability of FITC-SS31 to cells was demonstrated by flow cytometry. The colocalization of FITC-SS31 and MitoTracker both in normal and oxidative cells was analyzed by a laser confocal microscope. We detected the DEGs between SS31+H2O2 and H2O2-alone-treated cells by RNA seq. GO and KEGG analyses were performed to predict the functional gene of SS31. The molecular weight of FITC-SS31 was 1142.2 with the 97.76% purity. The flow cytometry results showed that the MFI (mean fluorescence intensity) of FITC-SS31 in normal cells in the 4 h probe treatment group was higher than that in the 2 h and the 0 h group. The MFI in the 2 h probe treatment group was much higher than that in the 4 h and 0 h groups in damaged cells. The positive rate of 10 μM FITC-SS31 was higher than that of 1 μM and 5 μM. Fluorescein imaging analysis confirmed that FITC-SS31 was overlapped with MitoTracker. Through the analysis, DEGs were highly expressed in "localization, organelle, antioxidant activity, binding" functions and enriched in "AMPK signaling pathway, MAPK targets/nuclear events mediated by MAP kinase pathway and PI3K-Akt signaling pathway." It is speculated that SS31 exerts an antioxidant effect through one of these pathways. We hypothesized that SS31 could play a more efficient role in the pathological cells in the half-life period to avoid cell death due to oxidative damage. The functions of the DEGs in SS31+H2O2 and H2O2-alone samples are related to the localization and antioxidant activity of SS31. DEGs are mostly enriched in the AMPK signaling pathway, which needs further studies.
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Affiliation(s)
- Yuan He
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, China
- Xi'an Medical University, Xi'an, China
| | - Ruixue Zhang
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, China
- Xi'an Medical University, Xi'an, China
| | - Zhuoya Quan
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, China
- Xi'an Medical University, Xi'an, China
| | - Beilei He
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, China
- Xi'an Medical University, Xi'an, China
| | - Yun Xu
- Xi'an Medical University, Xi'an, China
| | | | - Yuan Ren
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, China
| | - Xu Liu
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, China
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