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Scott CJR, McGregor NGS, Leadbeater DR, Oates NC, Hoßbach J, Abood A, Setchfield A, Dowle A, Overkleeft HS, Davies GJ, Bruce NC. Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates. Microbiol Spectr 2024; 12:e0394323. [PMID: 38757984 DOI: 10.1128/spectrum.03943-23] [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: 11/14/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.
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Affiliation(s)
- Conor J R Scott
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Janina Hoßbach
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Alexander Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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Ferchiou S, Caza F, Sinha K, Sauvageau J, St-Pierre Y. Assessing Marine Ecosystem Health Using Multi-Omic Analysis of Blue Mussel Liquid Biopsies: A Case Study within a National Marine Park. CHEMOSPHERE 2024; 362:142714. [PMID: 38950751 DOI: 10.1016/j.chemosphere.2024.142714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024]
Abstract
Marine ecosystems are under escalating threats from myriad environmental stressors, necessitating a deeper understanding of their impact on biodiversity and the health of sentinel organisms. In this study, we carried out a spatiotemporal multi-omic analysis of liquid biopsies collected from mussels (Mytilus spp.) in marine ecosystems of a national park. We delved into the epigenomic, transcriptomic, glycomic, proteomic, and microbiomic profiles to unravel the intricate interplay between ecosystem biodiversity and mussels' biological response to their environments. Our analysis revealed temporal fluctuations in the alpha diversity of the circulating microbiome associated with human activities. Analysis of the hemolymphatic circulating cell-free DNA (ccfDNA) provided information on the biodiversity and the presence of potential pathogens. Epigenomic analysis revealed widespread hypomethylation sites within the mitochondrial (mtDNA). Comparative transcriptomic and glycomic analyses highlighted differences in metabolic pathways and genes associated with immune and wound healing functions. This study demonstrates the potential of multi-omic analysis of liquid biopsy in sentinel to provide a holistic view of human activities' environmental impacts on marine coastal ecosystems. Overall, this approach has the potential to enhance the effectiveness and efficiency of various conservation efforts, leading to more informed decision-making and better outcomes for biodiversity and ecosystem conservation.
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Affiliation(s)
- Sophia Ferchiou
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, Canada, H7V 1B7
| | - France Caza
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, Canada, H7V 1B7
| | - Kumardip Sinha
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Janelle Sauvageau
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Yves St-Pierre
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, Canada, H7V 1B7.
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Woodworth DC, Nguyen KM, Sordo L, Scambray KA, Head E, Kawas CH, Corrada MM, Nelson PT, Sajjadi SA. Comprehensive assessment of TDP-43 neuropathology data in the National Alzheimer's Coordinating Center database. Acta Neuropathol 2024; 147:103. [PMID: 38896163 PMCID: PMC11186885 DOI: 10.1007/s00401-024-02728-8] [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: 10/23/2023] [Revised: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 06/21/2024]
Abstract
TDP-43 proteinopathy is a salient neuropathologic feature in a subset of frontotemporal lobar degeneration (FTLD-TDP), in amyotrophic lateral sclerosis (ALS-TDP), and in limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC), and is associated with hippocampal sclerosis of aging (HS-A). We examined TDP-43-related pathology data in the National Alzheimer's Coordinating Center (NACC) in two parts: (I) availability of assessments, and (II) associations with clinical diagnoses and other neuropathologies in those with all TDP-43 measures available. Part I: Of 4326 participants with neuropathology data collected using forms that included TDP-43 assessments, data availability was highest for HS-A (97%) and ALS (94%), followed by FTLD-TDP (83%). Regional TDP-43 pathologic assessment was available for 77% of participants, with hippocampus the most common region. Availability for the TDP-43-related measures increased over time, and was higher in centers with high proportions of participants with clinical FTLD. Part II: In 2142 participants with all TDP-43-related assessments available, 27% of participants had LATE-NC, whereas ALS-TDP or FTLD-TDP (ALS/FTLD-TDP) was present in 9% of participants, and 2% of participants had TDP-43 related to other pathologies ("Other TDP-43"). HS-A was present in 14% of participants, of whom 55% had LATE-NC, 20% ASL/FTLD-TDP, 3% Other TDP-43, and 23% no TDP-43. LATE-NC, ALS/FTLD-TDP, and Other TDP-43, were each associated with higher odds of dementia, HS-A, and hippocampal atrophy, compared to those without TDP-43 pathology. LATE-NC was associated with higher odds for Alzheimer's disease (AD) clinical diagnosis, AD neuropathologic change (ADNC), Lewy bodies, arteriolosclerosis, and cortical atrophy. ALS/FTLD-TDP was associated with higher odds of clinical diagnoses of primary progressive aphasia and behavioral-variant frontotemporal dementia, and cortical/frontotemporal lobar atrophy. When using NACC data for TDP-43-related analyses, researchers should carefully consider the incomplete availability of the different regional TDP-43 assessments, the high frequency of participants with ALS/FTLD-TDP, and the presence of other forms of TDP-43 pathology.
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Affiliation(s)
- Davis C Woodworth
- Department of Neurology, University of California, Irvine, Office 364, Med Surge II Building, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Katelynn M Nguyen
- Department of Neurology, University of California, Irvine, Office 364, Med Surge II Building, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Lorena Sordo
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Kiana A Scambray
- Department of Neurology, University of California, Irvine, Office 364, Med Surge II Building, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Elizabeth Head
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Claudia H Kawas
- Department of Neurology, University of California, Irvine, Office 364, Med Surge II Building, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - María M Corrada
- Department of Neurology, University of California, Irvine, Office 364, Med Surge II Building, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
- Department of Epidemiology and Biostatistics, University of California, Irvine, CA, USA
| | - Peter T Nelson
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - S Ahmad Sajjadi
- Department of Neurology, University of California, Irvine, Office 364, Med Surge II Building, Irvine, CA, 92697, USA.
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA.
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
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Alharbi M, Lai A, Godbole N, Guanzon D, Nair S, Zuñiga F, Quinn A, Yang M, Wu SY, Salomon C. Enhancing precision targeting of ovarian cancer tumor cells in vivo through extracellular vesicle engineering. Int J Cancer 2024. [PMID: 38848494 DOI: 10.1002/ijc.35055] [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: 10/27/2023] [Revised: 04/29/2024] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
Extracellular vesicles (EVs) function as natural mediators of intercellular communication, secreted by cells to facilitate cell-cell signaling. Due to their low toxicity, immunogenicity, biodegradability, and potential to encapsulate therapeutic drugs, EVs hold significant therapeutic promise. Nevertheless, their limited targeting ability often diminishes their therapeutic impact. Therefore, enhancing EVs by incorporating targeting units onto their membranes could bolster their targeting capabilities, enabling them to accumulate in specific cells and tissues. In this study, we engineered EVs to fuse ephrin-B2 with the EV membrane protein LAMP2b. This modification aimed to direct the engineered EVs toward the ephrin-B4 receptor expressed on the surface of ovarian cancer cells. The engineered EVs retained their inherent properties, including size, expression of EV membrane proteins, and morphology, upon isolation. In vitro experiments using real-time imaging revealed that EVs engineered with the ephrin-B2 ligand exhibited substantial internalization and uptake by ovarian cancer cells, in stark contrast to native EVs. In vivo, the engineered EVs carrying the ephrin-B2 ligand effectively targeted ovarian cancer cells, surpassing the targeting efficiency of control EVs. This innovative approach establishes a novel targeting system, enhancing the uptake of EVs by ovarian cancer cells. Our findings underscore the potential of using EVs to target cancer cells, thereby enhancing the effectiveness of anti-cancer therapies while minimizing off-target effects and toxicity in normal cells and organs.
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Affiliation(s)
- Mona Alharbi
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Andrew Lai
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Nihar Godbole
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Dominic Guanzon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Soumyalekshmi Nair
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
| | - Felipe Zuñiga
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepción, Concepción, Chile
| | - Alexander Quinn
- Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
| | - Mengliu Yang
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Sherry Y Wu
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, University of Queensland Centre for Clinical Research, Faculty of Medicine, Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, Australia
- UQ Centre for Extracellular Vesicle Nanomedicine, The University of Queensland, Brisbane, QLD, Australia
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Yu H, Zhang K, Cheng G, Mei C, Wang H, Zan L. Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle. BMC Genomics 2024; 25:558. [PMID: 38834950 DOI: 10.1186/s12864-024-10482-0] [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: 08/26/2023] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Indigenous Chinese cattle have abundant genetic diversity and a long history of artificial selection, giving local breeds advantages in adaptability, forage tolerance and resistance. The detection of selective sweeps and comparative genome analysis of selected breeds and ancestral populations provide a basis for understanding differences among breeds and for the identification and utilization of candidate genes. We investigated genetic diversity, population structure, and signatures of selection using genome-wide sequencing data for a new breed of Qinchuan cattle (QNC, n = 21), ancestral Qinchuan cattle (QCC, n = 20), and Zaosheng cattle (ZSC, n = 19). RESULTS A population structure analysis showed that the ancestry components of QNC and ZSC were similar. In addition, the QNC and ZSC groups showed higher proportions of European taurine ancestry than that of QCC, and this may explain the larger body size of QNC, approaching that of European cattle under long-term domestication and selection. A neighbor-joining tree revealed that QCC individuals were closely related, whereas QNC formed a distinct group. To search for signatures of selection in the QNC genome, we evaluated nucleotide diversity (θπ), the fixation index (FST) and Tajima's D. Overlapping selective sweeps were enriched for one KEGG pathway, the apelin signaling pathway, and included five candidate genes (MEF2A, SMAD2, CAMK4, RPS6, and PIK3CG). We performed a comprehensive review of genomic variants in QNC, QCC, and ZSC using whole-genome sequencing data. QCC was rich in novel genetic diversity, while diversity in QNC and ZSC cattle was reduced due to strong artificial selection, with divergence from the original cattle. CONCLUSIONS We identified candidate genes associated with production traits. These results support the success of selective breeding and can guide further breeding and resource conservation of Qinchuan cattle.
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Affiliation(s)
- Hengwei Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, No.22 Xinong Road, Yangling, 712100, China
- National Beef Cattle Improvement Center, Yangling, 712100, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- National Beef Cattle Improvement Center, Yangling, 712100, China.
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Ganhör C, Rezk M, Doppler C, Ruthmeier T, Wechselberger C, Müller M, Kotnik M, Puh Š, Messner B, Bernhard D. Aluminum, a colorful gamechanger: Uptake of an aluminum-containing food color in human cells and its implications for human health. Food Chem 2024; 442:138404. [PMID: 38237295 DOI: 10.1016/j.foodchem.2024.138404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 02/15/2024]
Abstract
Aluminum is added to many food colors to change their solubility. This study compares the aluminum-containing food color carmine with its aluminum-free version carminic acid (both E 120), hypothesizing that the addition of aluminum does not only change the color's solubility, but also its effects on human cells. We could show that carmine, but not carminic acid, is taken up by gastrointestinal Caco-2 and umbilical vein endothelial cells (HUVEC). Clear differences between gene expression profiles of Caco-2 cells exposed to carmine, carminic acid or control were shown. KEGG analysis revealed that carmine-specific genes suppress oxidative phosphorylation, and showed that this suppression is associated with neurodegenerative diseases such as Alzheimer and Parkinson disease. Furthermore, carmine, but not carminic acid, increased proliferation of Caco-2 cells. Our findings show that a food color containing aluminum induces different cellular effects compared to its aluminum-free form, which is currently not considered in EU legislation.
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Affiliation(s)
- Clara Ganhör
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Marlene Rezk
- Experimental Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria.
| | - Christian Doppler
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Teresa Ruthmeier
- Cardiac Surgery Research Laboratory, Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria.
| | - Christian Wechselberger
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Marina Müller
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Michaela Kotnik
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Špela Puh
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria.
| | - Barbara Messner
- Cardiac Surgery Research Laboratory, Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria.
| | - David Bernhard
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, Krankenhausstrasse 5, 4020 Linz, Austria; Clinical Research Institute for Cardiovascular and Metabolic Diseases, Medical Faculty, Johannes Kepler University Linz, Linz, Austria.
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Giannakis K, Richards L, Dauda KA, Johnston IG. Connecting Species-Specific Extents of Genome Reduction in Mitochondria and Plastids. Mol Biol Evol 2024; 41:msae097. [PMID: 38758976 PMCID: PMC11144018 DOI: 10.1093/molbev/msae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024] Open
Abstract
Mitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types have been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but quantitative data and statistical analyses exploring this picture remain limited outside of some specific cases like parasitism. Here, we use cross-eukaryote organelle genome data to explore evidence for coevolution of mitochondrial and plastid genome reduction. Controlling for differences between clades and pseudoreplication due to relatedness, we find that extents of mtDNA and ptDNA gene retention are related to each other across taxa, in a generally positive correlation that appears to differ quantitatively across eukaryotes, for example, between algal and nonalgal species. We find limited evidence for coevolution of specific mtDNA and ptDNA gene pairs, suggesting that the similarities between the two organelle types may be due mainly to independent responses to consistent evolutionary drivers.
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Affiliation(s)
| | - Luke Richards
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Kazeem A Dauda
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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Liu Z, Xie H, Li L, Jiang D, Qian Y, Zhu X, Dai M, Li Y, Wei R, Luo Z, Xu W, Zheng Q, Shen J, Zhou M, Zeng W, Chen W. Single-cell landscape reveals the epithelial cell-centric pro-inflammatory immune microenvironment in dry eye development. Mucosal Immunol 2024; 17:491-507. [PMID: 38007004 DOI: 10.1016/j.mucimm.2023.11.008] [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: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Dry eye disease (DED) is a prevalent chronic eye disease characterized by an aberrant inflammatory response in ocular surface mucosa. The immunological alterations underlying DED remain largely unknown. In this study, we employed single-cell transcriptome sequencing of conjunctival tissue from environment-induced DED mice to investigate multicellular ecosystem and functional changes at different DED stages. Our results revealed an epithelial subtype with fibroblastic characteristics and pro-inflammatory effects emerging in the acute phase of DED. We also found that T helper (Th)1, Th17, and regulatory T cells (Treg) were the dominant clusters of differentiation (CD)4+ T-cell types involved in regulating immune responses and identified three distinct macrophage subtypes, with the CD72+CD11c+ subtype enhancing chronic inflammation. Furthermore, bulk transcriptome analysis of video display terminal-induced DED consistently suggested the presence of the pro-inflammatory epithelial subtype in human conjunctiva. Our findings have uncovered a DED-associated pro-inflammatory microenvironment in the conjunctiva, centered around epithelial cells, involving interactions with macrophages and CD4+ T cells, which deepens our understanding of ocular surface mucosal immune responses during DED progression.
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Affiliation(s)
- Zihao Liu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - He Xie
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ling Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China; The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, Ningbo, Zhejiang, China
| | - Dan Jiang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yuna Qian
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Xinhao Zhu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Mali Dai
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yanxiao Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ruifen Wei
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zan Luo
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Weihao Xu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qinxiang Zheng
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianliang Shen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Meng Zhou
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenwen Zeng
- Institute for Immunology, School of Medicine, and Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Wei Chen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China.
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9
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Huang Q, Han W, Posada-Florez F, Evans JD. Microbiomes, diet flexibility, and the spread of a beetle parasite of honey bees. Front Microbiol 2024; 15:1387248. [PMID: 38881661 PMCID: PMC11176428 DOI: 10.3389/fmicb.2024.1387248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
Invasive pests may disturb and destructively reformat the local ecosystem. The small hive beetle (SHB), Aethina tumida, originated in Africa and has expanded to America, Australia, Europe, and Asia. A key factor facilitating its fast global expansion is its ability to subsist on diverse food inside and outside honey bee colonies. SHBs feed on various plant fruits and exudates in the environment while searching for bee hives. After sneaking into a bee hive, they switch their diet to honey, pollen, and bee larvae. How SHBs survive on such a broad range of food remains unclear. In this study, we simulated the outside and within hive stages by providing banana and hive resources and quantified the SHB associated microbes adjusted by the diet. We found that SHBs fed on bananas were colonized by microbes coding more carbohydrate-active enzymes and a higher alpha diversity than communities from SHBs feeding on hive products or those collected directly from bee hives. SHBs fed on bananas and those collected from the hive showed high symbiont variance, indicated by the beta diversity. Surprisingly, we found the honey bee core symbiont Snodgrassella alvi in the guts of SHBs collected in bee hives. To determine the role of S. alvi in SHB biology, we inoculated SHBs with a genetically tagged culture of S. alvi, showing that this symbiont is a likely transient of SHBs. In contrast, the fungus Kodamaea ohmeri is the primary commensal of SHBs. Diet-based microbiome shifts are likely to play a key role in the spread and success of SHBs.
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Affiliation(s)
- Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Wensu Han
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Francisco Posada-Florez
- USDA, Beltsville Agricultural Research Center, Bee Research Laboratory, Agricultural Research Service, Beltsville, MD, United States
| | - Jay D Evans
- USDA, Beltsville Agricultural Research Center, Bee Research Laboratory, Agricultural Research Service, Beltsville, MD, United States
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10
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Serambeque B, Mestre C, Correia-Barros G, Teixo R, Marto CM, Gonçalves AC, Caramelo F, Silva I, Paiva A, Beck HC, Carvalho AS, Botelho MF, Carvalho MJ, Matthiesen R, Laranjo M. Influence of Aldehyde Dehydrogenase Inhibition on Stemness of Endometrial Cancer Stem Cells. Cancers (Basel) 2024; 16:2031. [PMID: 38893151 PMCID: PMC11171353 DOI: 10.3390/cancers16112031] [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: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Endometrial cancer is one of the most common gynaecological malignancies. Although often diagnosed at an early stage, there is a subset of patients with recurrent and metastatic disease for whom current treatments are not effective. Cancer stem cells (CSCs) play a pivotal role in triggering tumorigenesis, disease progression, recurrence, and metastasis, as high aldehyde dehydrogenase (ALDH) activity is associated with invasiveness and chemotherapy resistance. Therefore, this study aimed to evaluate the effects of ALDH inhibition in endometrial CSCs. ECC-1 and RL95-2 cells were submitted to a sphere-forming protocol to obtain endometrial CSCs. ALDH inhibition was evaluated through ALDH activity and expression, sphere-forming capacity, self-renewal, projection area, and CD133, CD44, CD24, and P53 expression. A mass spectrometry-based proteomic study was performed to determine the proteomic profile of endometrial cancer cells upon N,N-diethylaminobenzaldehyde (DEAB). DEAB reduced ALDH activity and expression, along with a significant decrease in sphere-forming capacity and projection area, with increased CD133 expression. Additionally, DEAB modulated P53 expression. Endometrial cancer cells display a distinct proteomic profile upon DEAB, sharing 75 up-regulated and 30 down-regulated proteins. In conclusion, DEAB inhibits ALDH activity and expression, influencing endometrial CSC phenotype. Furthermore, ALDH18A1, SdhA, and UBAP2L should be explored as novel molecular targets for endometrial cancer.
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Affiliation(s)
- Beatriz Serambeque
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Catarina Mestre
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Gabriela Correia-Barros
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Ricardo Teixo
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Carlos Miguel Marto
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Univ Coimbra, Institute of Experimental Pathology, Faculty of Medicine, 3000-548 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Laboratory of Oncobiology and Hematology (LOH) and University Clinics of Hematology and Oncology, Faculty of Medicine, 3000-548 Coimbra, Portugal
| | - Francisco Caramelo
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO) and Laboratory of Biostatistics and Medical Informatics (LBIM), Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Isabel Silva
- Cytometry Operational Management Unit, Clinical Pathology Department, Unidade de Saúde Local de Coimbra, 3004-561 Coimbra, Portugal;
| | - Artur Paiva
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Cytometry Operational Management Unit, Clinical Pathology Department, Unidade de Saúde Local de Coimbra, 3004-561 Coimbra, Portugal;
- Polytechnic Institute of Coimbra, Coimbra Health School, Laboratory Biomedical Sciences, 3045-043 Coimbra, Portugal
| | - Hans C. Beck
- Department of Clinical Biochemistry, Odense University Hospital, 5000 Odense, Denmark;
| | - Ana Sofia Carvalho
- iNOVA4Health, NOVA Medical School (NMS), Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, 1150-082 Lisboa, Portugal; (A.S.C.); (R.M.)
| | - Maria Filomena Botelho
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Univ Coimbra, Institute of Experimental Pathology, Faculty of Medicine, 3000-548 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Maria João Carvalho
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Univ Coimbra, Universitary Clinic of Gynecology, Faculty of Medicine, 3004-561 Coimbra, Portugal
- Gynecology Service, Department of Gynecology, Obstetrics, Reproduction and Neonatology, Unidade Local de Saúde de Coimbra, 3004-561 Coimbra, Portugal
| | - Rune Matthiesen
- iNOVA4Health, NOVA Medical School (NMS), Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, 1150-082 Lisboa, Portugal; (A.S.C.); (R.M.)
| | - Mafalda Laranjo
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
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Schätzl T, Todorow V, Kaiser L, Weinschrott H, Schoser B, Deigner HP, Meinke P, Kohl M. Meta-analysis towards FSHD reveals misregulation of neuromuscular junction, nuclear envelope, and spliceosome. Commun Biol 2024; 7:640. [PMID: 38796645 PMCID: PMC11127974 DOI: 10.1038/s42003-024-06325-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/13/2024] [Indexed: 05/28/2024] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common autosomal dominant muscle disorders, yet no cure or amelioration exists. The clinical presentation is diverse, making it difficult to identify the actual driving pathomechanism among many downstream events. To unravel this complexity, we performed a meta-analysis of 13 original omics datasets (in total 171 FSHD and 129 control samples). Our approach confirmed previous findings about the disease pathology and specified them further. We confirmed increased expression of former proposed DUX4 biomarkers, and furthermore impairment of the respiratory chain. Notably, the meta-analysis provides insights about so far not reported pathways, including misregulation of neuromuscular junction protein encoding genes, downregulation of the spliceosome, and extensive alterations of nuclear envelope protein expression. Finally, we developed a publicly available shiny app to provide a platform for researchers who want to search our analysis for genes of interest in the future.
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Affiliation(s)
- Teresa Schätzl
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
| | - Vanessa Todorow
- Friedrich-Baur-Institute at the Department of Neurology, LMU University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
| | - Helga Weinschrott
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute at the Department of Neurology, LMU University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
- Faculty of Science, Eberhard-Karls-University Tuebingen, Tuebingen, Germany
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Rostock, Germany
| | - Peter Meinke
- Friedrich-Baur-Institute at the Department of Neurology, LMU University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Matthias Kohl
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany.
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12
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Liu S, Wang Y, Duan L, Cui D, Deng K, Dong Z, Wei S. Whole transcriptome sequencing identifies a competitive endogenous RNA network that regulates the immunity of bladder cancer. Heliyon 2024; 10:e29344. [PMID: 38681584 PMCID: PMC11053192 DOI: 10.1016/j.heliyon.2024.e29344] [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: 02/04/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/01/2024] Open
Abstract
Several types of non-coding RNAs such as circRNAs, lncRNAs, and miRNAs have been identified to regulate mRNAs through the mechanism known as the competitive endogenous RNA (ceRNA) network. To explore the role of the ceRNA regulatory network in the immune microenvironment of bladder cancer, whole-transcriptome sequencing of bladder tumor and its peritumoral tissues from 38 bladder cancer patients, with a total of 63 samples, was performed to screen differentially expressed circ-, lnc-, mi-, and mRNAs to construct a circ/lnc-mi-mRNA regulatory network with pruning algorithms. We excavated a key immune-related gene BDNF to build the final ceRNA network as hsa-miR-107 sponged by hsa-circ-000211, AC108488.1, and LINC00163. Finally, a meta-analysis of 7 public datasets demonstrated that low expression of BDNF and high expression of hsa-miR-107 were associated with longer survival. Our study identified a ceRNA regulatory network as a potentially new prognostic marker and molecular therapeutic target of bladder cancer.
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Affiliation(s)
- Sanhe Liu
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Yiqi Wang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Liqun Duan
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Diansheng Cui
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Kangli Deng
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Zhiqiang Dong
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Shaozhong Wei
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Urology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
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13
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Dopkins N, Fei T, Michael S, Liotta N, Guo K, Mickens KL, Barrett BS, Bendall ML, Dillon SM, Wilson CC, Santiago ML, Nixon DF. Endogenous retroelement expression in the gut microenvironment of people living with HIV-1. EBioMedicine 2024; 103:105133. [PMID: 38677181 PMCID: PMC11061259 DOI: 10.1016/j.ebiom.2024.105133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Endogenous retroelements (EREs), including human endogenous retroviruses (HERVs) and long interspersed nuclear elements (LINEs), comprise almost half of the human genome. Our previous studies of the interferome in the gut suggest potential mechanisms regarding how IFNb may drive HIV-1 gut pathogenesis. As ERE activity is suggested to partake in type 1 immune responses and is incredibly sensitive to viral infections, we sought to elucidate underlying interactions between ERE expression and gut dynamics in people living with HIV-1 (PLWH). METHODS ERE expression profiles from bulk RNA sequencing of colon biopsies and PBMC were compared between a cohort of PLWH not on antiretroviral therapy (ART) and uninfected controls. FINDINGS 59 EREs were differentially expressed in the colon of PLWH when compared to uninfected controls (padj <0.05 and FC ≤ -1 or ≥ 1) [Wald's Test]. Of these 59, 12 EREs were downregulated in PLWH and 47 were upregulated. Colon expression of the ERE loci LTR19_12p13.31 and L1FLnI_1q23.1s showed significant correlations with certain gut immune cell subset frequencies in the colon. Furthermore L1FLnI_1q23.1s showed a significant upregulation in peripheral blood mononuclear cells (PBMCs) of PLWH when compared to uninfected controls suggesting a common mechanism of differential ERE expression in the colon and PBMC. INTERPRETATION ERE activity has been largely understudied in genomic characterizations of human pathologies. We show that the activity of certain EREs in the colon of PLWH is deregulated, supporting our hypotheses that their underlying activity could function as (bio)markers and potential mediators of pathogenesis in HIV-1 reservoirs. FUNDING US NIH grants NCI CA260691 (DFN) and NIAID UM1AI164559 (DFN).
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Liotta
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kejun Guo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kaylee L Mickens
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Brad S Barrett
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie M Dillon
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Cara C Wilson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mario L Santiago
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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14
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Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector CD8 T cells during chronic infection and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.579535. [PMID: 38659890 PMCID: PMC11042319 DOI: 10.1101/2024.04.18.579535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During chronic infections and tumor progression, CD8 T cells gradually lose their effector functions and become exhausted. These exhausted CD8 T cells are heterogeneous and comprised of different subsets, including self-renewing progenitors that give rise to Ly108 - CX3CR1 + effector-like cells. Generation of these effector-like cells is essential for the control of chronic infections and tumors, albeit limited. However, the precise cues and mechanisms directing the formation and maintenance of exhausted effector-like are incompletely understood. Using genetic mouse models challenged with LCMV Clone 13 or syngeneic tumors, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in exhausted CD8 T cells, which in turn regulates the formation of exhausted effector-like cells. Gfi1 deletion in T cells dysregulates the chromatin accessibility and transcriptomic programs associated with the differentiation of LCMV Clone 13-specific CD8 T cell exhaustion, preventing the formation of effector-like and terminally exhausted cells while maintaining progenitors and a newly identified Ly108 + CX3CR1 + state. These Ly108 + CX3CR1 + cells have a distinct chromatin profile and may represent an alternative target for therapeutic interventions to combat chronic infections and cancer. In sum, we show that Gfi1 is a critical regulator of the formation of exhausted effector-like cells.
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15
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Janes JK, van der Voort GE, Huber DPW. We know very little about pollination in the Platanthera Rich (Orchidaceae: Orchidoideae). Ecol Evol 2024; 14:e11223. [PMID: 38606342 PMCID: PMC11007262 DOI: 10.1002/ece3.11223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/06/2024] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
The Platanthera Rich. (Orchidoideae) comprise a speciose genus of orchids primarily in the northern hemisphere, with up to 200 known species worldwide. Individual species are known to self-pollinate, but many rely on insect pollinators with characteristics such as floral color, timing of floral odor emissions, nectar rewards, and spur length associated with particular pollination syndromes. As with many orchids, some orchid-pollinator associations are likely highly co-evolved, but we also know that some Platanthera spp. are the result of hybridization events, which implies a lack of pollinator fidelity in some cases. Some Platanthera spp. occur in large numbers which, coupled with the numerous Platanthera-pollinator systems, make them accessible as study species and useful for co-evolutionary studies. Due to the likely effects of climate change and ongoing development on Platanthera spp. habitats, these orchids and their associated pollinators should be a focus of conservation attention and management. However, while there is a fairly substantial literature coverage of Platanthera-pollinator occurrence and interactions, there are still wide gaps in our understanding of the species involved in these systems. In this systematic review, we outline what is current knowledge and provide guidance on further research that will increase our understanding of orchid-insect co-evolutionary relationships. Our review covers 157 orchid species and about 233 pollinator species interacting with 30 Platanthera spp. We provide analyses on aspects of these interactions such as flower morphology, known insect partners of Platanthera species, insect-Platanthera specificity, pollination visitor timing (diurnal vs. nocturnal), floral rewards, and insect behavior affecting pollination outcomes (e.g., pollinia placement). A substantial number of Platanthera spp. and at least a few of their known pollinators are of official (IUCN) conservation concern - and many of their pollinators remain unassessed or even currently unknown - which adds to the urgency of further research on these co-evolved relationships.
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Affiliation(s)
- Jasmine K Janes
- Biology Department Vancouver Island University Nanaimo British Columbia Canada
- Faculty of Environment University of Northern British Columbia Prince George British Columbia Canada
- IUCN, Species Survival Commission, Orchid Specialist Group
| | - Genevieve E van der Voort
- Faculty of Environment University of Northern British Columbia Prince George British Columbia Canada
| | - Dezene P W Huber
- Faculty of Environment University of Northern British Columbia Prince George British Columbia Canada
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16
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Gu K, Mok L, Wakefield MJ, Chong MMW. Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops. Sci Rep 2024; 14:6713. [PMID: 38509178 PMCID: PMC10954719 DOI: 10.1038/s41598-024-57330-5] [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: 11/12/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it is required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and appears to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha have yet to be characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs) and compared the features of non-canonical versus miRNA stem-loop substrates. mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these mRNA substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNA stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.
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Affiliation(s)
- Karen Gu
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Lawrence Mok
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mark M W Chong
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia.
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Cui Y, Wang L, Liang W, Huang L, Zhuang S, Shi H, Xu N, Hu J. Identification and Validation of the Pyroptosis-Related Hub Gene Signature and the Associated Regulation Axis in Diabetic Keratopathy. J Diabetes Res 2024; 2024:2920694. [PMID: 38529047 PMCID: PMC10963115 DOI: 10.1155/2024/2920694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/26/2024] [Accepted: 02/19/2024] [Indexed: 03/27/2024] Open
Abstract
Background Diabetic keratopathy (DK) poses a significant challenge in diabetes mellitus, yet its molecular pathways and effective treatments remain elusive. The aim of our research was to explore the pyroptosis-related genes in the corneal epithelium of the streptozocin-induced diabetic rats. Methods After sixteen weeks of streptozocin intraperitoneal injection, corneal epithelium from three diabetic rats and three normal groups underwent whole-transcriptome sequencing. An integrated bioinformatics pipeline, including differentially expressed gene (DEG) identification, enrichment analysis, protein-protein interaction (PPI) network, coexpression, drug prediction, and immune deconvolution analyses, identified hub genes and key drivers in DK pathogenesis. These hub genes were subsequently validated in vivo through RT-qPCR. Results A total of 459 DEGs were screened out from the diabetic group and nondiabetic controls. Gene Set Enrichment Analysis highlighted significant enrichment of the NOD-like receptor, Toll-like receptor, and NF-kappa B signaling pathways. Intersection of DEGs and pyroptosis-related datasets showed 33 differentially expressed pyroptosis-related genes (DEPRGs) associated with pathways such as IL-17, NOD-like receptor, TNF, and Toll-like receptor signaling. A competing endogenous RNA network comprising 16 DEPRGs, 22 lncRNAs, 13 miRNAs, and 3 circRNAs was constructed. After PPI network, five hub genes (Nfkb1, Casp8, Traf6, Ptgs2, and Il18) were identified as upregulated in the diabetic group, and their expression was validated by RT-qPCR in streptozocin-induced rats. Immune infiltration characterization showed that diabetic corneas owned a higher proportion of resting mast cells, activated NK cells, and memory-resting CD4 T cells. Finally, several small compounds including all-trans-retinoic acid, Chaihu Shugan San, dexamethasone, and resveratrol were suggested as potential therapies targeting these hub genes for DK. Conclusions The identified and validated hub genes, Nfkb1, Casp8, Traf6, Ptgs2, and Il18, may play crucial roles in DK pathogenesis and serve as therapeutic targets.
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Affiliation(s)
- Yi Cui
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Li Wang
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Wentao Liang
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Li Huang
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Shuting Zhuang
- College of Integrated Traditional Chinese and Western Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Hong Shi
- College of Integrated Traditional Chinese and Western Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Nuo Xu
- Department of Ophthalmology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Jianzhang Hu
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
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Bigger-Allen A, Gheinani AH, Adam RM. Investigation of the impact of bromodomain inhibition on cytoskeleton stability and contraction. Cell Commun Signal 2024; 22:184. [PMID: 38493137 PMCID: PMC10944605 DOI: 10.1186/s12964-024-01553-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Injury to contractile organs such as the heart, vasculature, urinary bladder and gut can stimulate a pathological response that results in loss of normal contractility. PDGF and TGFβ are among the most well studied initiators of the injury response and have been shown to induce aberrant contraction in mechanically active cells of hollow organs including smooth muscle cells (SMC) and fibroblasts. However, the mechanisms driving contractile alterations downstream of PDGF and TGFβ in SMC and fibroblasts are incompletely understood, limiting therapeutic interventions. METHODS To identify potential molecular targets, we have leveraged the analysis of publicly available data, comparing transcriptomic changes in mechanically active cells stimulated with PDGF and TGFβ. Additional Analysis of publicly available data sets were performed on SMC and fibroblasts treated in the presence or absence of the MYC inhibitor JQ1. Validation of in silico findings were performed with qPCR, immunoblots, and collagen gel contraction assays measure the effect of JQ1 on cytoskeleton associated genes, proteins and contractility in mechanically active cells. Likelihood ratio test and FDR adjusted p-values were used to determine significant differentially expressed genes. Student ttest were used to calculate statistical significance of qPCR and contractility analyses. RESULTS Comparing PDGF and TGFβ stimulated SMC and fibroblasts identified a shared molecular profile regulated by MYC and members of the AP-1 transcription factor complex. Additional in silico analysis revealed a unique set of cytoskeleton-associated genes that were sensitive to MYC inhibition with JQ1. In vitro validation demonstrated JQ1 was also able to attenuate TGFβ and PDGF induced changes to the cytoskeleton and contraction of smooth muscle cells and fibroblasts in vitro. CONCLUSIONS These findings identify MYC as a key driver of aberrant cytoskeletal and contractile changes in fibroblasts and SMC, and suggest that JQ1 could be used to restore normal contractile function in hollow organs.
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Affiliation(s)
- Alexander Bigger-Allen
- Urological Diseases Research Center, Boston Children's Hospital, Enders Bldg 1061.4, 300 Longwood Avenue, Boston, MA, 02115, USA
- Biological & Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Hashemi Gheinani
- Urological Diseases Research Center, Boston Children's Hospital, Enders Bldg 1061.4, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010, Bern, Switzerland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rosalyn M Adam
- Urological Diseases Research Center, Boston Children's Hospital, Enders Bldg 1061.4, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Yu SY, Luan Y, Xu PC, Zhang Y, Dong R, Abazarikia A, Kim SY. Metabolic characteristics of granulosa cell tumor: role of PPARγ signaling†. Biol Reprod 2024; 110:509-520. [PMID: 38123510 PMCID: PMC10941086 DOI: 10.1093/biolre/ioad173] [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: 08/11/2023] [Revised: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
Granulosa cell tumors are relatively rare, posing challenges for comprehension and therapeutic development due to limited cases and preclinical models. Metabolic reprogramming, a hallmark of cancer, manifests in granulosa cell tumors with notable lipid accumulation and increased expression of peroxisome proliferator-activated receptor gamma (PPARγ), a key lipid metabolism regulator. The roles of these features, however, remain unclear. In our previous work, we established a granulosa cell tumor model in mice by introducing a constitutively active Pik3ca mutant in oocytes, enabling the study of predictable tumor patterns from postnatal day 50. In this study, we characterized metabolic alterations during tumorigenesis (postnatal day 8 to day 50) and tumor growth (day 50 to day 65) in this model and explored the impact of PPARγ antagonism on human granulosa cell tumor proliferation. The tumor exhibited significant lipid accumulation, with PPARγ and the proliferation marker Ki67 co-localizing at postnatal day 65. Transcriptome analysis demonstrates that pathways for lipid metabolism and mitochondrial oxidation are promoted during tumorigenesis and tumor growth, respectively. Overlappingly upregulated genes during tumorigenesis and tumor growth are associated with lipid metabolism pathways. Correspondingly, mouse granulosa cell tumor shows overexpression of peroxisome proliferator-activated receptor gamma and DGAT2 proteins at postnatal day 65. Furthermore, GW9662 reduces the proliferation of KGN human granulosa cell tumor cells and decreases the phosphorylation of AKT and SMAD3. Our findings identify metabolic abnormalities in ooPIK3CA* granulosa cell tumor model and suggest peroxisome proliferator-activated receptor gamma as a potential driver for primary granulosa cell tumor growth.
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Affiliation(s)
- Seok-Yeong Yu
- Department of Obstetrics and Gynecology, Olson Center for Women’s Health, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yi Luan
- Department of Obstetrics and Gynecology, Olson Center for Women’s Health, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pauline C Xu
- Department of Obstetrics and Gynecology, Olson Center for Women’s Health, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yaqi Zhang
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rosemary Dong
- Department of Obstetrics and Gynecology, Olson Center for Women’s Health, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Amirhossein Abazarikia
- Department of Obstetrics and Gynecology, Olson Center for Women’s Health, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - So-Youn Kim
- Department of Obstetrics and Gynecology, Olson Center for Women’s Health, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985860 Nebraska Med Center, Omaha, NE, 68198, USA
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Ali M, Garcia P, Lunkes LP, Sciortino A, Thomas M, Heurtaux T, Grzyb K, Halder R, Coowar D, Skupin A, Buée L, Blum D, Buttini M, Glaab E. Single cell transcriptome analysis of the THY-Tau22 mouse model of Alzheimer's disease reveals sex-dependent dysregulations. Cell Death Discov 2024; 10:119. [PMID: 38453894 PMCID: PMC10920792 DOI: 10.1038/s41420-024-01885-9] [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: 01/11/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Alzheimer's disease (AD) progression and pathology show pronounced sex differences, but the factors driving these remain poorly understood. To gain insights into early AD-associated molecular changes and their sex dependency for tau pathology in the cortex, we performed single-cell RNA-seq in the THY-Tau22 AD mouse model. By examining cell type-specific and cell type-agnostic AD-related gene activity changes and their sex-dimorphism for individual genes, pathways and cellular sub-networks, we identified both statistically significant alterations and interpreted the upstream mechanisms controlling them. Our results confirm several significant sex-dependent alterations in gene activity in the THY-Tau22 model mice compared to controls, with more pronounced alterations in females. Both changes shared across multiple cell types and cell type-specific changes were observed. The differential genes showed significant over-representation of known AD-relevant processes, such as pathways associated with neuronal differentiation, programmed cell death and inflammatory responses. Regulatory network analysis of these genes revealed upstream regulators that modulate many of the downstream targets with sex-dependent changes. Most key regulators have been previously implicated in AD, such as Egr1, Klf4, Chchd2, complement system genes, and myelin-associated glycoproteins. Comparing with similar data from the Tg2576 AD mouse model and human AD patients, we identified multiple genes with consistent, cell type-specific and sex-dependent alterations across all three datasets. These shared changes were particularly evident in the expression of myelin-associated genes such as Mbp and Plp1 in oligodendrocytes. In summary, we observed significant cell type-specific transcriptomic changes in the THY-Tau22 mouse model, with a strong over-representation of known AD-associated genes and processes. These include both sex-neutral and sex-specific patterns, characterized by consistent shifts in upstream master regulators and downstream target genes. Collectively, these findings provide insights into mechanisms influencing sex-specific susceptibility to AD and reveal key regulatory proteins that could be targeted for developing treatments addressing sex-dependent AD pathology.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Laetitia P Lunkes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Melanie Thomas
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Tony Heurtaux
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 8 avenue du Swing, L-4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, L-3555, Dudelange, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Djalil Coowar
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Alex Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, UMR-S1172 Lille Neuroscience & Cognition (LilNCog), Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - David Blum
- University of Lille, Inserm, CHU Lille, UMR-S1172 Lille Neuroscience & Cognition (LilNCog), Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.
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21
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Peters TJ, Meyer B, Ryan L, Achinger-Kawecka J, Song J, Campbell EM, Qu W, Nair S, Loi-Luu P, Stricker P, Lim E, Stirzaker C, Clark SJ, Pidsley R. Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 2024; 25:251. [PMID: 38448820 PMCID: PMC10916044 DOI: 10.1186/s12864-024-10027-5] [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: 10/12/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples. RESULTS We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding. CONCLUSIONS Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.
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Affiliation(s)
- Timothy J Peters
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Braydon Meyer
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Lauren Ryan
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Jenny Song
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Elyssa M Campbell
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Shalima Nair
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Phuc Loi-Luu
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Phillip Stricker
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
- Department of Urology, St. Vincent's Prostate Cancer Centre, Sydney, NSW, 2050, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia.
| | - Ruth Pidsley
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia.
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22
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Kajan K, Fuchs BM, Orlić S. Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre. Microbiol Spectr 2024; 12:e0301623. [PMID: 38334383 PMCID: PMC10913754 DOI: 10.1128/spectrum.03016-23] [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: 08/04/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.
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Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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Kotah JM, Kater MSJ, Brosens N, Lesuis SL, Tandari R, Blok TM, Marchetto L, Yusaf E, Koopmans FTW, Smit AB, Lucassen PJ, Krugers HJ, Verheijen MHG, Korosi A. Early-life stress and amyloidosis in mice share pathogenic pathways involving synaptic mitochondria and lipid metabolism. Alzheimers Dement 2024; 20:1637-1655. [PMID: 38055782 PMCID: PMC10984508 DOI: 10.1002/alz.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
INTRODUCTION Early-life stress (ES) increases the risk for Alzheimer's disease (AD). We and others have shown that ES aggravates amyloid-beta (Aβ) pathology and promotes cognitive dysfunction in APP/PS1 mice, but underlying mechanisms remain unclear. METHODS We studied how ES affects the hippocampal synaptic proteome in wild-type (WT) and APP/PS1 mice at early and late pathological stages, and validated hits using electron microscopy and immunofluorescence. RESULTS The hippocampal synaptosomes of both ES-exposed WT and early-stage APP/PS1 mice showed a relative decrease in actin dynamics-related proteins and a relative increase in mitochondrial proteins. ES had minimal effects on older WT mice, while strongly affecting the synaptic proteome of advanced stage APP/PS1 mice, particularly the expression of astrocytic and mitochondrial proteins. DISCUSSION Our data show that ES and amyloidosis share pathogenic pathways involving synaptic mitochondrial dysfunction and lipid metabolism, which may underlie the observed impact of ES on the trajectory of AD.
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Affiliation(s)
- Janssen M. Kotah
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Mandy S. J. Kater
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Niek Brosens
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sylvie L. Lesuis
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Roberta Tandari
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Thomas M. Blok
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Luca Marchetto
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ella Yusaf
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Frank T. W. Koopmans
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - August B. Smit
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Paul J. Lucassen
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Harm J. Krugers
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Mark H. G. Verheijen
- Department of Molecular and Cellular NeurobiologyCenter for Neurogenomics and Cognitive ResearchAmsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Aniko Korosi
- Brain Plasticity GroupSwammerdam Institute for Life Sciences – Center for NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
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Zhang X, Ekwealor JTB, Mishler BD, Silva AT, Yu L, Jones AK, Nelson ADL, Oliver MJ. Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants. THE NEW PHYTOLOGIST 2024. [PMID: 38415863 DOI: 10.1111/nph.19620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation-tolerant moss, provides valuable insights into survival of water-limited conditions. We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana. The genome was assembled into 12 chromosomes encompassing 21 169 protein-coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation-associated gene families, and highlighted genome-level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)-responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA-insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA-dependent stress response in Arabidopsis. The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.
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Affiliation(s)
- Xiaodan Zhang
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Jenna T B Ekwealor
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Brent D Mishler
- University and Jepson Herbaria, Berkeley, CA, 94720-2465, USA
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | | | - Li'ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Andrea K Jones
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew D L Nelson
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Melvin J Oliver
- Division of Plant Sciences and Technology and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
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Wang X, Li X, Tan L, Zhang F, Zhang J, Zhao X, Zhang Y, Du G, Liu W. Identification and Validation of Lipid Metabolism Gene FASN-Associated miRNA in Wilms Tumor. Biochem Genet 2024:10.1007/s10528-024-10703-x. [PMID: 38416272 DOI: 10.1007/s10528-024-10703-x] [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: 08/09/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
miRNA has been a research hotspot in recent years and its scope of action is very wide, involving the regulation of cell proliferation, differentiation, apoptosis, and other biological behaviors. This study intends to explore the role of miRNA in the lipid metabolism and development of Wilms tumor (WT) by detecting and analyzing the differences in the expression profiles of miRNAs between the tumor and adjacent normal tissue. Gene detection was performed in tumor tissues and adjacent normal tissues of three cases of WT to screen differentially expressed miRNAs (DEMs). According to our previous research, FASN, which participates in the lipid metabolism pathway, may be a target of WT. The starBase database was used to predict FASN-targeted miRNAs. The above two groups of miRNAs were intersected to obtain FASN-targeted DEMs and then GO Ontology (GO) functional enrichment analysis of FASN-targeted DEMs was performed. Finally, the FASN-targeted DEMs were compared and further verified by qRT‒PCR. Through gene sequencing and differential analysis, 287 DEMs were obtained, including 132 upregulated and 155 downregulated miRNAs. The top ten DEMs were all downregulated. Fourteen miRNAs targeted by the lipid metabolism-related gene FASN were predicted by starBase. After intersection with the DEMs, three miRNAs were finally obtained, namely, miR-107, miR-27a-3p, and miR-335-5p. GO enrichment analysis was mainly concentrated in the Parkin-FBXW7-Cul1 ubiquitin ligase complex and response to prostaglandin E. Further experimental verification showed that miR-27a-3p was significantly correlated with WT (P = 0.0018). Imbalanced expression of miRNAs may be involved in the occurrence and development of WT through lipid metabolism. The expression of miR-27a-3p is related to the malignant degree of WT, and it may become the target of diagnosis, prognosis, and treatment of WT in the later stage.
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Affiliation(s)
- Xiaoqing Wang
- Department of Pediatric Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Street, Jinan, 250021, Shandong, People's Republic of China
- Post-Doctoral Research Station of Clinical Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Xiao Li
- Department of Pediatric Surgery, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, 271000, Shandong, People's Republic of China
| | - Lin Tan
- Department of Gastroenterology, The Affiliated Zhuzhou Hospital Xiangya Medical College CSU, Zhuzhou, 412007, Hunan, People's Republic of China
| | - Fengjun Zhang
- College of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, Jinan, 250355, Shandong, People's Republic of China
| | - Jing Zhang
- Department of Pediatrics, Shandong Second Provincial General Hospital, Jinan, 250022, Shandong, People's Republic of China
| | - Xu Zhao
- Department of Anesthesiology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, People's Republic of China
| | - Yongfei Zhang
- Department of Dermatology, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250021, Shandong, People's Republic of China
| | - Guoqiang Du
- Department of Pediatric Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Street, Jinan, 250021, Shandong, People's Republic of China.
| | - Wei Liu
- Department of Pediatric Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Street, Jinan, 250021, Shandong, People's Republic of China.
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Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [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: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Warin J, Vedrenne N, Tam V, Zhu M, Yin D, Lin X, Guidoux-D’halluin B, Humeau A, Roseiro L, Paillat L, Chédeville C, Chariau C, Riemers F, Templin M, Guicheux J, Tryfonidou MA, Ho JW, David L, Chan D, Camus A. In vitro and in vivo models define a molecular signature reference for human embryonic notochordal cells. iScience 2024; 27:109018. [PMID: 38357665 PMCID: PMC10865399 DOI: 10.1016/j.isci.2024.109018] [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: 08/11/2023] [Revised: 11/13/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding the emergence of human notochordal cells (NC) is essential for the development of regenerative approaches. We present a comprehensive investigation into the specification and generation of bona fide NC using a straightforward pluripotent stem cell (PSC)-based system benchmarked with human fetal notochord. By integrating in vitro and in vivo transcriptomic data at single-cell resolution, we establish an extended molecular signature and overcome the limitations associated with studying human notochordal lineage at early developmental stages. We show that TGF-β inhibition enhances the yield and homogeneity of notochordal lineage commitment in vitro. Furthermore, this study characterizes regulators of cell-fate decision and matrisome enriched in the notochordal niche. Importantly, we identify specific cell-surface markers opening avenues for differentiation refinement, NC purification, and functional studies. Altogether, this study provides a human notochord transcriptomic reference that will serve as a resource for notochord identification in human systems, diseased-tissues modeling, and facilitating future biomedical research.
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Affiliation(s)
- Julie Warin
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Nicolas Vedrenne
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
- Inserm, Univ. Limoges, Pharmacology & Transplantation, U1248, CHU Limoges, Service de Pharmacologie, toxicologie et pharmacovigilance, FHU SUPORT, 87000 Limoges, France
| | - Vivian Tam
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Mengxia Zhu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Danqing Yin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Xinyi Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Bluwen Guidoux-D’halluin
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Antoine Humeau
- Inserm, Univ. Limoges, Pharmacology & Transplantation, U1248, CHU Limoges, Service de Pharmacologie, toxicologie et pharmacovigilance, FHU SUPORT, 87000 Limoges, France
| | - Luce Roseiro
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Lily Paillat
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Claire Chédeville
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Caroline Chariau
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, 44000 Nantes, France
| | - Frank Riemers
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Markus Templin
- NMI Natural and Medical Sciences Institute, Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Jérôme Guicheux
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
| | - Marianna A. Tryfonidou
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joshua W.K. Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, 44000 Nantes, France
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Danny Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Anne Camus
- Nantes Université, Oniris, CHU Nantes, Inserm, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000 Nantes, France
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Gao Y, Zhang G, Jiang S, Liu Y. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. IMETA 2024; 3:e175. [PMID: 38868508 PMCID: PMC10989175 DOI: 10.1002/imt2.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 06/14/2024]
Abstract
The increasing application of meta-omics approaches to investigate the structure, function, and intercellular interactions of microbial communities has led to a surge in available data. However, this abundance of human and environmental microbiome data has exposed new scalability challenges for existing bioinformatics tools. In response, we introduce Wekemo Bioincloud-a specialized platform for -omics studies. This platform offers a comprehensive analysis solution, specifically designed to alleviate the challenges of tool selection for users in the face of expanding data sets. As of now, Wekemo Bioincloud has been regularly equipped with 22 workflows and 65 visualization tools, establishing itself as a user-friendly and widely embraced platform for studying diverse data sets. Additionally, the platform enables the online modification of vector outputs, and the registration-independent personalized dashboard system ensures privacy and traceability. Wekemo Bioincloud is freely available at https://www.bioincloud.tech/.
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Affiliation(s)
- Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Guoxing Zhang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Shunyao Jiang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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29
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Huang PJ, Weng YC, Huang KY, Lee CC, Yeh YM, Chen YT, Chiu CH, Tang P. ProFun: A web server for functional enrichment analysis of parasitic protozoan genes. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00008-2. [PMID: 38311498 DOI: 10.1016/j.jmii.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/05/2024] [Accepted: 01/24/2024] [Indexed: 02/06/2024]
Abstract
BACKGROUND The initial step to interpreting putative biological functions from comparative multi-omics studies usually starts from a differential expressed gene list followed by functional enrichment analysis (FEA). However, most FEA packages are designed exclusively for humans and model organisms. Although parasitic protozoan is the most important pathogen in the tropics, no FEA package is available for protozoan functional (ProFun) enrichment analysis. To speed up comparative multi-omics research on parasitic protozoans, we constructed ProFun, a web-based, user-friendly platform for the research community. METHODS ProFun utilizes the Docker container, ShinyProxy, and R Shiny to construct a scalable web service with load-balancing infrastructure. We have integrated a series of visual analytic functions, in-house scripts, and custom-made annotation packages to create three analytical modules for 40 protozoan species: (1) Gene Overlaps; (2) Over-representation Analysis (ORA); (3) Gene Set Enrichment Analysis (GSEA). RESULTS We have established ProFun, a web server for functional enrichment analysis of differentially expressed genes. FEA becomes as simple as pasting a list of gene IDs into the textbox of our website. Users can customize enrichment parameters and results with just one click. The intuitive web interface and publication-ready charts enable users to reveal meaningful biological events and pinpoint potential targets for further studies. CONCLUSION ProFun is the first web application that enables gene functional enrichment analysis of parasitic protozoans. In addition to supporting FEA analysis, ProFun also allows the comparison of FEA results across complicated experimental designs. ProFun is freely available at http://dalek.cgu.edu.tw:8080/app/profun.
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Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Yi-Chen Weng
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan.
| | - Chi-Ching Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan.
| | - Yuan-Ming Yeh
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Yu-Tong Chen
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
| | - Petrus Tang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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30
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Gao C, Chen C, Akyol T, Dusa A, Yu G, Cao B, Cai P. ggVennDiagram: Intuitive Venn diagram software extended. IMETA 2024; 3:e177. [PMID: 38868514 PMCID: PMC10989133 DOI: 10.1002/imt2.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 06/14/2024]
Abstract
Highlights of ggVennDiagram include: (1) Subset/Region filling Venn diagram up to seven sets; (2) Upset plot with unlimited sets; (3) Venn Calculator for two or more sets; (4) Provide as R package, Shiny App, and TBtools plugin.
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Affiliation(s)
- Chun‐Hui Gao
- National Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- College of Resources and EnvironmentHuazhong Agricultural UniversityWuhanChina
- School of Civil and Environmental Engineering and Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Turgut Akyol
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Adrian Dusa
- Department of SociologyUniversity of BucharestBucharestRomania
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Bin Cao
- School of Civil and Environmental Engineering and Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Peng Cai
- National Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- College of Resources and EnvironmentHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Soil Environment and Pollution RemediationHuazhong Agricultural UniversityWuhanChina
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31
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Ogbodo AK, Mustafov D, Arora M, Lambrou GI, Braoudaki M, Siddiqui SS. Analysis of SIGLEC12 expression, immunomodulation and prognostic value in renal cancer using multiomic databases. Heliyon 2024; 10:e24286. [PMID: 38268823 PMCID: PMC10803920 DOI: 10.1016/j.heliyon.2024.e24286] [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: 06/04/2023] [Revised: 11/30/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
Siglecs belong to a family of immune regulatory receptors predominantly found on hematopoietic cells. They interact with Sia, resulting in the activation or inhibition of the immune response. Previous reports have suggested that the SIGLEC12 gene, which encodes the Siglec-XII protein, is expressed in the epithelial tissues and upregulated in carcinomas. However, studies deciphering the role of Siglec-XII in renal cancer (RC) are still unavailable, and here we provide insights on this question. We conducted expression analysis using the Human Protein Atlas and UALCAN databases. The impact of SIGLEC12 on RC prognosis was determined using the KM plotter, and an assessment of immune infiltration with SIGLEC12 was performed using the TIMER database. GSEA was conducted to identify the pathways affected by SIGLEC12. Finally, using GeneMania, we identified Siglec-XII interacting proteins. Our findings indicated that macrophages express SIGLEC12 in the kidney. Furthermore, we hypothesize that Siglec-XII expression might be involved in the increase of primary RC, but this effect may not be dependent on the age of the patient. In the tumour microenvironment, oncogenic pathways appeared to be upregulated by SIGLEC12. Similarly, our analysis suggested that SIGLEC12-related kidney renal papillary cell carcinomas may be more suitable for targeted immunotherapy, such as CTLA-4 and PD-1/PD-L1 inhibitors. These preliminary results suggested that high expression of SIGLEC12 is associated with poor prognosis for RC. Future studies to assess its clinical utility are necessitated.
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Affiliation(s)
- Amobichukwu K. Ogbodo
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
- #Current Address: Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Old Road Campus, Oxford OX3 7LF, United Kingdom
| | - Denis Mustafov
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
- College of Health, Medicine, and Life Science, Brunel University London UB8 3PH, United Kingdom
| | - Mohit Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - George I. Lambrou
- Choremeio Research Laboratory, First Department of Paediatrics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece, Thivon & Levadeias 8, 11527, Goudi, Athens, Greece
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, Thivon & Levadeias 8, 11527 Athens, Greece
| | - Maria Braoudaki
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
| | - Shoib S. Siddiqui
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
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32
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Olmo R, Quijada NM, Morán-Diez ME, Hermosa R, Monte E. Identification of Tomato microRNAs in Late Response to Trichoderma atroviride. Int J Mol Sci 2024; 25:1617. [PMID: 38338899 PMCID: PMC10855890 DOI: 10.3390/ijms25031617] [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: 11/30/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21-24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant-pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects.
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Affiliation(s)
| | | | | | | | - Enrique Monte
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185 Villamayor, Salamanca, Spain; (R.O.); (N.M.Q.); (M.E.M.-D.); (R.H.)
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33
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Liu T, Ul-Haq W, Tang Q, Li W, Wang Z, Shan Q, Serfraz S, Shakir Y, Ullah Kakar M, Sun L. Novel integrated Omics based computational approach for drug repurposing for non-muscle invasive bladder cancer (NMIBC). J Biomol Struct Dyn 2024:1-11. [PMID: 38247255 DOI: 10.1080/07391102.2024.2302343] [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: 06/07/2023] [Accepted: 10/04/2023] [Indexed: 01/23/2024]
Abstract
Non-muscle invasive bladder cancer (NMIBC) refers to a subtype of bladder carcinoma where cancer is localized in the inner lining of bladder. NMIBC consider as one of most costly malignancy and requires significant surgical and therapeutic measure. However, recurrence and progression of tumor is common in treated patients. Here we presented an integrated OMICs approach for the identification and inhibition of NMIBC specific genes. We utilized a case study where three group of patients were compared: 1) Relapsed tumors 2) recurrent tumors and 3) tumor in progression. Common transcriptome signature between patients facing recurrence and progression allowed us to identify three NMIBC specific genes FLT-1, WHSC-1 and CD34. We further utilized novel approach of Co-expressed gene-set enrichment analysis (COGENA) on the differentially expressed genes of this case study. Three drugs (paroxetine, adiphenine and H-89) with role of receptors inhibition were identified and predicted as repurposed drugs for the inhibition NMIBC specific genes. We further tested this hypothesis by performing molecular docking and simulation analysis between cancer specific proteins and drugs. FLT-1 have shown significant stable interaction with both drugs paroxetine and adiphenine whereas WHSC-1 have shown compact interaction with adiphenine and H-89. In the light of these evidence, we suggest that adiphenine could be repositioned as alternate targeted medicine for the treatment of NMIBC. In the future, this study will help for strengthening the strategies development at the molecular level for the control of carcinomas at early as well as detection of active and binding site, receptor-ligand interaction and also make drug repurposing for the early treatment of the carcinomas.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tiantian Liu
- The Department of Oncology, Affiliated with Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Waqar- Ul-Haq
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Pakistan
| | - Qing Tang
- The Department of Oncology, Affiliated with Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Wei Li
- The Department of Oncology, Affiliated with Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Zhixia Wang
- The Department of Oncology, Affiliated with Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Qiujie Shan
- The Department of Oncology, Affiliated with Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Saad Serfraz
- Evolutionary Biology Lab, CABB, University of Agriculture Faisalabad, Pakistan
| | - Yasmeen Shakir
- Department of Biochemistry, Hazara University, Mansehra, Khyber Pakhtunkhua, Pakistan
| | - Mohib Ullah Kakar
- Faculty of Marine Sciences, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Balochistan, Pakistan
| | - Lizhu Sun
- The Department of Oncology, Affiliated with Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
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Curd EE, Gal L, Gallego R, Silliman K, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2024; 6:e489. [PMID: 38370872 PMCID: PMC10871694 DOI: 10.1002/edn3.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/19/2023] [Indexed: 02/20/2024]
Abstract
The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Katherine Silliman
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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Schauberger C, Thamdrup B, Lemonnier C, Trouche B, Poulain J, Wincker P, Arnaud-Haond S, Glud RN, Maignien L. Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions. ISME COMMUNICATIONS 2024; 4:ycad005. [PMID: 38282644 PMCID: PMC10809760 DOI: 10.1093/ismeco/ycad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024]
Abstract
Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.
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Affiliation(s)
- Clemens Schauberger
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Bo Thamdrup
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Clarisse Lemonnier
- Microbiology of Extreme Environments Laboratory, CNRS, IFREMER, Univ Brest, F-29280 Plouzané, France
| | - Blandine Trouche
- Microbiology of Extreme Environments Laboratory, CNRS, IFREMER, Univ Brest, F-29280 Plouzané, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS,University of Évry, Université Paris-Saclay, 91057 Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS,University of Évry, Université Paris-Saclay, 91057 Evry, France
| | - Sophie Arnaud-Haond
- MARBEC, CNRS, IRD, Institut Français de Recherche pour L'Exploitation de la Mer, Univ Montpellier, 34200 Sète, France
| | - Ronnie N Glud
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Lois Maignien
- Microbiology of Extreme Environments Laboratory, CNRS, IFREMER, Univ Brest, F-29280 Plouzané, France
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Xiong Z, Chen P, Yuan M, Yao L, Wang Z, Liu P, Jiang Y. Integrated Bioinformatics and Validation Reveal IFI27 and Its Related Molecules as Potential Identifying Genes in Liver Cirrhosis. Biomolecules 2023; 14:13. [PMID: 38275754 PMCID: PMC10813755 DOI: 10.3390/biom14010013] [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: 10/29/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 01/27/2024] Open
Abstract
Liver cirrhosis remains a significant global public health concern, with liver transplantation standing as the foremost effective treatment currently available. Therefore, investigating the pathogenesis of liver cirrhosis and developing novel therapies is imperative. Mitochondrial dysfunction stands out as a pivotal factor in its development. This study aimed to elucidate the relationship between mitochondria dysfunction and liver cirrhosis using bioinformatic methods to unveil its pathogenesis. Initially, we identified 460 co-expressed differential genes (co-DEGs) from the GSE14323 and GSE25097 datasets, alongside their combined datasets. Functional analysis revealed that these co-DEGs were associated with inflammatory cytokines and cirrhosis-related signaling pathways. Utilizing weighted gene co-expression network analysis (WCGNA), we screened module genes, intersecting them with co-DEGs and oxidative stress-related mitochondrial genes. Two algorithms (least absolute shrinkage and selection operator (LASSO) regression and SVE-RFE) were then employed to further analyze the intersecting genes. Finally, COX7A1 and IFI27 emerged as identifying genes for liver cirrhosis, validated through a receiver operating characteristic (ROC) curve analysis and related experiments. Additionally, immune infiltration highlighted a strong correlation between macrophages and cirrhosis, with the identifying genes (COX7A1 and IFI27) being significantly associated with macrophages. In conclusion, our findings underscore the critical role of oxidative stress-related mitochondrial genes (COX7A1 and IFI27) in liver cirrhosis development, highlighting their association with macrophage infiltration. This study provides novel insights into understanding the pathogenesis of liver cirrhosis.
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Affiliation(s)
| | | | | | | | | | | | - Yingan Jiang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Z.X.); (P.C.); (M.Y.); (L.Y.); (Z.W.); (P.L.)
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37
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Morrill A, Forbes MR, Vesterinen EJ, Tamminen M, Sääksjärvi IE, Kaunisto KM. Molecular Characterisation of Faecal Bacterial Assemblages Among Four Species of Syntopic Odonates. MICROBIAL ECOLOGY 2023; 87:16. [PMID: 38108886 PMCID: PMC10728244 DOI: 10.1007/s00248-023-02328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Factors such as host species, phylogeny, diet, and both timing and location of sampling are thought to influence the composition of gut-associated bacteria in insects. In this study, we compared the faecal-associated bacterial taxa for three Coenagrion and one Enallagma damselfly species. We expected high overlap in representation of bacterial taxa due to the shared ecology and diet of these species. Using metabarcoding based on the 16S rRNA gene, we identified 1513 sequence variants, representing distinct bacterial 'taxa'. Intriguingly, the damselfly species showed somewhat different magnitudes of richness of ZOTUs, ranging from 480 to 914 ZOTUs. In total, 921 (or 60.8% of the 1513) distinct ZOTUs were non-shared, each found only in one species, and then most often in only a single individual. There was a surfeit of these non-shared incidental ZOTUs in the Enallagma species accounting for it showing the highest bacterial richness and accounting for a sample-wide pattern of more single-species ZOTUs than expected, based on comparisons to the null model. Future studies should address the extent to which faecal bacteria represent non-incidental gut bacteria and whether abundant and shared taxa are true gut symbionts. Pictures of odonates adopted from Norske Art databank under Creative Commons License (CC BY 4.0).
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Affiliation(s)
- A Morrill
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - M R Forbes
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - E J Vesterinen
- Department of Biology, University of Turku, Turku, Finland
| | - M Tamminen
- Department of Biology, University of Turku, Turku, Finland
| | | | - K M Kaunisto
- Biodiversity Unit, University of Turku, Turku, Finland.
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Bahrami E, Geiger T, Steixner-Kumar AA, Santacruz D, Viollet C, Dick A, Roth Y, Schlingeloff P, Schmidberger J, Haenle M, Kratzer W, Kitt K, Neubauer H, Simon E, Krenkel O, Werner M. An optimized protocol for isolation of hepatic leukocytes retrieved from murine and NASH liver biopsies. STAR Protoc 2023; 4:102597. [PMID: 37740914 PMCID: PMC10520930 DOI: 10.1016/j.xpro.2023.102597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/27/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023] Open
Abstract
Immune dysregulation and inflammation by hepatic-resident leukocytes is considered a key step in disease progression of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis toward cirrhosis and hepatocellular carcinoma. Here, we provide a protocol for isolation and characterization of liver-resident immune cells from fine-needle biopsies obtained from a rodent model and humans. We describe steps for isolating leukocytes, cell sorting, and RNA extraction and sequencing. We then detail procedures for low-input mRNA sequencing analyses.
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Affiliation(s)
- Ehsan Bahrami
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tobias Geiger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Diana Santacruz
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Coralie Viollet
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Alec Dick
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Yvonne Roth
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | | | - Mark Haenle
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Wolfgang Kratzer
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Kerstin Kitt
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Heike Neubauer
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Eric Simon
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Oliver Krenkel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Markus Werner
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany.
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Zhou R, Chen X, Huang M, Chen H, Zhang L, Xu D, Wang D, Gao P, Wang B, Dai X. ATR-FTIR spectroscopy combined with chemometrics to assess the spectral markers of irradiated baijius and their potential application in irradiation dose control. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123162. [PMID: 37478760 DOI: 10.1016/j.saa.2023.123162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023]
Abstract
Although some methods have been proposed for the identification of irradiated baijius, they are often costly, time-consuming, and destructive. It is also unclear what instrumentation can be used to fully characterize the quality changes in irradiated baijius. To address this issue, this study pioneers the use of attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy in combination with chemometrics to open up new avenues for characterizing irradiated baijius and their quality control. Principal component analysis, five spectral pre-processing methods (Savitzky-Golay smoothing (S-G), second-order derivative (SD), multiple scattering correction (MSC), S-G + SD and S-G + MSC), five wavelength selection methods (random forest variable importance (RFVI), two-dimensional correlation spectroscopy (2D-COS), variable importance in projection (VIP), ReliefF, and Venn), and three classification models (partial least squares-discriminant analysis (PLS-DA), random forest (RF), and grasshopper optimization algorithm-based support vector machine (GOA-SVM)) were integrated into the analytical framework of ATR-FTIR spectroscopy, aiming to accurately identify baijiu samples according to different irradiation doses and to search for irradiation-induced spectral difference characteristics (spectral markers). The results showed that SD was the best spectral pre-processing method, and RF models constructed using the 20 most competitive and discriminative spectral markers (selected by Venn) could achieve accurate identification of baijiu samples based on irradiation dose (0, 4, 6, and 8 kGy). After Pearson correlation analysis, the five significantly (P<0.05) changed spectral markers (1596, 2025, 2309, 2329, and 2380 cm-1) were attributed to changes in the content of total acids, alcohols, and aromatic compounds. These findings demonstrate for the first time the potential of ATR-FTIR spectroscopy as a fast, low-cost, and non-destructive tool for the characterization and identification of irradiated baijiu samples. This approach may also offer a promising solution for labeling management of irradiated foods, vintage identification of baijius, and brand protection.
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Affiliation(s)
- Rui Zhou
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China
| | - Xiaoming Chen
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China.
| | - Min Huang
- Sichuan Institute of Atomic Energy, Chengdu 610101, Sichuan, PR China
| | - Hao Chen
- Sichuan Institute of Atomic Energy, Chengdu 610101, Sichuan, PR China
| | - Lili Zhang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China
| | - Defu Xu
- Luzhou Laojiao Co., Ltd, Luzhou 646699, Sichuan, PR China
| | - Dan Wang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China
| | - Peng Gao
- Sichuan Institute of Atomic Energy, Chengdu 610101, Sichuan, PR China
| | - Bensheng Wang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, PR China
| | - Xiaoxue Dai
- Luzhou Laojiao Co., Ltd, Luzhou 646699, Sichuan, PR China
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Cao Z, Zeng L, Wang Z, Zhou Y, Qian K. Role of miR -5010 -3p in predicting the prognosis of hepatocellular carcinoma. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:1281-1295. [PMID: 38044639 PMCID: PMC10929860 DOI: 10.11817/j.issn.1672-7347.2023.230042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 12/05/2023]
Abstract
OBJECTIVES Numerous miRNAs have been found to be abnormally expressed in hepatocellular carcinoma (HCC). However, clinical significance of miR-5010-3p in HCC is not elucidated. This study aims to explore the prognostic value and role of miR-5010-3p in HCC. METHODS The differential gene expression analysis of miR-5010-3p in HCC was performed based on the Cancer Genome Atlas (TCGA) database. The receiver operating characteristic (ROC) curve was used to evaluate the predictive value of miR-5010-3p expression level for HCC prognosis. The Kaplan-Meier, Cox univariate, and Cox multivariate analysis were used to predict its role in the prognosis of HCC. The downstream target genes were predicted. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to predict the potential functional pathways they may participate in. Finally, methyl thiazolyl tetrazolium (MTT) assay and 5-ethyl-2'-deoxyuridine (EDU) incorporation experiment were carried out to prove its effect on proliferation. RESULTS The expression of miR-5010-3p was associated with histological grade (P=0.019), vascular invasion degree (P=0.049), TP53 level (P=0.004), and alpha fetoprotein (AFP) level (P=0.012). A moderate ability to distinguish between tumor and paracancerous tissues of miR-5010-3p in HCC was perceived by ROC curve (AUC: 0.712, 95% CI 0.649 to 0.776). High expression of miR-5010-3p was associated with shorter overall survival (OS) (P=0.003). The results of functional enrichment analysis showed that miR-5010-3p was related to the tumorigenesis process. In vitro experiments verified that miR-5010-3p promoted the proliferation of hepatocellular carcinoma cells. CONCLUSIONS MiR-5010-3p promotes the proliferation of liver cancer cells, and its high expression is associated with poor prognosis, which may be a potential prognostic marker.
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Affiliation(s)
- Zhenyu Cao
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha 410011.
| | - Liyun Zeng
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha 410011
| | - Zicheng Wang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha 410011
- Department of General Surgery, Hunan Provincial People's Hospital, First Affiliated Hospital of Hunan Normal University, Changsha 410016
| | - Yi Zhou
- Department of General Surgery, Affiliated Hospital of Guilin Medical University, Guilin Guangxi 541000, China
| | - Ke Qian
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha 410011.
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Ting KK, Coleman P, Kim HJ, Zhao Y, Mulangala J, Cheng NC, Li W, Gunatilake D, Johnstone DM, Loo L, Neely GG, Yang P, Götz J, Vadas MA, Gamble JR. Vascular senescence and leak are features of the early breakdown of the blood-brain barrier in Alzheimer's disease models. GeroScience 2023; 45:3307-3331. [PMID: 37782439 PMCID: PMC10643714 DOI: 10.1007/s11357-023-00927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/27/2023] [Indexed: 10/03/2023] Open
Abstract
Alzheimer's disease (AD) is an age-related disease, with loss of integrity of the blood-brain barrier (BBB) being an early feature. Cellular senescence is one of the reported nine hallmarks of aging. Here, we show for the first time the presence of senescent cells in the vasculature in AD patients and mouse models of AD. Senescent endothelial cells and pericytes are present in APP/PS1 transgenic mice but not in wild-type littermates at the time of amyloid deposition. In vitro, senescent endothelial cells display altered VE-cadherin expression and loss of cell junction formation and increased permeability. Consistent with this, senescent endothelial cells in APP/PS1 mice are present at areas of vascular leak that have decreased claudin-5 and VE-cadherin expression confirming BBB breakdown. Furthermore, single cell sequencing of endothelial cells from APP/PS1 transgenic mice confirms that adhesion molecule pathways are among the most highly altered pathways in these cells. At the pre-plaque stage, the vasculature shows significant signs of breakdown, with a general loss of VE-cadherin, leakage within the microcirculation, and obvious pericyte perturbation. Although senescent vascular cells were not directly observed at sites of vascular leak, senescent cells were close to the leak area. Thus, we would suggest in AD that there is a progressive induction of senescence in constituents of the neurovascular unit contributing to an increasing loss of vascular integrity. Targeting the vasculature early in AD, either with senolytics or with drugs that improve the integrity of the BBB may be valid therapeutic strategies.
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Affiliation(s)
- Ka Ka Ting
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia.
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
| | - Paul Coleman
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Hani Jieun Kim
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Yang Zhao
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jocelyne Mulangala
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
| | - Ngan Ching Cheng
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
| | - Wan Li
- Department of General Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Dilini Gunatilake
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
| | - Daniel M Johnstone
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, & School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, & School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Mathew A Vadas
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
- Heart Research Institute, Sydney, NSW, Australia
| | - Jennifer R Gamble
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia.
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
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Brinker P, Chen F, Chehida YB, Beukeboom LW, Fontaine MC, Salles JF. Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia. Mol Ecol 2023; 32:6644-6658. [PMID: 36125236 DOI: 10.1111/mec.16699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022]
Abstract
The microbial community composition is crucial for diverse life-history traits in many organisms. However, we still lack a sufficient understanding of how the host microbiome is acquired and maintained, a pressing issue in times of global environmental change. Here we investigated to what extent host genotype, environmental conditions, and the endosymbiont Wolbachia influence the bacterial communities in the parasitic wasp Asobara japonica. We sampled multiple wasp populations across 10 locations in their natural distribution range in Japan and sequenced the host genome (whole genome sequencing) and microbiome (16S rRNA gene). We compared the host population structure and bacterial community composition of wasps that reproduce sexually and are uninfected with Wolbachia with wasps that reproduce asexually and carry Wolbachia. The bacterial communities in asexual wasps were highly similar due to a strong effect of Wolbachia rather than host genomic structure. In contrast, in sexual wasps, bacterial communities appear primarily shaped by a combination of population structure and environmental conditions. Our research highlights that multiple factors shape the bacterial communities of an organism and that the presence of a single endosymbiont can strongly alter their compositions. This information is crucial to understanding how organisms and their associated microbiome will react in the face of environmental change.
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Affiliation(s)
- Pina Brinker
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Fangying Chen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, UK
- Department of Biology, University of York, York, UK
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
| | - Joana Falcao Salles
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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43
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Hink L, Holzinger A, Sandfeld T, Weig AR, Schramm A, Feldhaar H, Horn MA. Microplastic ingestion affects hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber. Environ Microbiol 2023; 25:2776-2791. [PMID: 37041018 DOI: 10.1111/1462-2920.16386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/31/2023] [Indexed: 04/13/2023]
Abstract
Microplastic (MP) is an environmental burden and enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. Isopods represent ubiquitously abundant, ecologically important detritivores. However, MP-polymer specific effects on the host and its gut microbiota are unknown. We tested the hypothesis that biodegradable (polylactic acid [PLA]) and non-biodegradable (polyethylene terephthalate [PET]; polystyrene [PS]) MPs have contrasting effects on P. scaber mediated by changes of the gut microbiota. The isopod fitness after an 8-week MP-exposure was generally unaffected, although the isopods showed avoidance behaviour to PS-food. MP-polymer specific effects on gut microbes were detected, including a stimulation of microbial activity by PLA compared with MP-free controls. PLA stimulated hydrogen emission from isopod guts, while PET and PS were inhibitory. We roughly estimated 107 kg year-1 hydrogen emitted from the isopods globally and identified their guts as anoxic, significant mobile sources of reductant for soil microbes despite the absence of classical obligate anaerobes, likely due to Enterobacteriaceae-related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of important isopod hydrogen emissions by MP pollution and the potential of MP to affect terrestrial food webs.
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Affiliation(s)
- Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | - Anja Holzinger
- Animal Population Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Tobias Sandfeld
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Alfons R Weig
- Genomics and Bioinformatics, University of Bayreuth, Bayreuth, Germany
| | - Andreas Schramm
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Heike Feldhaar
- Animal Population Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
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44
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Sun S, Cai X, Shao J, Zhang G, Liu S, Wang H. Machine learning-based approach for efficient prediction of diagnosis, prognosis and lymph node metastasis of papillary thyroid carcinoma using adhesion signature selection. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:20599-20623. [PMID: 38124567 DOI: 10.3934/mbe.2023911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The association between adhesion function and papillary thyroid carcinoma (PTC) is increasingly recognized; however, the precise role of adhesion function in the pathogenesis and prognosis of PTC remains unclear. In this study, we employed the robust rank aggregation algorithm to identify 64 stable adhesion-related differentially expressed genes (ARDGs). Subsequently, using univariate Cox regression analysis, we identified 16 prognostic ARDGs. To construct PTC survival risk scoring models, we employed Lasso Cox and multivariate + stepwise Cox regression methods. Comparative analysis of these models revealed that the Lasso Cox regression model (LPSRSM) displayed superior performance. Further analyses identified age and LPSRSM as independent prognostic factors for PTC. Notably, patients classified as low-risk by LPSRSM exhibited significantly better prognosis, as demonstrated by Kaplan-Meier survival analyses. Additionally, we investigated the potential impact of adhesion feature on energy metabolism and inflammatory responses. Furthermore, leveraging the CMAP database, we screened 10 drugs that may improve prognosis. Finally, using Lasso regression analysis, we identified four genes for a diagnostic model of lymph node metastasis and three genes for a diagnostic model of tumor. These gene models hold promise for prognosis and disease diagnosis in PTC.
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Affiliation(s)
- Shuo Sun
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Beihua University, Beihua University, Jilin 132013, China
| | - Xiaoni Cai
- Department of General Surgery, Shangyu People's Hospital of Shaoxing, the Second Affiliated Hospital of Zhejiang University Medical College Hospital, Shaoxing 312399, China
| | - Jinhai Shao
- Department of General Surgery, Shangyu People's Hospital of Shaoxing, the Second Affiliated Hospital of Zhejiang University Medical College Hospital, Shaoxing 312399, China
| | - Guimei Zhang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Jilin University, Changchun 130061, China
| | - Shan Liu
- Department of Nuclear Medicine, The Second Hospital of Jilin University, Jilin University, Changchun 130041, China
| | - Hongsheng Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Beihua University, Beihua University, Jilin 132013, China
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45
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Bigger-Allen A, Gheinani AH, Adam RM. Investigation of the impact of bromodomain inhibition on cytoskeleton stability and contraction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567076. [PMID: 38014184 PMCID: PMC10680757 DOI: 10.1101/2023.11.14.567076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Injury to contractile organs such as the heart, vasculature, urinary bladder and gut can stimulate a pathological response that results in loss of normal contractility. PDGF and TGFβ are among the most well studied initiators of the injury response and have been shown to induce aberrant contraction in mechanically active cells of hollow organs including smooth muscle cells (SMC) and fibroblasts. However the mechanisms driving contractile alterations downstream of PDGF and TGFβ in SMC and fibroblasts are incompletely understood, limiting therapeutic interventions. To identify potential molecular targets, we have leveraged the analysis of publicly available data, comparing transcriptomic changes in mechanically active cells stimulated with PDGF and TGFβ and identified a shared molecular profile regulated by MYC and members of the AP-1 transcription factor complex. We also analyzed data sets from SMC and fibroblasts treated in the presence or absence of the MYC inhibitor JQ1. This analysis revealed a unique set of cytoskeleton-associated genes that were sensitive to MYC inhibition. JQ1 was also able to attenuate TGFβ and PDGF induced changes to the cytoskeleton and contraction of smooth muscle cells and fibroblasts in vitro. These findings identify MYC as a key driver of aberrant cytoskeletal and contractile changes in fibroblasts and SMC, and suggest that JQ1 could be used to restore normal contractile function in hollow organs.
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Affiliation(s)
- Alexander Bigger-Allen
- Urological Diseases Research Center, Boston Children’s Hospital, Boston, MA, USA
- Biological & Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Hashemi Gheinani
- Urological Diseases Research Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rosalyn M. Adam
- Urological Diseases Research Center, Boston Children’s Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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46
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Tarnowski MJ, Varliero G, Scown J, Phelps E, Gorochowski TE. Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230963. [PMID: 38026022 PMCID: PMC10646459 DOI: 10.1098/rsos.230963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.
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Affiliation(s)
- Matthew J. Tarnowski
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biosciences, Geography and Physics, Swansea University, Swansea SA2 8PP, UK
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Jim Scown
- Humanities and Social Sciences, University of Exeter, Cornwall TR10 9FE, UK
| | - Emily Phelps
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Thomas E. Gorochowski
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- BrisEngBio, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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47
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Yeo S, Jang J, Jung HJ, Lee H, Choe Y. Primary cilia-mediated regulation of microglial secretion in Alzheimer's disease. Front Mol Biosci 2023; 10:1250335. [PMID: 37942288 PMCID: PMC10627801 DOI: 10.3389/fmolb.2023.1250335] [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: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
Alzheimer's disease (AD) is a brain disorder manifested by a gradual decline in cognitive function due to the accumulation of extracellular amyloid plaques, disruptions in neuronal substance transport, and the degeneration of neurons. In affected neurons, incomplete clearance of toxic proteins by neighboring microglia leads to irreversible brain inflammation, for which cellular signaling is poorly understood. Through single-cell transcriptomic analysis, we discovered distinct regional differences in the ability of microglia to clear damaged neurites. Specifically, microglia in the septal region of wild type mice exhibited a transcriptomic signature resembling disease-associated microglia (DAM). These lateral septum (LS)-enriched microglia were associated with dense axonal bundles originating from the hippocampus. Further transcriptomic and proteomic approaches revealed that primary cilia, small hair-like structures found on cells, played a role in the regulation of microglial secretory function. Notably, primary cilia were transiently observed in microglia, and their presence was significantly reduced in microglia from AD mice. We observed significant changes in the secretion and proteomic profiles of the secretome after inhibiting the primary cilia gene intraflagellar transport particle 88 (Ift88) in microglia. Intriguingly, inhibiting primary cilia in the septal microglia of AD mice resulted in the expansion of extracellular amyloid plaques and damage to adjacent neurites. These results indicate that DAM-like microglia are present in the LS, a critical target region for hippocampal nerve bundles, and that the primary ciliary signaling system regulates microglial secretion, affecting extracellular proteostasis. Age-related primary ciliopathy probably contributes to the selective sensitivity of microglia, thereby exacerbating AD. Targeting the primary ciliary signaling system could therefore be a viable strategy for modulating neuroimmune responses in AD treatments.
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Affiliation(s)
- Seungeun Yeo
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jaemyung Jang
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyun Jin Jung
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-eui University, Busan, Republic of Korea
| | - Youngshik Choe
- Korea Brain Research Institute, Daegu, Republic of Korea
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48
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Doonan JM, Kosawang C, Eisenring M, Ladd T, Roe AD, Budde KB, Jørgensen HJL, Queloz V, Gossner MM, Nielsen LR. Transcriptome profiling of Fraxinus excelsior genotypes infested by emerald ash borer. Sci Data 2023; 10:680. [PMID: 37798274 PMCID: PMC10556020 DOI: 10.1038/s41597-023-02588-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
European ash, Fraxinus excelsior is facing the double threat of ongoing devastation by the invasive fungal pathogen, Hymenoscyphus fraxineus and the imminent arrival of the non-native emerald ash borer (EAB), Agrilus planipennis. The spread of EAB which is currently moving westwards from European Russia and Ukraine into central Europe, poses an additional substantial threat to European ash, F. excelsior. While the molecular basis for resistance or variation in resistance among European ash genotypes is heavily investigated, comparatively little is known about the molecular ash traits involved in resistance against EAB. In this study we have gathered transcriptomic data from EAB inoculated genotypes of F. excelsior that have previously shown different levels of susceptibility to EAB. Resultant datasets show differential gene expression in susceptible and resistant genotypes in response to EAB infestation. This data will provide important information on the molecular basis of resistance to the EAB and allow the development of management plans to combat a pending threat of a culturally and ecologically important European tree species.
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Affiliation(s)
- James M Doonan
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
| | - Chatchai Kosawang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Michael Eisenring
- Forest Health and biotic Interactions, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Tim Ladd
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Amanda D Roe
- Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Katharina B Budde
- Buesgen Institute of Forest Genetics and Forest Tree Breeding, Georg-August Universität Göttingen, Buesgenweg 2, 37077, Goettingen, Germany
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Valentin Queloz
- Forest Health and biotic Interactions, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Martin M Gossner
- Forest Health and biotic Interactions, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätstrasse 16, 8092, Zürich, Switzerland
| | - Lene R Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
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49
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Saydullaeva I, Butuner BD, Korkmaz KS. NKX3.1 Expression Contributes to Epithelial-Mesenchymal Transition of Prostate Cancer Cells. ACS OMEGA 2023; 8:32580-32592. [PMID: 37720744 PMCID: PMC10500679 DOI: 10.1021/acsomega.3c03127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
Abstract
Studies demonstrate that inflammation synergizes with high-grade aggressive prostate tumor development and ultimately metastatic spread, in which a lot of work has been done in recent years. However, the clear mechanism of inflammation inciting prostate cancer remains largely uncharacterized. Our previous study has shown that the conditioned media (CM)-mediated LNCaP cell migration is partially correlated with the loss of expression of the tumor suppressor NKX3.1. Here, we continue to investigate the inflammation-mediated migration of prostate cancer cells, and the role of NKX3.1 in this process to gain insights into cell migration-related changes comprehensively. Earlier, the model of inflammation in the tumor microenvironment have been optimized by our research group; here, we continue to investigate the time-dependent effect of CM exposure together with NKX3.1 changes, in which we observed that these changes play important roles in gaining heterogeneous epithelial-to-mesenchymal transition (EMT) phenotype. Hence, this is an important parameter of tumor progression; we depleted NKX3.1 expression using the CRISPR/Cas9 system and examined the migrating cell clusters after exposure to inflammatory cytokines. We found that the migrated cells clearly demonstrate reversible loss of E-cadherin expression, which is consistent with subsequent vimentin expression alterations in comparison to control cells. Moreover, the data suggest that the AR-mediated transcriptional program also contributes to mesenchymal-to-epithelial transition (MET) in prostate cancer progression. Furthermore, the quantitative proteomic analysis showed that migrated subpopulations from the same cell line presented different phenotypes in which the proteins overexpressed are involved in cell metabolism and RNA processing. According to KEGG pathway analysis, the ABC transporters were found to be the most significant. Thus, the dynamic process of cellular migration favors diverse genetic compositions under changing tumor microenvironments. The different levels of invasiveness are supported by shifting the cells in between these EMT and MET phenotypes.
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Affiliation(s)
- Iroda Saydullaeva
- Faculty
of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir 35040, Turkey
| | - Bilge Debelec Butuner
- Faculty
of Pharmacy, Department of Pharmaceutical Biotechnology, Ege University, Izmir 35040, Turkey
| | - Kemal Sami Korkmaz
- Faculty
of Engineering, Department of Bioengineering, Cancer Biology Laboratory, Ege University, Izmir 35040, Turkey
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50
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Berková L, Fazilaty H, Yang Q, Kubovčiak J, Stastna M, Hrckulak D, Vojtechova M, Dalessi T, Brügger MD, Hausmann G, Liberali P, Korinek V, Basler K, Valenta T. Terminal differentiation of villus tip enterocytes is governed by distinct Tgfβ superfamily members. EMBO Rep 2023; 24:e56454. [PMID: 37493498 PMCID: PMC10481656 DOI: 10.15252/embr.202256454] [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: 11/09/2022] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/27/2023] Open
Abstract
The protective and absorptive functions of the intestinal epithelium rely on differentiated enterocytes in the villi. The differentiation of enterocytes is orchestrated by sub-epithelial mesenchymal cells producing distinct ligands along the villus axis, in particular Bmps and Tgfβ. Here, we show that individual Bmp ligands and Tgfβ drive distinct enterocytic programs specific to villus zonation. Bmp4 is expressed from the centre to the upper part of the villus and activates preferentially genes connected to lipid uptake and metabolism. In contrast, Bmp2 is produced by villus tip mesenchymal cells and it influences the adhesive properties of villus tip epithelial cells and the expression of immunomodulators. Additionally, Tgfβ induces epithelial gene expression programs similar to those triggered by Bmp2. Bmp2-driven villus tip program is activated by a canonical Bmp receptor type I/Smad-dependent mechanism. Finally, we establish an organoid cultivation system that enriches villus tip enterocytes and thereby better mimics the cellular composition of the intestinal epithelium. Our data suggest that not only a Bmp gradient but also the activity of individual Bmp drives specific enterocytic programs.
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Affiliation(s)
- Linda Berková
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Hassan Fazilaty
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Qiutan Yang
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and Regeneration, Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jan Kubovčiak
- Laboratory of Genomics and BioinformaticsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Monika Stastna
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Dusan Hrckulak
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Martina Vojtechova
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Tosca Dalessi
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | | | - George Hausmann
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Vladimir Korinek
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Konrad Basler
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Tomas Valenta
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
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