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Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Comput Struct Biotechnol J 2024; 23:1129-1143. [PMID: 38510973 PMCID: PMC10950807 DOI: 10.1016/j.csbj.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
We introduce drexml, a command line tool and Python package for rational data-driven drug repurposing. The package employs machine learning and mechanistic signal transduction modeling to identify drug targets capable of regulating a particular disease. In addition, it employs explainability tools to contextualize potential drug targets within the functional landscape of the disease. The methodology is validated in Fanconi Anemia and Familial Melanoma, two distinct rare diseases where there is a pressing need for solutions. In the Fanconi Anemia case, the model successfully predicts previously validated repurposed drugs, while in the Familial Melanoma case, it identifies a promising set of drugs for further investigation.
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Affiliation(s)
- Marina Esteban-Medina
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Víctor Manuel de la Oliva Roque
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Sara Herráiz-Gil
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U714, Madrid, Spain
- Departamento de Bioingeniería, Universidad Carlos III de Madrid (UC3M), Madrid, Spain
- Regenerative Medicine and Tissue Engineering Group, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - María Peña-Chilet
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Platform of Big Data, AI and Biostatistics, Health Research Institute La Fe (IISLAFE), Valencia, Spain
| | - Joaquín Dopazo
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Seville, Spain
| | - Carlos Loucera
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
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2
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Zhang S, Shu M, Gong Z, Liu X, Zhang C, Liang Y, Lin Q, Zhou B, Guo T, Liu J. Enhancing extracellular monascus pigment production in submerged fermentation with engineered microbial consortia. Food Microbiol 2024; 121:104499. [PMID: 38637070 DOI: 10.1016/j.fm.2024.104499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/13/2023] [Accepted: 02/21/2024] [Indexed: 04/20/2024]
Abstract
In this study, we investigated the impact of microbial interactions on Monascus pigment (MP) production. We established diverse microbial consortia involving Monascus purpureus and Lactobacillus fermentum. The addition of Lactobacillus fermentum (4% at 48 h) to the submerged fermentation of M. purpureus resulted in a significantly higher MP production compared to that achieved using the single-fermentation system. Co-cultivation with immobilized L. fermentum led to a remarkable increase of 59.18% in extracellular MP production, while mixed fermentation with free L. fermentum caused a significant decrease of 66.93% in intracellular MPs, contrasting with a marginal increase of 4.52% observed during co-cultivation with immobilized L. fermentum and the control group respectively. The findings indicate an evident enhancement in cell membrane permeability of M. purpureus when co-cultivated with immobilized L. fementum. Moreover, integrated transcriptomic and metabolomic analyses were conducted to elucidate the regulatory mechanisms underlying MP biosynthesis and secretion following inoculation with immobilized L. fementum, with specific emphasis on glycolysis, steroid biosynthesis, fatty acid biosynthesis, and energy metabolism.
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Affiliation(s)
- Song Zhang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Meng Shu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Zihan Gong
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Xinyi Liu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Chenyu Zhang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ying Liang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Qinlu Lin
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Bo Zhou
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ting Guo
- Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Jun Liu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China.
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3
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Ji Z, Zhang J, Deng C, Guo T, Han R, Yang Y, Zang C, Chen Y. Identification of pasteurized mare milk and powder adulteration with bovine milk using quantitative prote omics and metabolomics approaches. Food Chem X 2024; 22:101265. [PMID: 38468636 PMCID: PMC10926301 DOI: 10.1016/j.fochx.2024.101265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
Adulteration in dairy products presents food safety challenges, driven by economic factors. Processing may change specific biomarkers, thus affecting their effectiveness in detection. In this study, proteomics and metabolomics approaches were to investigate the detection of bovine milk (BM) constituents adulteration in pasteurized mare milk (PMM) and mare milk powder (MMP). Several bovine proteins and metabolites were identified, with their abundances in PMM and MMP increasing upon addition of BM. Proteins like osteopontin (OPN) and serotransferrin (TF) detected adulteration down to 1 % in PMM, whereas these proteins in MMP were utilized to identify 10 % adulteration. Biotin and N6-Me-adenosine were effective in detecting adulteration in PMM as low as 10 % and 1 % respectively, while in MMP, their detection limits extend down to 0.1 %. These findings offer insights for authenticating mare milk products and underscore the influence of processing methods on biomarker levels, stressing the need to consider these effects in milk product authentication.
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Affiliation(s)
- Zhongyuan Ji
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, Shandong, China
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junyu Zhang
- Institute of Feed Research, Xinjiang Academy of Animal Science, Urumqi 830052, Xinjiang, China
| | - Chunxia Deng
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Tongjun Guo
- Institute of Feed Research, Xinjiang Academy of Animal Science, Urumqi 830052, Xinjiang, China
| | - Rongwei Han
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Yongxin Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, Shandong, China
| | - Changjiang Zang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
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Saeed M, Masood Quraishi U, Mustafa G, Farooqi A, Greger M, Naseem Malik R. Metabol omics profiling reveals the detoxification and tolerance behavior of two bread wheat (Triticum aestivum L.) varieties under arsenate stress. Food Chem 2024; 443:138612. [PMID: 38306910 DOI: 10.1016/j.foodchem.2024.138612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
The present study conducted metabolomics profiling (targeted and untargeted) in the roots of two wheat varieties (BARANI-70 and NARC-09) under arsenate stress in a hydroponic experiment. The findings indicated a better growth response of BARANI-70 compared to the NARC-09. From amino acid profiling, a total of 26 amino acids (AAs) were quantified in roots. BARANI-70 showed higher induction of stress-responsive AAs compared to the NARC-09. From untargeted metabolomics, a total of 136 metabolites were identified: AAs, fatty acids, purines, carnitines, LysoPCs, and others. The KEGG pathway identified pathways such as linoleic acid metabolism, TCA cycle, glutathione metabolism, and aminoacyl-tRNA biosynthesis that were regulated to improve the defense of tolerant variety. BARANI-70 emerged as a tolerant variety based on the psychological response, As accumulation, and behavior of stress-responsive metabolites. This study should facilitate the breeding of low-As accumulating wheat varieties for future application to ensure sustainable production and food safety.
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Affiliation(s)
- Muhammad Saeed
- Environmental Biology and Ecotoxicology Laboratory, Department of Environmental Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Umar Masood Quraishi
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Ghazala Mustafa
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Abida Farooqi
- Environmental Geochemistry Laboratory, Department of Environmental Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Maria Greger
- Plant Metal Laboratory, Department of Ecology, Environment, and Plant Sciences (DEEP), Stockholm University, Stockholm, Sweden
| | - Riffat Naseem Malik
- Environmental Biology and Ecotoxicology Laboratory, Department of Environmental Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Li L, Xie G, Dong P, Tang H, Wu L, Zhang L. Anticyanobacterial effect of p-coumaric acid on Limnothrix sp. determined by proteomic and metabolomic analysis. Sci Total Environ 2024; 926:171632. [PMID: 38471589 DOI: 10.1016/j.scitotenv.2024.171632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Regulating photosynthetic machinery is a powerful but challenging strategy for selectively inhibiting bloom-forming cyanobacteria, in which photosynthesis mainly occurs in thylakoids. P-coumaric acid (p-CA) has several biological properties, including free radical scavenging and antibacterial effects, and studies have shown that it can damage bacterial cell membranes, reduce chlorophyll a in cyanobacteria, and effectively inhibit algal growth at concentrations exceeding 0.127 g/L. Allelochemicals typically inhibit cyanobacteria by inhibiting photosynthesis; however, research on inhibiting harmful algae using phenolic acids has focused mainly on their inhibitory and toxic effects and metabolite levels, and the molecular mechanism by which p-CA inhibits photosynthesis remains unclear. Thus, we examined the effect of p-CA on the photosynthesis of Limnothrix sp. in detail. We found that p-CA inhibits algal growth and damages photosynthesis-related proteins in Limnothrix sp., reduces carotenoid and allophycocyanin levels, and diminishes the actual quantum yield of Photosystem II (PSII). Moreover, p-CA significantly altered algal cell membrane protein systems, and PSII loss resulting from p-CA exposure promoted reactive oxygen species production. It significantly altered algae cell membrane protein systems. Finally, p-CA was found to be environmentally nontoxic; 80 % of 48-h-old Daphnia magna larvae survived when exposed to 0.15 g/L p-CA. These findings provide insight into the mechanism of cyanobacterial inhibition by p-CA, providing a more practical approach to controlling harmful algal blooms.
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Affiliation(s)
- Lingzhi Li
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Gengxin Xie
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
| | - Pan Dong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Hui Tang
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Liping Wu
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Liang Zhang
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
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Louie JD, Barrios-Camacho CM, Bromberg BH, Hintschich CA, Schwob JE. Spatiotemporal dynamics exhibited by horizontal basal cells reveal a pro-neurogenic pathway during injury-induced olfactory epithelium regeneration. iScience 2024; 27:109600. [PMID: 38650985 PMCID: PMC11033173 DOI: 10.1016/j.isci.2024.109600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 12/21/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Horizontal basal cells (HBCs) mediate olfactory epithelium (OE) regeneration following severe tissue injury. The dynamism of the post-injury environment is well illustrated by in silico modeling of RNA sequencing data that demonstrate an evolving HBC transcriptome. Unfortunately, spatiotemporally dynamic processes occurring within HBCs in situ remain poorly understood. Here, we show that HBCs at 24 h post-OE injury spatially redistribute a constellation of proteins, which, in turn, helped to nominate Rac1 as a regulator of HBC differentiation during OE regeneration. Using our primary culture model to activate HBCs pharmacologically, we demonstrate that concurrent Rac1 inhibition attenuates HBC differentiation potential. This in vitro functional impairment manifested in vivo as decreased HBC differentiation into olfactory sensory neurons following HBC-specific Rac1 conditional knockout. Taken together, our data potentiate the design of hyposmia-alleviating therapies and highlight aspects of in situ HBC spatiotemporal dynamics that deserve further investigation.
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Affiliation(s)
- Jonathan D. Louie
- Medical Scientist Training Program, Tufts University School of Medicine, Boston, MA 02111, USA
- Neuroscience Graduate Program, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
- Department of Developmental, Molecular & Chemical Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Camila M. Barrios-Camacho
- Neuroscience Graduate Program, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
- Department of Developmental, Molecular & Chemical Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Benjamin H. Bromberg
- Department of Developmental, Molecular & Chemical Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Constantin A. Hintschich
- Department of Developmental, Molecular & Chemical Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
- Department of Otorhinolaryngology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - James E. Schwob
- Department of Developmental, Molecular & Chemical Biology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
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Chen H, Sahu SK, Wang S, Liu J, Yang J, Cheng L, Chiu TY, Liu H. Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids. iScience 2024; 27:109599. [PMID: 38646178 PMCID: PMC11033161 DOI: 10.1016/j.isci.2024.109599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.
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Affiliation(s)
- Haixia Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jinlong Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tsan-Yu Chiu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
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Qiu O, Zhao J, Shi Z, Li H, Wang S, Liao K, Tang M, Xie J, Huang X, Zhang W, Zhou L, Yang X, Zhou Z, Xu L, Huang R, Miao Y, Qiu Y, Lin Y. Asparagine endopeptidase deficiency mitigates radiation-induced brain injury by suppressing microglia-mediated neuronal senescence. iScience 2024; 27:109698. [PMID: 38655198 PMCID: PMC11035374 DOI: 10.1016/j.isci.2024.109698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
Mounting evidence supports the role of neuroinflammation in radiation-induced brain injury (RIBI), a chronic disease characterized by delayed and progressive neurological impairment. Asparagine endopeptidase (AEP), also known as legumain (LGMN), participates in multiple malignancies and neurodegenerative diseases and may potentially be involved in RIBI. Here, we found AEP expression was substantially elevated in the cortex and hippocampus of wild-type (Lgmn+/+) mice following whole-brain irradiation. Lgmn knockout (Lgmn-/-) alleviated neurological impairment caused by whole-brain irradiation by suppressing neuronal senescence. Bulk RNA and metabolomic sequencing revealed AEP's involvement in the antigen processing and presentation pathway and neuroinflammation. This was further confirmed by co-culturing Lgmn+/+ primary neurons with the conditioned media derived from irradiated Lgmn+/+ or Lgmn-/- primary microglia. Furthermore, esomeprazole inhibited the enzymatic activity of AEP and RIBI. These findings identified AEP as a critical factor of neuroinflammation in RIBI, highlighting the prospect of targeting AEP as a therapeutic approach.
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Affiliation(s)
- Ouwen Qiu
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Jianyi Zhao
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Zhonggang Shi
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Huan Li
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Siyuan Wang
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Keman Liao
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Minchao Tang
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Guangxi 530021, P.R. China
| | - Jieqiong Xie
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi 530007, P.R. China
| | - Xi Huang
- Department of Digestive Oncology, Guangxi Medical University Cancer Hospital, Guangxi 530021, P.R. China
| | - Wenrui Zhang
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Li Zhou
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Xi Yang
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Zhiyi Zhou
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Lei Xu
- Department of Radiation, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Renhua Huang
- Department of Radiation, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Yifeng Miao
- Department of Neurosurgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Yongming Qiu
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Yingying Lin
- Brain Injury Center, Shanghai Institute of Head Trauma, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
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9
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Steinhoff M, Buddenkotte J. Flushing New Light on Rosacea. J Invest Dermatol 2024; 144:934-935. [PMID: 38099889 DOI: 10.1016/j.jid.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/13/2023] [Accepted: 11/03/2023] [Indexed: 04/23/2024]
Affiliation(s)
- Martin Steinhoff
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha, Qatar; Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Weill Cornell Medicine-Qatar, Doha, Qatar; Department of Medicine, Qatar University, Doha, Qatar; Department of Life Sciences, Hamad-bin-Khalifa University, Doha, Qatar; Department of Dermatology, Weill Cornell Medicine, New York, New York, USA.
| | - Joerg Buddenkotte
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha, Qatar; Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
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Liu Z, Wang J, Yue Z, Wang J, Dou T, Chen T, Li J, Dai H, Yu J. Study of cabbage antioxidant system response on early infection stage of Xanthomonas campestris pv. campestris. BMC Plant Biol 2024; 24:324. [PMID: 38658831 DOI: 10.1186/s12870-024-04994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) significantly affects the production of cabbage and other cruciferous vegetables. Plant antioxidant system plays an important role in pathogen invasion and is one of the main mechanisms underlying resistance to biological stress. Therefore, it is important to study the resistance mechanisms of the cabbage antioxidant system during the early stages of Xcc. In this study, 108 CFU/mL (OD600 = 0.1) Xcc race1 was inoculated on "zhonggan 11" cabbage using the spraying method. The effects of Xcc infection on the antioxidant system before and after Xcc inoculation (0, 1, 3, and 5 d) were studied by physiological indexes determination, transcriptome and metabolome analyses. We concluded that early Xcc infection can destroy the balance of the active oxygen metabolism system, increase the generation of free radicals, and decrease the scavenging ability, leading to membrane lipid peroxidation, resulting in the destruction of the biofilm system and metabolic disorders. In response to Xcc infection, cabbage clears a series of reactive oxygen species (ROS) produced during Xcc infection via various antioxidant pathways. The activities of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) increased after Xcc infection, and the ROS scavenging rate increased. The biosynthesis of non-obligate antioxidants, such as ascorbic acid (AsA) and glutathione (GSH), is also enhanced after Xcc infection. Moreover, the alkaloid and vitamin contents increased significantly after Xcc infection. We concluded that cabbage could resist Xcc invasion by maintaining the stability of the cell membrane system and improving the biosynthesis of antioxidant substances and enzymes after infection by Xcc. Our results provide theoretical basis and data support for subsequent research on the cruciferous vegetables resistance mechanism and breeding to Xcc.
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Affiliation(s)
- Zeci Liu
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Jie Wang
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Zhibin Yue
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Jue Wang
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Tingting Dou
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Tongyan Chen
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Jinbao Li
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Haojie Dai
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China
| | - Jihua Yu
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, People's Republic of China.
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11
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Ernst TR, Blischak JD, Nordlund P, Dalen J, Moore J, Bhamidipati A, Dwivedi P, LoGrasso J, Curado MR, Engelmann BW. OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies. BMC Bioinformatics 2024; 25:162. [PMID: 38658834 DOI: 10.1186/s12859-024-05743-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND The results of high-throughput biology ('omic') experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features. RESULTS We present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access. CONCLUSIONS OmicNavigator can be found at https://github.com/abbvie-external/OmicNavigator.
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Affiliation(s)
| | - John D Blischak
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Paul Nordlund
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Joe Dalen
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Justin Moore
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
- Current Address: Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Pankaj Dwivedi
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
- Proteovant Therapeutics, 2500 Renaissance Blvd, King of Prussia, PA, USA
| | - Joe LoGrasso
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
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12
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Deng M, Hou T, Zhang J, Mao X, Yang F, Wei Y, Tang Y, Zeng W, Huang W, Li N, Xiao L, Feng Y, Guo Y. Cultivation, cryopreservation, and transcriptomic studies of host-adapted Cryptosporidium parvum and Cryptosporidium hominis using enteroids. iScience 2024; 27:109563. [PMID: 38623332 PMCID: PMC11016910 DOI: 10.1016/j.isci.2024.109563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/21/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Cryptosporidium hominis and Cryptosporidium parvum are major causes of severe diarrhea. Comparative studies of them are hampered by the lack of effective cultivation and cryopreservation methods, especially for C. hominis. Here, we describe adapted murine enteroids for the cultivation and complete development of host-adapted C. parvum and C. hominis subtypes, producing oocysts infectious to mice. Using the system, we developed a cryopreservation method for Cryptosporidium isolates. In comparative RNA-seq analyses of C. hominis cultures, the enteroid system generated significantly more host and pathogen responses than the conventional HCT-8 cell system. In particular, the infection was shown to upregulate PI3K-Akt, Ras, TNF, NF-κB, IL-17, MAPK, and innate immunity signaling pathways and downregulate host cell metabolism, and had significantly higher expression of parasite genes involved in oocyst formation. Therefore, the enteroid system provides a valuable tool for comparative studies of the biology of divergent Cryptosporidium species and isolates.
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Affiliation(s)
- Miner Deng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Tianyi Hou
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie Zhang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xinjie Mao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fuxian Yang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yanting Wei
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yongping Tang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wanting Zeng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wanyi Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, Guangdong, China
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13
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Juteršek M, Gerasymenko IM, Petek M, Haumann E, Vacas S, Kallam K, Gianoglio S, Navarro-Llopis V, Heethoff M, Fuertes IN, Patron N, Orzáez D, Gruden K, Warzecha H, Baebler Š. Transcriptome-informed identification and characterization of Planococcus citri cis- and trans-isoprenyl diphosphate synthase genes. iScience 2024; 27:109441. [PMID: 38523795 PMCID: PMC10960109 DOI: 10.1016/j.isci.2024.109441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/13/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS coding sequences of the pest mealybug Planococcus citri. We queried the available genomic and newly generated short- and long-read P. citri transcriptomic data and identified 18 putative IDS genes, whose phylogenetic analysis indicates several gene family expansion events. In vitro testing confirmed regular short-chain coupling activity with five gene products. With the candidate with highest IDS activity, we also detected low amounts of irregular coupling products, and determined amino acid residues important for chain-length preference and irregular coupling activity. This work therefore provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, including the sex pheromone biosynthesis in P. citri.
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Affiliation(s)
- Mojca Juteršek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Iryna M. Gerasymenko
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Marko Petek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Elisabeth Haumann
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Sandra Vacas
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Vicente Navarro-Llopis
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Michael Heethoff
- Animal Evolutionary Ecology, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | | | - Nicola Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Diego Orzáez
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Špela Baebler
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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14
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Artigas-Jerónimo S, Villar M, Estrada-Peña A, Alberdi P, de la Fuente J. Subolesin knockdown in tick cells provides insights into vaccine protective mechanisms. Vaccine 2024; 42:2801-2809. [PMID: 38508929 DOI: 10.1016/j.vaccine.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/19/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Ticks as obligate blood-feeding arthropod vectors of pathogenic viruses, bacteria, protozoa and helminths associated with prevalent tick-borne diseases (TBDs) worldwide. These arthropods constitute the second vector after mosquitoes that transmit pathogens to humans and the first vector in domestic animals. Vaccines constitute the safest and more effective approach to control tick infestations and TBDs, but research is needed to identify new antigens and improve vaccine formulations. The tick protein Subolesin (Sub) is a well-known vaccine protective antigen with a highly conserved sequence at both gene and protein levels in the Ixodidae and among arthropods and vertebrates. In this study, transcriptomics and proteomics analyses were conducted together with graph theory data analysis in wild type and Sub knockdown (KD) tick ISE6 cells in order to identify and characterize the functional implications of Sub in tick cells. The results support a key role for Sub in the regulation of gene expression in ticks and the relevance of this antigen in vaccine development against ticks and TBDs. Proteins with differential representation in response to Sub KD provide insights into vaccine protective mechanisms and candidate tick protective antigens.
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Affiliation(s)
- Sara Artigas-Jerónimo
- Biochemistry Section, Faculty of Science and Chemical Technologies, University of Castilla- La Mancha, 13071 Ciudad Real, Spain.
| | - Margarita Villar
- Biochemistry Section, Faculty of Science and Chemical Technologies, University of Castilla- La Mancha, 13071 Ciudad Real, Spain; SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | | | - Pilar Alberdi
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain; Center for Veterinary Health Sciences, Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA.
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15
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Hurtado Silva M, van Waardenberg AJ, Mostafa A, Schoch S, Dietrich D, Graham ME. Multi omics of early epileptogenesis in mice reveals phosphorylation and dephosphorylation-directed growth and synaptic weakening. iScience 2024; 27:109534. [PMID: 38600976 PMCID: PMC11005001 DOI: 10.1016/j.isci.2024.109534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 01/26/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024] Open
Abstract
To investigate the phosphorylation-based signaling and protein changes occurring early in epileptogenesis, the hippocampi of mice treated with pilocarpine were examined by quantitative mass spectrometry at 4 and 24 h post-status epilepticus at vast depth. Hundreds of posttranscriptional regulatory proteins were the major early targets of increased phosphorylation. At 24 h, many protein level changes were detected and the phosphoproteome continued to be perturbed. The major targets of decreased phosphorylation at 4 and 24 h were a subset of postsynaptic density scaffold proteins, ion channels, and neurotransmitter receptors. Many proteins targeted by dephosphorylation at 4 h also had decreased protein abundance at 24 h, indicating a phosphatase-mediated weakening of synapses. Increased translation was indicated by protein changes at 24 h. These observations, and many additional indicators within this multiomic resource, suggest that early epileptogenesis is characterized by signaling that stimulates both growth and a homeostatic response that weakens excitability.
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Affiliation(s)
- Mariella Hurtado Silva
- Synapse Proteomics, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | | | - Aya Mostafa
- Department of Neuropathology, University Hospital Bonn, Synaptic Neuroscience Unit, 53127 Bonn, North Rhine-Westphalia, Germany
| | - Susanne Schoch
- Department of Neuropathology, University Hospital Bonn, Synaptic Neuroscience Unit, 53127 Bonn, North Rhine-Westphalia, Germany
| | - Dirk Dietrich
- Department of Neurosurgery, University Hospital Bonn, Synaptic Neuroscience Unit, 53127 Bonn, North Rhine-Westphalia, Germany
| | - Mark E. Graham
- Synapse Proteomics, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
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16
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Baig S, Nadaf J, Allache R, Le PU, Luo M, Djedid A, Nkili-Meyong A, Safisamghabadi M, Prat A, Antel J, Guiot MC, Petrecca K. Identity and nature of neural stem cells in the adult human subventricular zone. iScience 2024; 27:109342. [PMID: 38495819 PMCID: PMC10940989 DOI: 10.1016/j.isci.2024.109342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/26/2023] [Accepted: 02/22/2024] [Indexed: 03/19/2024] Open
Abstract
The existence of neural stem cells (NSCs) in adult human brain neurogenic regions remains unresolved. To address this, we created a cell atlas of the adult human subventricular zone (SVZ) derived from fresh neurosurgical samples using single-cell transcriptomics. We discovered 2 adult radial glia (RG)-like populations, aRG1 and aRG2. aRG1 shared features with fetal early RG (eRG) and aRG2 were transcriptomically similar to fetal outer RG (oRG). We also captured early neuronal and oligodendrocytic NSC states. We found that the biological programs driven by their transcriptomes support their roles as early lineage NSCs. Finally, we show that these NSCs have the potential to transition between states and along lineage trajectories. These data reveal that multipotent NSCs reside in the adult human SVZ.
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Affiliation(s)
- Salma Baig
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Javad Nadaf
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Redouane Allache
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Phuong U. Le
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Michael Luo
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Annisa Djedid
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Andriniaina Nkili-Meyong
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Maryam Safisamghabadi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Alex Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC H2X0A9, Canada
| | - Jack Antel
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Marie-Christine Guiot
- Department of Neuropathology, Montreal Neurological Institute-Hospital, McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
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17
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Dorgau B, Collin J, Rozanska A, Boczonadi V, Moya-Molina M, Unsworth A, Hussain R, Coxhead J, Dhanaseelan T, Armstrong L, Queen R, Lako M. Deciphering the spatiotemporal transcriptional and chromatin accessibility of human retinal organoid development at the single-cell level. iScience 2024; 27:109397. [PMID: 38510120 PMCID: PMC10952046 DOI: 10.1016/j.isci.2024.109397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/28/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Molecular information on the early stages of human retinal development remains scarce due to limitations in obtaining early human eye samples. Pluripotent stem cell-derived retinal organoids (ROs) provide an unprecedented opportunity for studying early retinogenesis. Using a combination of single cell RNA-seq and spatial transcriptomics we present for the first-time a single cell spatiotemporal transcriptome of RO development. Our data demonstrate that ROs recapitulate key events of retinogenesis including optic vesicle/cup formation, presence of a putative ciliary margin zone, emergence of retinal progenitor cells and their orderly differentiation to retinal neurons. Combining the scRNA- with scATAC-seq data, we were able to reveal cell-type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development, and to show that chromatin accessibility is highly correlated to the developing human retina, but with some differences in the temporal emergence and abundance of some of the retinal neurons.
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Affiliation(s)
- Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Agata Rozanska
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Veronika Boczonadi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Marina Moya-Molina
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
- Newcells Biotech, Newcastle upon Tyne NE4 5BX, UK
| | - Adrienne Unsworth
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Rafiqul Hussain
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Tamil Dhanaseelan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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18
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Niu R, Guo Y, Shang X. GLIMS: A two-stage gradual-learning method for cancer genes prediction using multi- omics data and co-splicing network. iScience 2024; 27:109387. [PMID: 38510118 PMCID: PMC10951990 DOI: 10.1016/j.isci.2024.109387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Identifying cancer genes is vital for cancer diagnosis and treatment. However, because of the complexity of cancer occurrence and limited cancer genes knowledge, it is hard to identify cancer genes accurately using only a few omics data, and the overall performance of existing methods is being called for further improvement. Here, we introduce a two-stage gradual-learning strategy GLIMS to predict cancer genes using integrative features from multi-omics data. Firstly, it uses a semi-supervised hierarchical graph neural network to predict the initial candidate cancer genes by integrating multi-omics data and protein-protein interaction (PPI) network. Then, it uses an unsupervised approach to further optimize the initial prediction by integrating the co-splicing network in post-transcriptional regulation, which plays an important role in cancer development. Systematic experiments on multi-omics cancer data demonstrated that GLIMS outperforms the state-of-the-art methods for the identification of cancer genes and it could be a useful tool to help advance cancer analysis.
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Affiliation(s)
- Rui Niu
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
| | - Yang Guo
- School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
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19
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Ishiguro H, Ushiki T, Honda A, Yoshimatsu Y, Ohashi R, Okuda S, Kawasaki A, Cho K, Tamura S, Suwabe T, Katagiri T, Ling Y, Iijima A, Mikami T, Kitagawa H, Uemura A, Sango K, Masuko M, Igarashi M, Sone H. Reduced chondroitin sulfate content prevents diabetic neuropathy through transforming growth factor-β signaling suppression. iScience 2024; 27:109528. [PMID: 38595797 PMCID: PMC11002665 DOI: 10.1016/j.isci.2024.109528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/08/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024] Open
Abstract
Diabetic neuropathy (DN) is a major complication of diabetes mellitus. Chondroitin sulfate (CS) is one of the most important extracellular matrix components and is known to interact with various diffusible factors; however, its role in DN pathology has not been examined. Therefore, we generated CSGalNAc-T1 knockout (T1KO) mice, in which CS levels were reduced. We demonstrated that diabetic T1KO mice were much more resistant to DN than diabetic wild-type (WT) mice. We also found that interactions between pericytes and vascular endothelial cells were more stable in T1KO mice. Among the RNA-seq results, we focused on the transforming growth factor β signaling pathway and found that the phosphorylation of Smad2/3 was less upregulated in T1KO mice than in WT mice under hyperglycemic conditions. Taken together, a reduction in CS level attenuates DN progression, indicating that CS is an important factor in DN pathogenesis.
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Affiliation(s)
- Hajime Ishiguro
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
| | - Takashi Ushiki
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
- Division of Hematology and Oncology, Graduate School of Health Sciences, Niigata University, Niigata, Japan
- Departments of Transfusion Medicine, Cell Therapy and Regenerative Medicine, Medical and Dental Hospital, Niigata University, Niigata, Japan
| | - Atsuko Honda
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Center for Research Promotion, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Yasuhiro Yoshimatsu
- Division of Pharmacology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Riuko Ohashi
- Divisions of Molecular and Diagnostic Pathology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Asami Kawasaki
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Kaori Cho
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
| | - Suguru Tamura
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
| | - Tatsuya Suwabe
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
| | - Takayuki Katagiri
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
| | - Yiwei Ling
- Division of Bioinformatics, Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Atsuhiko Iijima
- Neurophysiology & Biomedical Engineering Lab, Interdisciplinary Program of Biomedical Engineering, Assistive Technology and Art and Sports Sciences, Faculty of Engineering, Niigata University Niigata, Niigata, Japan
| | - Tadahisa Mikami
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, Japan
| | - Hiroshi Kitagawa
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, Japan
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kazunori Sango
- Diabetic Neuropathy Project, Department of Diseases and Infection, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masayoshi Masuko
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
- Hematopoietic Cell Transplantation Niigata University Medical and Dental Hospital, , Niigata University, Niigata, Japan
| | - Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hirohito Sone
- Departments of Hematology, Endocrinology, and Metabolism, Graduate School of Medical and Dental Sciences, Niigata university, Niigata, Japan
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20
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Li T, Wu Y, Yang J, Jing J, Ma C, Sun L. N6-methyladenosine-associated genetic variants in NECTIN2 and HPCAL1 are risk factors for abdominal aortic aneurysm. iScience 2024; 27:109419. [PMID: 38510151 PMCID: PMC10952030 DOI: 10.1016/j.isci.2024.109419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/07/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
Although N6-methyladenosine (m6A) modification has been implicated in the pathogenesis of abdominal aortic aneurysm (AAA), the relationship between m6A-associated single nucleotide polymorphisms (m6A-SNPs) and AAA remains unknown. This study used integrative multi-omics analysis and clinical validation approaches to systematically identify potential m6A-SNPs connected with AAA risk. We found that rs6859 and rs10198139 could modulate the expression of local genes, NECTIN2 and HPCAL1, respectively, which exhibited upregulation in AAA tissues, and their risk variants were significantly correlated with an increased susceptibility to AAA. Incorporating rs6859 and rs10198139 improved the efficiency of AAA risk prediction compared to the model considering only conventional risk factors. Additionally, these two SNPs were predicted to be located within the regulatory sequences, and rs6859 showed a substantial impact on m6A modification levels. Our findings suggest that m6A-SNPs rs6859 and rs10198139 confer an elevated risk of AAA, possibly by promoting local gene expression through an m6A-mediated manner.
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Affiliation(s)
- Tan Li
- Department of Cardiovascular Ultrasound, the First Hospital of China Medical University, Shenyang 110001, China
- Clinical Medical Research Center of Imaging in Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
| | - Yijun Wu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang 110001, China
| | - Jun Yang
- Department of Cardiovascular Ultrasound, the First Hospital of China Medical University, Shenyang 110001, China
- Clinical Medical Research Center of Imaging in Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang 110001, China
| | - Chunyan Ma
- Department of Cardiovascular Ultrasound, the First Hospital of China Medical University, Shenyang 110001, China
- Clinical Medical Research Center of Imaging in Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang 110001, China
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21
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Oh J, Kim DK, Ahn SH, Kim HM, Cho H. A dual role of the conserved PEX19 helix in safeguarding peroxisomal membrane proteins. iScience 2024; 27:109537. [PMID: 38585659 PMCID: PMC10995880 DOI: 10.1016/j.isci.2024.109537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Accurate localization of membrane proteins is essential for proper cellular functioning and the integrity of cellular membranes. Post-translational targeting of peroxisomal membrane proteins (PMPs) is mediated by the cytosolic chaperone PEX19 and its membrane receptor PEX3. However, the molecular mechanisms underlying PMP targeting are poorly understood. Here, using biochemical and mass spectrometry analysis, we find that a conserved PEX19 helix, αd, is critical to prevent improper exposure of the PEX26 transmembrane domain (TMD) to cytosolic chaperones. Furthermore, the αd helix of PEX19 interacts with the cytosolic domain of the PEX3 receptor, thereby triggering PEX26 release at the correct destination membrane. The peroxisome-deficient PEX3-G138E mutant completely abolishes this secondary interaction, leading to lack of PEX3-induced PEX26 release from PEX19. These findings elucidate a dual molecular mechanism that is essential to membrane protein protection and destination-specific release by a molecular chaperone.
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Affiliation(s)
- Jeonghyun Oh
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Do Kyung Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Seung Hae Ahn
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunju Cho
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
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22
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Morey R, Bui T, Cheung VC, Dong C, Zemke JE, Requena D, Arora H, Jackson MG, Pizzo D, Theunissen TW, Horii M. iPSC-based modeling of preeclampsia identifies epigenetic defects in extravillous trophoblast differentiation. iScience 2024; 27:109569. [PMID: 38623329 PMCID: PMC11016801 DOI: 10.1016/j.isci.2024.109569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Preeclampsia (PE) is a hypertensive pregnancy disorder with increased risk of maternal and fetal morbidity and mortality. Abnormal extravillous trophoblast (EVT) development and function is considered to be the underlying cause of PE, but has not been previously modeled in vitro. We previously derived induced pluripotent stem cells (iPSCs) from placentas of PE patients and characterized abnormalities in formation of syncytiotrophoblast and responses to changes in oxygen tension. In this study, we converted these primed iPSC to naïve iPSC, and then derived trophoblast stem cells (TSCs) and EVT to evaluate molecular mechanisms underlying PE. We found that primed (but not naïve) iPSC-derived PE-EVT have reduced surface HLA-G, blunted invasive capacity, and altered EVT-specific gene expression. These abnormalities correlated with promoter hypermethylation of genes associated with the epithelial-mesenchymal transition pathway, specifically in primed-iPSC derived PE-EVT. Our findings indicate that abnormal epigenetic regulation might play a role in PE pathogenesis.
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Affiliation(s)
- Robert Morey
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Tony Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Virginia Chu Cheung
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph E. Zemke
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniela Requena
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Harneet Arora
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeline G. Jackson
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
| | - Donald Pizzo
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Thorold W. Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mariko Horii
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Center for Perinatal Discovery, University of California San Diego, La Jolla, CA 92093, USA
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23
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Trinks J, Mascardi MF, Gadano A, Marciano S. Omics-based biomarkers as useful tools in metabolic dysfunction-associated steatotic liver disease clinical practice: How far are we? World J Gastroenterol 2024; 30:1982-1989. [DOI: 10.3748/wjg.v30.i14.1982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/19/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Unmet needs exist in metabolic dysfunction-associated steatotic liver disease (MASLD) risk stratification. Our ability to identify patients with MASLD with advanced fibrosis and at higher risk for adverse outcomes is still limited. Incorporating novel biomarkers could represent a meaningful improvement to current risk predictors. With this aim, omics technologies have revolutionized the process of MASLD biomarker discovery over the past decades. While the research in this field is thriving, much of the publication has been haphazard, often using single-omics data and specimen sets of convenience, with many identified candidate biomarkers but lacking clinical validation and utility. If we incorporate these biomarkers to direct patients’ management, it should be considered that the roadmap for translating a newly discovered omics-based signature to an actual, analytically valid test useful in MASLD clinical practice is rigorous and, therefore, not easily accomplished. This article presents an overview of this area’s current state, the conceivable opportunities and challenges of omics-based laboratory diagnostics, and a roadmap for improving MASLD biomarker research.
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Affiliation(s)
- Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica - Consejo Nacional de Investigaciones Científicas y Técnicas - Instituto Universitario del Hospital Italiano - Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199ACL, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - María F Mascardi
- Instituto de Medicina Traslacional e Ingeniería Biomédica - Consejo Nacional de Investigaciones Científicas y Técnicas - Instituto Universitario del Hospital Italiano - Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199ACL, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Adrián Gadano
- Liver Unit, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199DF, Argentina
- Department of Research, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199DF, Argentina
| | - Sebastián Marciano
- Instituto de Medicina Traslacional e Ingeniería Biomédica - Consejo Nacional de Investigaciones Científicas y Técnicas - Instituto Universitario del Hospital Italiano - Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199ACL, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Liver Unit, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199DF, Argentina
- Department of Research, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires C1199DF, Argentina
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24
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Mauceri A, Puccio G, Faddetta T, Abbate L, Polito G, Caldiero C, Renzone G, Lo Pinto M, Alibrandi P, Vaccaro E, Abenavoli MR, Scaloni A, Sunseri F, Cavalieri V, Palumbo Piccionello A, Gallo G, Mercati F. Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium. Plant Physiol Biochem 2024; 210:108609. [PMID: 38615442 DOI: 10.1016/j.plaphy.2024.108609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.
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Affiliation(s)
- Antonio Mauceri
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Guglielmo Puccio
- National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy; University of Palermo, SAAF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Teresa Faddetta
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Loredana Abbate
- National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Giulia Polito
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Ciro Caldiero
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Giovanni Renzone
- National Research Council, Proteomics, Metabolomics and Mass Spectrometry Laboratory (ISPAAM), Piazzale E. Fermi 1, 80055, Portici, (Napoli), Italy
| | - Margot Lo Pinto
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Pasquale Alibrandi
- Mugavero Teresa S.A.S., Corso Umberto e Margherita 1B, 90018, Termini Imerese, (Palermo), Italy
| | - Edoardo Vaccaro
- Mugavero Teresa S.A.S., Corso Umberto e Margherita 1B, 90018, Termini Imerese, (Palermo), Italy
| | - Maria Rosa Abenavoli
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Andrea Scaloni
- National Research Council, Proteomics, Metabolomics and Mass Spectrometry Laboratory (ISPAAM), Piazzale E. Fermi 1, 80055, Portici, (Napoli), Italy
| | - Francesco Sunseri
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Vincenzo Cavalieri
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | | | - Giuseppe Gallo
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
| | - Francesco Mercati
- National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy.
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25
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Qu R, Liu N, Wen Q, Guo J, Ge F. Molecular mechanism of dissolvable metal nanoparticles-enhanced CO 2 fixation by algae: Metal-chlorophyll synthesis. Environ Pollut 2024; 349:123987. [PMID: 38621453 DOI: 10.1016/j.envpol.2024.123987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/09/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024]
Abstract
Algae-driven photosynthetic CO2 fixation is a promising strategy to mitigate global climate changes and energy crises. Yet, the presence of metal nanoparticles (NPs), particularly dissolvable NPs, in aquatic ecosystems introduces new complexities due to their tendency to release metal ions that may perturb metabolic processes related to algal CO2 fixation. This study selected six representative metal NPs (Fe3O4, ZnO, CuO, NiO, MgO, and Ag) to investigate their impacts on CO2 fixation by algae (Chlorella vulgaris). We discovered an intriguing phenomenon that bivalent metal ions released from the metal NPs, especially from ZnO NPs, substituted Mg2+ within the porphyrin ring. This interaction led to 81.8% and 76.1% increases in Zinc-chlorophyll and Magnesium-chlorophyll contents within algal cells at 0.01 mM ZnO NPs, respectively. Integrating metabolomics and transcriptomics analyses revealed that ZnO NPs mainly promoted the photosynthesis-antenna protein pathway, porphyrin and chlorophyll metabolism, and carbon fixation pathway, thereby mitigating the adverse effects of Zn2+ substitution in light harvesting and energy transfer for CO2 fixation. Ultimately, the genes encoding Rubisco large subunit (rbcL) responsible for CO2 fixation were upregulated to 2.60-fold, resulting in a 76.3% increase in carbon fixation capacity. Similar upregulations of rbcL expression (1.13-fold) and carbon fixation capacity (76.1%) were observed in algal cells even at 0.001 mM ZnO NPs, accompanied by valuable lipid accumulation. This study offers novel insights into the molecular mechanism underlying NPs on CO2 fixation by algae and potentially introduces strategies for global carbon sequestration.
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Affiliation(s)
- Ruohua Qu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
| | - Na Liu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
| | - Qiong Wen
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
| | - Jingyi Guo
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
| | - Fei Ge
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of Environmental Eco-Health, Hunan, College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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26
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de Las Vecillas L, Quirce S. The Multiple Trajectories of the Allergic March. J Investig Allergol Clin Immunol 2024; 34:75-84. [PMID: 38113128 DOI: 10.18176/jiaci.0983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
The allergic march comprises the sequential appearance of a series of allergic comorbidities. However, variability in the onset and progression of allergic diseases generates a heterogeneous scenario that does not follow a linear and single trajectory. Almost half of the pediatric population presents at least 1 allergy symptom. However, only 4%-6% present multimorbidity, with several allergic diseases co-occurring. It has recently been shown that although they share etiological mechanisms and risk factors, allergic diseases arise independently. In most cases, progression is not consecutive, or at least not the same in all patients. TH2-mediated inflammation, epithelial barrier dysfunction, and genetic predisposition play a fundamental role in the etiology of allergic diseases, on which the interaction with the exposome acts decisively. Therefore, studying diseases from an omics point of view is essential when attempting to describe the various trajectories of allergic progression and to propose effective interventions to prevent multimorbidity. In this narrative review, we provide an overview of the current perception of the allergic march, including clinical observations, omics data, risk factors, and measures aimed at modifying its course or even preventing its onset.
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Affiliation(s)
- L de Las Vecillas
- Department of Allergy, La Paz University Hospital, Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - S Quirce
- Department of Allergy, La Paz University Hospital, Madrid, Spain
- IdiPAZ, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Spain
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27
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Roder T, Pimentel G, Fuchsmann P, Stern MT, von Ah U, Vergères G, Peischl S, Brynildsrud O, Bruggmann R, Bär C. Scoary2: rapid association of phenotypic multi- omics data with microbial pan-genomes. Genome Biol 2024; 25:93. [PMID: 38605417 PMCID: PMC11007987 DOI: 10.1186/s13059-024-03233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 03/29/2024] [Indexed: 04/13/2024] Open
Abstract
Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.
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Affiliation(s)
- Thomas Roder
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012, Bern, Switzerland
| | - Grégory Pimentel
- Methods development and analytics, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland
| | - Pascal Fuchsmann
- Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland
| | - Mireille Tena Stern
- Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland
| | - Ueli von Ah
- Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland
| | - Guy Vergères
- Food microbial systems, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, CH-3012, Switzerland
| | - Ola Brynildsrud
- Norwegian Institute of Public Health, Oslo and Norwegian University of Life Science, Ås, Norway
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, CH-3012, Switzerland.
| | - Cornelia Bär
- Methods development and analytics, Agroscope, Schwarzenburgstrasse 161, Bern, CH-3003, Switzerland
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Hassan S, Bhadwal SS, Khan M, Sabreena, Nissa KU, Shah RA, Bhat HM, Bhat SA, Lone IM, Ganai BA. Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches. Chemosphere 2024; 356:141889. [PMID: 38583533 DOI: 10.1016/j.chemosphere.2024.141889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Siloni Singh Bhadwal
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Misba Khan
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Sabreena
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Khair-Ul Nissa
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Rameez Ahmad Shah
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Haneef Mohammad Bhat
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Shabir Ahmad Bhat
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Ishfaq Maqbool Lone
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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Liu Z, Zhou Y, Wang H, Liu C, Wang L. Recent advances in understanding the fitness and survival mechanisms of Vibrio parahaemolyticus. Int J Food Microbiol 2024; 417:110691. [PMID: 38631283 DOI: 10.1016/j.ijfoodmicro.2024.110691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
The presence of Vibrio parahaemolyticus (Vp) in different production stages of seafood has generated negative impacts on both public health and the sustainability of the industry. To further better investigate the fitness of Vp at the phenotypical level, a great number of studies have been conducted in recent years using plate counting methods. In the meantime, with the increasing accessibility of the next generation sequencing and the advances in analytical chemistry techniques, omics-oriented biotechnologies have further advanced our knowledge in the survival and virulence mechanisms of Vp at various molecular levels. These observations provide insights to guide the development of novel prevention and control strategies and benefit the monitoring and mitigation of food safety risks associated with Vp contamination. To timely capture these recent advances, this review firstly summarizes the most recent phenotypical level studies and provide insights about the survival of Vp under important in vitro stresses and on aquatic products. After that, molecular survival mechanisms of Vp at transcriptomic and proteomic levels are summarized and discussed. Looking forward, other newer omics-biotechnology such as metabolomics and secretomics show great potential to be used for confirming the cellular responses of Vp. Powerful data mining tools from the field of machine learning and artificial intelligence, that can better utilize the omics data and solve complex problems in the processing, analysis, and interpretation of omics data, will further improve our mechanistic understanding of Vp.
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Affiliation(s)
- Zhuosheng Liu
- Department of Food Science and Technology, University of California Davis, Davis, CA 95618, USA
| | - Yi Zhou
- Department of Food Science and Technology, University of California Davis, Davis, CA 95618, USA
| | - Hongye Wang
- Department of Food Science and Technology, University of California Davis, Davis, CA 95618, USA
| | - Chengchu Liu
- University of Maryland Sea Grant Extension Program, UMES Center for Food Science and Technology, Princess Anne, MD, United States
| | - Luxin Wang
- Department of Food Science and Technology, University of California Davis, Davis, CA 95618, USA.
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Brennan PG, Mota L, Aridi T, Patel N, Liang P, Ferran C. Advancements in Omics and Breakthrough Gene Therapies: A Glimpse into the Future of Peripheral Artery Disease. Ann Vasc Surg 2024:S0890-5096(24)00156-0. [PMID: 38582204 DOI: 10.1016/j.avsg.2024.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 01/01/2024] [Indexed: 04/08/2024]
Abstract
Peripheral artery disease (PAD), a highly prevalent global disease, associates with significant morbidity and mortality in affected patients. Despite progress in endovascular and open revascularization techniques for advanced PAD, these interventions grapple with elevated rates of arterial restenosis and vein graft failure attributed to intimal hyperplasia (IH). Novel multi-omics technologies, coupled with sophisticated analyses tools recently powered by advances in artificial intelligence, have enabled the study of atherosclerosis and intimal hyperplasia with unprecedented single cell and spatial precision. Numerous studies have pinpointed gene hubs regulating pivotal atherogenic and atheroprotective signaling pathways as potential therapeutic candidates. Leveraging advancements in viral and non-viral gene therapy platforms, gene editing technologies, and cutting-edge biomaterial reservoirs for delivery uniquely positions us to develop safe, efficient, and targeted gene therapies for PAD-related diseases. Gene therapies appear particularly fitting for ex vivo genetic engineering of IH-resistant vein grafts. This manuscript highlights currently available state-of-the-art multi-omics approaches, explores promising gene therapy-based candidates, and details gene therapy delivery modalities employed by our laboratory and others to thwart mid-term vein graft failure caused by IH, as well as other PAD-related conditions. The potential clinical translation of these targeted gene therapies holds the promise to revolutionize PAD treatment, thereby enhancing patients' quality of life and life expectancy.
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Affiliation(s)
- Phillip G Brennan
- Division of Vascular and Endovascular Surgery, and Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lucas Mota
- Division of Vascular and Endovascular Surgery, and Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Tarek Aridi
- Division of Vascular and Endovascular Surgery, and Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Nyah Patel
- Division of Vascular and Endovascular Surgery, and Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Patric Liang
- Division of Vascular and Endovascular Surgery, and Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christiane Ferran
- Division of Vascular and Endovascular Surgery, and Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Division of Nephrology and the Transplant Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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31
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Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
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Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
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Prattichizzo F, Frigé C, Pellegrini V, Scisciola L, Santoro A, Monti D, Rippo MR, Ivanchenko M, Olivieri F, Franceschi C. Organ-specific biological clocks: Ageotyping for personalized anti-aging medicine. Ageing Res Rev 2024; 96:102253. [PMID: 38447609 DOI: 10.1016/j.arr.2024.102253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Aging is a complex multidimensional, progressive remodeling process affecting multiple organ systems. While many studies have focused on studying aging across multiple organs, assessment of the contribution of individual organs to overall aging processes is a cutting-edge issue. An organ's biological age might influence the aging of other organs, revealing a multiorgan aging network. Recent data demonstrated a similar yet asynchronous inter-organs and inter-individuals progression of aging, thereby providing a foundation to track sources of declining health in old age. The integration of multiple omics with common clinical parameters through artificial intelligence has allowed the building of organ-specific aging clocks, which can predict the development of specific age-related diseases at high resolution. The peculiar individual aging-trajectory, referred to as ageotype, might provide a novel tool for a personalized anti-aging, preventive medicine. Here, we review data relative to biological aging clocks and omics-based data, suggesting different organ-specific aging rates. Additional research on longitudinal data, including young subjects and analyzing sex-related differences, should be encouraged to apply ageotyping analysis for preventive purposes in clinical practice.
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Affiliation(s)
| | | | | | - Lucia Scisciola
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Aurelia Santoro
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Daniela Monti
- Department of Experimental and Clinical, Biomedical Sciences "Mario Serio" University of Florence, Florence, Italy
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, and Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy; Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy.
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, and Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia
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Abstract
Improving human healthspan in our rapidly aging population has never been more imperative. Telomeres, protective "caps" at the ends of linear chromosomes, are essential for maintaining genome stability of eukaryotic genomes. Due to their physical location and the "end-replication problem" first envisioned by Dr. Alexey Olovnikov, telomeres shorten with cell division, the implications of which are remarkably profound. Telomeres are hallmarks and molecular drivers of aging, as well as fundamental integrating components of the cumulative effects of genetic, lifestyle, and environmental factors that erode telomere length over time. Ongoing telomere attrition and the resulting limit to replicative potential imposed by cellular senescence serves a powerful tumor suppressor function, and also underlies aging and a spectrum of age-related degenerative pathologies, including reduced fertility, dementias, cardiovascular disease and cancer. However, very little data exists regarding the extraordinary stressors and exposures associated with long-duration space exploration and eventual habitation of other planets, nor how such missions will influence telomeres, reproduction, health, disease risk, and aging. Here, we briefly review our current understanding, which has advanced significantly in recent years as a result of the NASA Twins Study, the most comprehensive evaluation of human health effects associated with spaceflight ever conducted. Thus, the Twins Study is at the forefront of personalized space medicine approaches for astronauts and sets the stage for subsequent missions. We also extrapolate from current understanding to future missions, highlighting potential biological and biochemical strategies that may enable human survival, and consider the prospect of longevity in the extreme environment of space.
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Affiliation(s)
- Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Henry J Feng
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
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Ozerov MY, Noreikiene K, Kahar S, Flajšhans M, Gross R, Vasemägi A. Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis). Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110941. [PMID: 38218377 DOI: 10.1016/j.cbpb.2024.110941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.
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Affiliation(s)
- M Y Ozerov
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893 Drottningholm, Sweden; Biodiversity Unit, University of Turku, 20014 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland
| | - K Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia; Department of Botany and Genetics, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania. https://twitter.com/snaudale
| | - S Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - M Flajšhans
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, 38925 Vodňany, Czech Republic
| | - R Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - A Vasemägi
- Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, 17893 Drottningholm, Sweden; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia.
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Nguyen TV, Trang PN, Kumar A. Understanding PFAS toxicity through cell culture metabol omics: Current applications and future perspectives. Environ Int 2024; 186:108620. [PMID: 38579451 DOI: 10.1016/j.envint.2024.108620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/07/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS), ubiquitous environmental contaminants, pose significant challenges to ecosystems and human health. While cell cultures have emerged as new approach methodologies (NAMs) in ecotoxicity research, metabolomics is an emerging technique used to characterize the small-molecule metabolites present in cells and to understand their role in various biological processes. Integration of metabolomics with cell cultures, known as cell culture metabolomics, provides a novel and robust tool to unravel the complex molecular responses induced by PFAS exposure. In vitro testing also reduces reliance on animal testing, aligning with ethical and regulatory imperatives. The current review summarizes key findings from recent studies utilizing cell culture metabolomics to investigate PFAS toxicity, highlighting alterations in metabolic pathways, biomarker identification, and the potential linkages between metabolic perturbations. Additionally, the paper discusses different types of cell cultures and metabolomics methods used for studies of environmental contaminants and particularly PFAS. Future perspectives on the combination of metabolomics with other advanced technologies, such as single-cell metabolomics (SCM), imaging mass spectrometry (IMS), extracellular flux analysis (EFA), and multi-omics are also explored, which offers a holistic understanding of environmental contaminants. The synthesis of current knowledge and identification of research gaps provide a foundation for future investigations that aim to elucidate the complexities of PFAS-induced cellular responses and contribute to the development of effective strategies for mitigating their adverse effects on human health.
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Affiliation(s)
- Thao V Nguyen
- Environment, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Waite Campus, South Australia 5064, Australia; NTT Institute of High Technology, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 4, Ho Chi Minh City, Viet Nam.
| | - Phan Nguyen Trang
- Department of Food Technology, Institute of Food and Biotechnology, Can Tho University, Campus II, 3/2 Street, Ninh Kieu District, Can Tho, Viet Nam.
| | - Anu Kumar
- Environment, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Waite Campus, South Australia 5064, Australia.
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Mota VT, Delforno TP, Ribeiro JC, Zaiat M, Oliveira VMD. Understanding microbiome dynamics and functional responses during acidogenic fermentation of sucrose and sugarcane vinasse through metatranscriptomic analysis. Environ Res 2024; 246:118150. [PMID: 38218518 DOI: 10.1016/j.envres.2024.118150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/15/2024]
Abstract
Improving anaerobic digestion of sugarcane vinasse - a high-strength wastewater from ethanol distillation - is a subject of great interest, in view of the reduction of the pollutants and recovery of methane and valuable metabolites as byproducts. Through metatranscriptomic analysis, this study evaluated the active microbiome and metabolic pathways in a continuous acidogenic reactor: Stage 1S (control): 100% sucrose-based substrate (SBS); Stage 2SV (acclimation): 50% SBS and 50% vinasse; Stage 3V: 100% vinasse. Metatranscriptome obtained from each Stage was subjected to taxonomic and functional annotations. Under SBS feeding, pH dropped to pH 2.7 and biohydrogen production was observed. As vinasse was added, pH increased to 4.1-4.5, resulting in community structure and metabolite changes. In Stage 3V, biohydrogen production ceased, and propionate and acetate prevailed among the volatile fatty acids. Release of homoacetogenesis enzymes by Clostridium ljungdahlii and of uptake hydrogenase (EC 1.12.99.6) by Pectinatus frisingensis were linked to hydrogen consumption in Stages 2SV and 3V. Metabolic pathways of vinasse compounds, such as carbohydrates, malate, oxalate, glycerol, sulfate and phenol, were investigated in detail. In pyruvate metabolism, gene transcripts of oadA (oxaloacetate decarboxylase) and mdh (malate dehydrogenase), were upregulated in Stage 3V, being mostly attributed to P. frisingensis. Acetate formation from vinasse degradation was mainly attributed to Megasphaera and Clostridium, and propionate formation to P. frisingensis. Glycerol removal from vinasse exceeded 99%, and gene transcripts encoding for glpF (glycerol uptake facilitator protein), glpK (glycerol kinase) and glpABC (glycerol-3-phosphate dehydrogenase) were expressed mostly by Pectinatus and Prevotella. mRNA profiling showed that active bacteria and gene expression greatly changed when vinasse replaced sucrose, and Pectinatus was the main active bacterium degrading the searched compounds from vinasse. The identification of the main metabolic routes and the associated microorganisms achieved in this work contributes with valuable information to support further optimization of fermentation towards the desired metabolites.
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Affiliation(s)
- Vera T Mota
- Research Center for Chemistry, Biology and Agriculture Research, University of Campinas (CPQBA/Unicamp), Paulínia, SP, Brazil.
| | - Tiago P Delforno
- SENAI Innovation Institute for Biotechnology, São Paulo, SP, Brazil
| | - Jaqueline C Ribeiro
- Biological Processes Laboratory, São Carlos School of Engineering, University of São Paulo (LPB/EESC/USP), São Carlos, SP, Brazil
| | - Marcelo Zaiat
- Biological Processes Laboratory, São Carlos School of Engineering, University of São Paulo (LPB/EESC/USP), São Carlos, SP, Brazil
| | - Valéria M de Oliveira
- Research Center for Chemistry, Biology and Agriculture Research, University of Campinas (CPQBA/Unicamp), Paulínia, SP, Brazil
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Raab N, Zeh N, Kretz R, Weiß L, Stadermann A, Lindner B, Fischer S, Stoll D, Otte K. Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi- omics comparison with plasma cells. Metab Eng 2024; 83:110-122. [PMID: 38561148 DOI: 10.1016/j.ymben.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Especially for the production of artificial, difficult to express molecules a further development of the CHO production cell line is required to keep pace with the continuously increasing demands. However, the identification of novel targets for cell line engineering to improve CHO cells is a time and cost intensive process. Since plasma cells are evolutionary optimized for a high antibody expression in mammals, we performed a comprehensive multi-omics comparison between CHO and plasma cells to exploit optimized cellular production traits. Comparing the transcriptome, proteome, miRNome, surfaceome and secretome of both cell lines identified key differences including 392 potential overexpression targets for CHO cell engineering categorized in 15 functional classes like transcription factors, protein processing or secretory pathway. In addition, 3 protein classes including 209 potential knock-down/out targets for CHO engineering were determined likely to affect aggregation or proteolysis. For production phenotype engineering, several of these novel targets were successfully applied to transient and transposase mediated overexpression or knock-down strategies to efficiently improve productivity of CHO cells. Thus, substantial improvement of CHO productivity was achieved by taking nature as a blueprint for cell line engineering.
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Affiliation(s)
- Nadja Raab
- Biberach University of Applied Sciences, Germany.
| | - Nikolas Zeh
- Biberach University of Applied Sciences, Germany; Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Robin Kretz
- Hochschule Albstadt Sigmaringen, Germany; NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Linus Weiß
- Biberach University of Applied Sciences, Germany
| | - Anna Stadermann
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Benjamin Lindner
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Dieter Stoll
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Kerstin Otte
- Biberach University of Applied Sciences, Germany
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38
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Su G, Yu C, Liang S, Wang W, Wang H. Multi- omics in food safety and authenticity in terms of food components. Food Chem 2024; 437:137943. [PMID: 37948800 DOI: 10.1016/j.foodchem.2023.137943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
One of the main goals of food science is to ensure the high quality and safety of food. The inspection technology for known hazards has matured, and the identification of unknown and potential food safety hazards, as well as the identification of their composition and origin, is a challenge faced by food safety. Food safety and authenticity require multi-omics methods to support the implementation of qualitative discrimination to precise quantitative analysis, from targeted screening to non-target detection, and from multi component to full component analysis to address these challenges. The present review aims to provide characterizations, advantages, the latest progress, and prospects of using omics (including genomics, proteomics, and metabonomics) in food safety and authenticity. Multi omics strategies used to detect and verify different standard biomarkers of food will contribute to understanding the basic relationship between raw materials, processing, foods, nutrition, food safety, and human health.
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Affiliation(s)
- Guangyue Su
- Shenyang Pharmaceutical University, Shenyang 110016, PR China; School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, 110016, PR of China
| | - Chong Yu
- Shenyang Pharmaceutical University, Shenyang 110016, PR China; Department of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Shuwen Liang
- Shenyang Pharmaceutical University, Shenyang 110016, PR China; Department of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Wei Wang
- Shenyang Pharmaceutical University, Shenyang 110016, PR China; Department of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Haifeng Wang
- Shenyang Pharmaceutical University, Shenyang 110016, PR China; Department of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, PR China.
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39
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Kodali MC, Antone J, Alsop E, Jayakumar R, Parikh K, Chiot A, Sanchez-Molina P, Ajami B, Arnold SE, Jensen K, Das S, Weinberg MS. Cryopreservation of cerebrospinal fluid cells preserves the transcriptional landscape for single-cell analysis. J Neuroinflammation 2024; 21:71. [PMID: 38521932 PMCID: PMC10960996 DOI: 10.1186/s12974-024-03047-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/14/2024] [Indexed: 03/25/2024] Open
Abstract
Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approach to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.
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Affiliation(s)
- Mahesh Chandra Kodali
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Jerry Antone
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Eric Alsop
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Khushi Parikh
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Aude Chiot
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Paula Sanchez-Molina
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Bahareh Ajami
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Steven E Arnold
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kendall Jensen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Marc S Weinberg
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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40
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Schulte EC, Schulze TG. How do lipids fit into the picture of severe mental health disorders? A missing pathophysiologic link or just a consequence of behavior and treatment. Eur Neuropsychopharmacol 2024; 83:27-29. [PMID: 38518409 DOI: 10.1016/j.euroneuro.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/24/2024]
Affiliation(s)
- Eva C Schulte
- Department of Psychiatry and Psychotherapy, University Hospital, Faculty of Medicine, University of Bonn, Bonn, Germany; Institute of Human Genetics, University Hospital, Faculty of Medicine, University of Bonn, Bonn, Germany; Institute of Psychiatric Phenomics & Genomics, LMU University Hospital, LMU Munich, Munich, Germany.
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics & Genomics, LMU University Hospital, LMU Munich, Munich, Germany; Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, United States; German Center for Mental Health (DZPG), partner site Munich, Germany
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41
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Hsu HC, Hsu SP, Hsu FY, Chang M, Chen JA. LncRNA Litchi is a regulator for harmonizing maturity and resilient functionality in spinal motor neurons. iScience 2024; 27:109207. [PMID: 38433925 PMCID: PMC10906515 DOI: 10.1016/j.isci.2024.109207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/08/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play pivotal roles in modulating gene expression during development and disease. Despite their high expression in the central nervous system (CNS), understanding the precise physiological functions of CNS-associated lncRNAs has been challenging, largely due to the in vitro-centric nature of studies in this field. Here, utilizing mouse embryonic stem cell (ESC)-derived motor neurons (MNs), we identified an unexplored MN-specific lncRNA, Litchi (Long Intergenic RNAs in Chat Intron). By employing an "exon-only" deletion strategy in ESCs and a mouse model, we reveal that Litchi deletion profoundly impacts MN dendritic complexity, axonal growth, and altered action potential patterns. Mechanistically, voltage-gated channels and neurite growth-related genes exhibited heightened sensitivity to Litchi deletion. Our Litchi-knockout mouse model displayed compromised motor behaviors and reduced muscle strength, highlighting Litchi's critical role in motor function. This study unveils an underappreciated function of lncRNAs in orchestrating MN maturation and maintaining robust electrophysiological properties.
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Affiliation(s)
- Ho-Chiang Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Fang-Yu Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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42
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Wang D, Ling J, Tan R, Wang H, Qu Y, Li X, Lin J, Zhang Q, Hu Q, Liu Z, Lu Z, Lin Y, Sun L, Wang D, Zhou M, Shi Z, Gao W, Ye H, Lin X. CD169 + classical monocyte as an important participant in Graves' ophthalmopathy through CXCL12-CXCR4 axis. iScience 2024; 27:109213. [PMID: 38439953 PMCID: PMC10910260 DOI: 10.1016/j.isci.2024.109213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/11/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Patients with Graves' disease (GD) can develop Graves' ophthalmopathy (GO), but the underlying pathological mechanisms driving this development remain unclear. In our study, which included patients with GD and GO, we utilized single-cell RNA sequencing (scRNA-seq) and multiplatform analyses to investigate CD169+ classical monocytes, which secrete proinflammatory cytokines and are expanded through activated interferon signaling. We found that CD169+ clas_mono was clinically significant in predicting GO progression and prognosis, and differentiated into CD169+ macrophages that promote inflammation, adipogenesis, and fibrosis. Our murine model of early-stage GO showed that CD169+ classical monocytes accumulated in orbital tissue via the Cxcl12-Cxcr4 axis. Further studies are needed to investigate whether targeting circulating monocytes and the Cxcl12-Cxcr4 axis could alleviate GO progression.
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Affiliation(s)
- Dongliang Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jie Ling
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - RongQiang Tan
- The First People’s Hospital of Zhaoqing, Zhaoqing 526000, China
| | - Huishi Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yixin Qu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Xingyi Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jinshan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Qiuling Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhaojing Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Li Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Dingqiao Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Ming Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wuyou Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Huijing Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Xianchai Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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43
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Dong Q, Wu Y, Wang H, Li B, Huang R, Li H, Tao Q, Li Q, Tang X, Xu Q, Luo Y, Wang C. Integrated morphological, physiological and transcriptomic analyses reveal response mechanisms of rice under different cadmium exposure routes. J Hazard Mater 2024; 466:133688. [PMID: 38310845 DOI: 10.1016/j.jhazmat.2024.133688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
Rice (Oryza sativa) is one of the major cereal crops and takes up cadmium (Cd) more readily than other crops. Understanding the mechanism of Cd uptake and defense in rice can help us avoid Cd in the food chain. However, studies comparing Cd uptake, toxicity, and detoxification mechanisms of leaf and root Cd exposure at the morphological, physiological, and transcriptional levels are still lacking. Therefore, experiments were conducted in this study and found that root Cd exposure resulted in more severe oxidative and photosynthetic damage, lower plant biomass, higher Cd accumulation, and transcriptional changes in rice than leaf Cd exposure. The activation of phenylpropanoids biosynthesis in both root and leaf tissues under different Cd exposure routes suggests that increased lignin is the response mechanism of rice under Cd stress. Moreover, the roots of rice are more sensitive to Cd stress and their adaptation responses are more pronounced than those of leaves. Quantitative PCR revealed that OsPOX, OsCAD, OsPAL and OsCCR play important roles in the response to Cd stress, which further emphasize the importance of lignin. Therefore, this study provides theoretical evidence for future chemical and genetic regulation of lignin biosynthesis in crop plants to reduce Cd accumulation.
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Affiliation(s)
- Qin Dong
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yingjie Wu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Haidong Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Rong Huang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Xu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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44
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Ko KD, Sartorelli V. A deep learning adversarial autoencoder with dynamic batching displays high performance in denoising and ordering scRNA-seq data. iScience 2024; 27:109027. [PMID: 38361616 PMCID: PMC10867661 DOI: 10.1016/j.isci.2024.109027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/17/2024] Open
Abstract
By providing high-resolution of cell-to-cell variation in gene expression, single-cell RNA sequencing (scRNA-seq) offers insights into cell heterogeneity, differentiating dynamics, and disease mechanisms. However, challenges such as low capture rates and dropout events can introduce noise in data analysis. Here, we propose a deep neural generative framework, the dynamic batching adversarial autoencoder (DB-AAE), which excels at denoising scRNA-seq datasets. DB-AAE directly captures optimal features from input data and enhances feature preservation, including cell type-specific gene expression patterns. Comprehensive evaluation on simulated and real datasets demonstrates that DB-AAE outperforms other methods in denoising accuracy and biological signal preservation. It also improves the accuracy of other algorithms in establishing pseudo-time inference. This study highlights DB-AAE's effectiveness and potential as a valuable tool for enhancing the quality and reliability of downstream analyses in scRNA-seq research.
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Affiliation(s)
- Kyung Dae Ko
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
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45
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Xie M, Guo F, Song L, Tan W, Han X, Xu S, Li X, Wang Y, Wang Y, Zhou L, Zhou X, Jiang H, Yu L. Noninvasive neuromodulation protects against doxorubicin-induced cardiotoxicity and inhibits tumor growth. iScience 2024; 27:109163. [PMID: 38425841 PMCID: PMC10904274 DOI: 10.1016/j.isci.2024.109163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/14/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Doxorubicin (Dox) poses a considerable threat to patients owing to its cardiotoxicity, thus limiting its clinical utility. Optimal cardioprotective intervention strategies are needed to suppress tumor growth but also minimize cardiac side effects. Here, we showed that tragus vagus nerve stimulation (tVNS) improved the imbalanced autonomic tone, ameliorated impaired cardiac function and fibrosis, attenuated myocyte apoptosis, and mitochondrial dysfunction compared to those in the Dox group. The beneficial effects were attenuated by methyllycaconitine citrate (MLA). The transcript profile revealed that there were 312 differentially expressed genes and the protection of tVNS and retardation of MLA were related to inflammatory response and NADPH oxidase activity. In addition, tVNS synergizing with Dox inhibited tumor growth and lung metastasis and promoted apoptosis of tumor cells in an anti-tumor immunity manner. These results indicated that non-invasive neuromodulation can play a dual role in preventing Dox-induced cardiotoxicity and suppressing tumor growth through inflammation and oxidative stress.
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Affiliation(s)
- Mengjie Xie
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Fuding Guo
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Lingpeng Song
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Wuping Tan
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Xinrui Han
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Saiting Xu
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Xujun Li
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Yijun Wang
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Yueyi Wang
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Liping Zhou
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Xiaoya Zhou
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Hong Jiang
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
| | - Lilei Yu
- Department of Cardiology, Renmin Hospital of Wuhan University; Institute of Molecular Medicine, Renmin Hospital of Wuhan University; Hubei Key Laboratory of Autonomic Nervous System Modulation; Taikang Center for Life and Medical Sciences, Wuhan University; Cardiac Autonomic Nervous System Research Center of Wuhan University; Hubei Key Laboratory of Cardiology; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, P.R. China
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Fan Q, Wang H, Gu T, Liu H, Deng P, Li B, Yang H, Mao Y, Shao Z. Modeling the precise interaction of glioblastoma with human brain region-specific organoids. iScience 2024; 27:109111. [PMID: 38390494 PMCID: PMC10882168 DOI: 10.1016/j.isci.2024.109111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/18/2023] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
Glioblastoma is a highly aggressive malignant tumor of the central nervous system, but the interaction between glioblastoma and different types of neurons remains unclear. Here, we established a co-culture model in vitro using 3D printed molds with microchannels, in which glioblastoma organoids (GB), dorsal forebrain organoids (DO, mainly composed of excitatory neurons), and ventral forebrain organoids (VO, mainly composed of inhibitory neurons) were assembled. Our results indicate that DO has a greater impact on altered gene expression profiles of GB, resulting in increased invasive potential. GB cells preferentially invaded DO along axons, whereas this phenomenon was not observed in VO. Furthermore, GB cells selectively inhibited neurite outgrowth in DOs and reduced the expression of the vesicular GABA transporter (VGAT), leading to neuronal hyperexcitability. By revealing how glioblastoma interacts with brain cells, our study provides a more comprehensive understanding of this disease.
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Affiliation(s)
- Qi Fan
- Institutes for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
| | - Hanze Wang
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Tianyi Gu
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201203, China
| | - Huihui Liu
- Institutes for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
| | - Peng Deng
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Bo Li
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Hui Yang
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
- Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhicheng Shao
- Institutes for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
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47
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De Sousa Linhares A, Sharma S, Steinberger P, Leitner J. Transcriptional reprogramming via signaling domains of CD2, CD28, and 4-1BB. iScience 2024; 27:109267. [PMID: 38455974 PMCID: PMC10918215 DOI: 10.1016/j.isci.2024.109267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/23/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Costimulatory signals provided to T cells during antigen encounter have a decisive role in the outcome of immune responses. Here, we used chimeric receptors harboring the extracellular domain of mouse inducible T cell costimulator (mICOS) to study transcriptional activation mediated by cytoplasmic sequences of the major T cell costimulatory receptors CD28, 4-1BB, and CD2. The chimeric receptors were introduced in a T cell reporter platform that allows to simultaneously evaluate nuclear factor κB (NF-κB), NFAT, and AP-1 activation. Engagement of the chimeric receptors induced distinct transcriptional profiles. CD28 signaling activated all three transcription factors, whereas 4-1BB strongly promoted NF-κB and AP-1 but downregulated NFAT activity. CD2 signals resulted in the strongest upregulation of NFAT. Transcriptome analysis revealed pronounced and distinct gene expression signatures upon CD2 and 4-1BB signaling. Using the intracellular sequence of CD28, we exemplify that distinct signaling motifs endow chimeric receptors with different costimulatory capacities.
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Affiliation(s)
- Annika De Sousa Linhares
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
- Loop lab Bio GmbH, Vienna, Austria
| | - Sumana Sharma
- MRC Translational Immune Discovery Unit John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Peter Steinberger
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Judith Leitner
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
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48
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Anurag M, Strandgaard T, Kim SH, Dou Y, Comperat E, Al-Ahmadie H, Inman BA, Taber A, Nordentoft I, Jensen JB, Dyrskjøt L, Lerner SP. Multi omics profiling of urothelial carcinoma in situ reveals CIS-specific gene signature and immune characteristics. iScience 2024; 27:109179. [PMID: 38439961 PMCID: PMC10910238 DOI: 10.1016/j.isci.2024.109179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/20/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
Urothelial carcinoma in situ (CIS) is an aggressive phenotype of non-muscle-invasive bladder cancer. Molecular features unique to CIS compared to high-grade papillary tumors are underexplored. RNA sequencing of CIS, papillary tumors, and normal urothelium showed lower immune marker expression in CIS compared to papillary tumors. We identified a 46-gene expression signature in CIS samples including selectively upregulated known druggable targets MTOR, TYK2, AXIN1, CPT1B, GAK, and PIEZO1 and selectively downregulated BRD2 and NDUFB2. High expression of selected genes was significantly associated with CIS in an independent dataset. Mutation analysis of matched CIS and papillary tumors revealed shared mutations between samples across time points and mutational heterogeneity. CCDC138 was the most frequently mutated gene in CIS. The immunological landscape showed higher levels of PD-1-positive cells in CIS lesions compared to papillary tumors. We identified CIS lesions to have distinct characteristics compared to papillary tumors potentially contributing to the aggressive phenotype.
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Affiliation(s)
- Meenakshi Anurag
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center and Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Trine Strandgaard
- Department of Molecular Medicine Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Sung Han Kim
- Scott Department of Urology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Urology, Urological Cancer Center, National Cancer Center, Goayng, Gyeonggi, Rep. Korea
| | - Yongchao Dou
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center and Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Eva Comperat
- Department of Pathology, Medical University Vienna, Vienna General Hospital, 1090 Wien, Austria
| | - Hikmat Al-Ahmadie
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brant A. Inman
- Department of Urologic Oncology, Western University, London, ON, USA
| | - Ann Taber
- Department of Molecular Medicine Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Seth P. Lerner
- Scott Department of Urology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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49
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Albizzati E, Breccia M, Florio E, Cabasino C, Postogna FM, Grassi R, Boda E, Battaglia C, De Palma C, De Quattro C, Pozzi D, Landsberger N, Frasca A. Mecp2 knock-out astrocytes affect synaptogenesis by interleukin 6 dependent mechanisms. iScience 2024; 27:109296. [PMID: 38469559 PMCID: PMC10926209 DOI: 10.1016/j.isci.2024.109296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 09/09/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
Synaptic abnormalities are a hallmark of several neurological diseases, and clarification of the underlying mechanisms represents a crucial step toward the development of therapeutic strategies. Rett syndrome (RTT) is a rare neurodevelopmental disorder, mainly affecting females, caused by mutations in the X-linked methyl-CpG-binding protein 2 (MECP2) gene, leading to a deep derangement of synaptic connectivity. Although initial studies supported the exclusive involvement of neurons, recent data have highlighted the pivotal contribution of astrocytes in RTT pathogenesis through non-cell autonomous mechanisms. Since astrocytes regulate synapse formation and functionality by releasing multiple molecules, we investigated the influence of soluble factors secreted by Mecp2 knock-out (KO) astrocytes on synapses. We found that Mecp2 deficiency in astrocytes negatively affects their ability to support synaptogenesis by releasing synaptotoxic molecules. Notably, neuronal inputs from a dysfunctional astrocyte-neuron crosstalk lead KO astrocytes to aberrantly express IL-6, and blocking IL-6 activity prevents synaptic alterations.
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Affiliation(s)
- Elena Albizzati
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
| | - Martina Breccia
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
| | - Elena Florio
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Cecilia Cabasino
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
| | - Francesca Maddalena Postogna
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
| | - Riccardo Grassi
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Enrica Boda
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10126 Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Regione Gonzole 10, 10043 Orbassano, Turin, Italy
| | - Cristina Battaglia
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
| | - Clara De Palma
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
| | - Concetta De Quattro
- Department of Biotechnology, University of Verona, Cà Vignal 1, 37134 Verona, Italy
| | - Davide Pozzi
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Nicoletta Landsberger
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Angelisa Frasca
- Department of Medical Biotechnology and Translational Medicine, University of Milan, via F.lli Cervi 93, 20054 Segrate, Milan, Italy
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50
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Liou TG, Argel N, Asfour F, Brown PS, Chatfield BA, Cox DR, Daines CL, Durham D, Francis JA, Glover B, Helms M, Heynekamp T, Hoidal JR, Jensen JL, Kartsonaki C, Keogh R, Kopecky CM, Lechtzin N, Li Y, Lysinger J, Molina O, Nakamura C, Packer KA, Paine R, Poch KR, Quittner AL, Radford P, Redway AJ, Sagel SD, Szczesniak RD, Sprandel S, Taylor-Cousar JL, Vroom JB, Yoshikawa R, Clancy JP, Elborn JS, Olivier KN, Adler FR. Airway inflammation accelerates pulmonary exacerbations in cystic fibrosis. iScience 2024; 27:108835. [PMID: 38384849 PMCID: PMC10879674 DOI: 10.1016/j.isci.2024.108835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/02/2023] [Accepted: 01/03/2024] [Indexed: 02/23/2024] Open
Abstract
Airway inflammation underlies cystic fibrosis (CF) pulmonary exacerbations. In a prospective multicenter study of randomly selected, clinically stable adolescents and adults, we assessed relationships between 24 inflammation-associated molecules and the future occurrence of CF pulmonary exacerbation using proportional hazards models. We explored relationships for potential confounding or mediation by clinical factors and assessed sensitivities to treatments including CF transmembrane regulator (CFTR) protein synthesis modulators. Results from 114 participants, including seven on ivacaftor or lumacaftor-ivacaftor, representative of the US CF population during the study period, identified 10 biomarkers associated with future exacerbations mediated by percent predicted forced expiratory volume in 1 s. The findings were not sensitive to anti-inflammatory, antibiotic, and CFTR modulator treatments. The analyses suggest that combination treatments addressing RAGE-axis inflammation, protease-mediated injury, and oxidative stress might prevent pulmonary exacerbations. Our work may apply to other airway inflammatory diseases such as bronchiectasis and the acute respiratory distress syndrome.
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Affiliation(s)
- Theodore G Liou
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
- Primary Children's Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113, USA
| | - Natalia Argel
- Cystic Fibrosis Center, Phoenix Children's Hospital, 1919 East Thomas Road, Phoenix, AZ 85016, USA
| | - Fadi Asfour
- Primary Children's Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113, USA
| | - Perry S Brown
- St. Luke's Cystic Fibrosis Center of Idaho, 610 W. Hays Street, Boise, ID 83702, USA
| | - Barbara A Chatfield
- Primary Children's Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113, USA
| | - David R Cox
- Nuffield College, 1 New Rd, Oxford OX1 1NF, UK
| | - Cori L Daines
- Division of Pediatric Pulmonary and Sleep Medicine, Department of Pediatrics, University of Arizona Health Sciences, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, AZ 85724, USA
| | | | - Jessica A Francis
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Barbara Glover
- Cystic Fibrosis Center, 3006 S. Maryland Pkwy, Suite #315, Las Vegas, NV 89109, USA
| | - My Helms
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Theresa Heynekamp
- Adult Cystic Fibrosis Program, Division of Pulmonary, Critical Care and Sleep Medicine, DoIM MSC10-5550, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - John R Hoidal
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Judy L Jensen
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Christiana Kartsonaki
- Clinical Trial Service Unit & Epidemiological Studies Unit and Medical Research Council Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Ruth Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Carol M Kopecky
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado Anschutz Medical Campus, 13123 East 16th Avenue, Aurora, CO 80045, USA
| | - Noah Lechtzin
- Division of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Baltimore, MD 21205, USA
| | - Yanping Li
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Jerimiah Lysinger
- Montana Cystic Fibrosis Center, Billings Clinic, 2800 10th Avenue N, Billings, MT 59101, USA
| | - Osmara Molina
- Division of Pediatric Pulmonary and Sleep Medicine, Department of Pediatrics, University of Arizona Health Sciences, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, AZ 85724, USA
| | - Craig Nakamura
- Cystic Fibrosis Center, 3006 S. Maryland Pkwy, Suite #315, Las Vegas, NV 89109, USA
| | - Kristyn A Packer
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Robert Paine
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
| | - Katie R Poch
- Division of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA
| | | | - Peggy Radford
- Cystic Fibrosis Center, Phoenix Children's Hospital, 1919 East Thomas Road, Phoenix, AZ 85016, USA
| | - Abby J Redway
- Adult Cystic Fibrosis Program, Division of Pulmonary, Critical Care and Sleep Medicine, DoIM MSC10-5550, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado Anschutz Medical Campus, 13123 East 16th Avenue, Aurora, CO 80045, USA
| | - Rhonda D Szczesniak
- Division of Biostatistics & Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shawna Sprandel
- Montana Cystic Fibrosis Center, Billings Clinic, 2800 10th Avenue N, Billings, MT 59101, USA
| | - Jennifer L Taylor-Cousar
- Division of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA
- Division of Pulmonology, Department of Pediatrics, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Jane B Vroom
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132, USA
- Primary Children's Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113, USA
| | - Ryan Yoshikawa
- Cystic Fibrosis Center, 3006 S. Maryland Pkwy, Suite #315, Las Vegas, NV 89109, USA
| | - John P Clancy
- Former: Division of Pulmonary Medicine, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - J Stuart Elborn
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Health Sciences Building, Lisburn Rd, Belfast BT9 7AE, UK
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart Lung and Blood Institute, National Institutes of Health, 10 Center Drive MSC1454, Building 10-CRC, Room 1408A, Bethesda, MD 20892, USA
| | - Frederick R Adler
- Department of Mathematics, 155 South 1400 East, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, 257 South 1400 East, University of Utah, Salt Lake City, UT 84112, USA
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