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Campos TL, Korhonen PK, Young ND, Chang BC, Gasser RB. Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions. Comput Struct Biotechnol J 2024; 23:3081-3089. [PMID: 39185442 PMCID: PMC11342751 DOI: 10.1016/j.csbj.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/27/2024] Open
Abstract
Detailed explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have substantially improved our knowledge and understanding of biological processes and pathways in metazoan organisms. Extensive functional genomic and multi-omic data sets have enabled the discovery and characterisation of 'essential' genes that are critical for the survival of these organisms. Recently, we showed that a machine learning (ML)-based pipeline could be utilised to predict essential genes in both C. elegans and D. melanogaster using features from DNA, RNA, protein and/or cellular data or associated information. As these distantly-related species are within the Ecdysozoa, we hypothesised that this approach could be suited for non-model organisms within the same group (phylum) of protostome animals. In the present investigation, we cross-predicted essential genes within the phylum Nematoda - between C. elegans and the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus, and then ranked and prioritised these genes. Highly ranked genes were linked to key biological pathways or processes, such as ribosome biogenesis, translation and RNA processing, and were expressed at relatively high levels in the germline, gonad, hypodermis and/or nerves. The present in silico workflow is hoped to expedite the identification of drug targets in parasitic organisms for subsequent experimental validation in the laboratory.
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Affiliation(s)
- Túlio L. Campos
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
- Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fiocruz., Av. Professor Moraes Rego, s/n, Cidade Universitária, Recife, PE CEP 50740–465, Brazil
| | - Pasi K. Korhonen
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
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2
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Zhao Y, Zhou Z, Cui X, Yu Y, Yan P, Zhao W. Enhancing insight into ferroptosis mechanisms in sepsis: A genomic and pharmacological approach integrating single-cell sequencing and Mendelian randomization. Int Immunopharmacol 2024; 140:112910. [PMID: 39121604 DOI: 10.1016/j.intimp.2024.112910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
This research investigated the intricate relationship between ferroptosis and sepsis by utilizing advanced genomic and pharmacological methodologies. Specifically, we obtained expression quantitative trait loci (eQTLs) for 435 genes associated with ferroptosis from the eQTLGen Consortium and detected notable cis-eQTLs for 281 of these genes. Next, we conducted a detailed analysis to assess the impact of these eQTLs on susceptibility to sepsis using Mendelian randomization (MR) with data from a cohort of 10,154 sepsis patients and 452,764 controls sourced from the UK Biobank. MR analysis revealed 16 ferroptosis-related genes that exhibited significant associations with sepsis outcomes. To bolster the robustness of these findings, sensitivity analyses were performed to assess pleiotropy and heterogeneity, thus confirming the reliability of the causal inferences. Furthermore, single-cell RNA sequencing data from sepsis patients offered a detailed examination of gene expression profiles, demonstrating varying levels of ferroptosis marker expression across different cell types. Pathway enrichment analysis utilizing gene set enrichment analysis (GSEA) further revealed the key biological pathways involved in the progression of sepsis. Additionally, the use of computational molecular docking facilitated the prediction of interactions between identified genes and potential therapeutic compounds, highlighting novel drug targets. In conclusion, our integrated approach combining genomics and pharmacology offers valuable insights into the involvement of ferroptosis in sepsis, laying the groundwork for potential therapeutic strategies targeting this cell death pathway to enhance sepsis management.
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Affiliation(s)
- Yuanqi Zhao
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Zijian Zhou
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Xiuyu Cui
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Yiwei Yu
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Ping Yan
- Department of Gastroenterology, First Affiliated Hospital of Dali University, Dali, China.
| | - Weidong Zhao
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China; Department of Clinical Laboratory, Second Infectious Disease Hospital of Yunnan Province, Dali, China; Immunology Discipline Team, School of Basic Medicine, Dali University, Dali, China.
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Ye Q, Xie J, Xiao H, Wang J, Tian W, Wang W, Zhang J, Chang Y, Wang L, Yin D, Ding J, Han B. Effects of Selenium, Iron, and Zinc Enrichment on Cultured Sea Cucumber (Apostichopus Japonicus). Biol Trace Elem Res 2024:10.1007/s12011-024-04352-9. [PMID: 39340597 DOI: 10.1007/s12011-024-04352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/18/2024] [Indexed: 09/30/2024]
Abstract
Selenium, iron, and zinc (Se, Fe, Zn) are essential trace elements crucial for animal growth, development, and immune protection, but they can be detrimental in excess. This study evaluates the impacts of Se, Fe and Zn on Apostichopus japonicus over a period of nine days, utilizing concentrations ranging from low to high: Se (0.20 µmol/L and 0.82 µmol/L), Fe (4.74 µmol/L and 18.96 µmol/L), Zn (1.88 µmol/L and 7.51 µmol/L). Concentrations of these trace elements in sea cucumbers increased with exposure time. Activities of CAT, SOD, and GSH-PX enzymes were enhanced. Transcriptomic analyses of sea cucumber body wall revealed significant gene expression changes, with differentially expressed genes (DEGs) numbering 294 at high and 945 at low Se concentrations, 906 at high and 210 at low Fe concentrations, and 423 at high and 123 at low Zn concentrations. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses highlighted DEGs enrichment in critical metabolic and immune-related pathways, including DNA replication, arachidonic acid metabolism, and oxidative phosphorylation. These results suggest that energy metabolism and immune regulation are pivotal in managing these elements, potentially enhancing sea cucumber immunity. This study enhances our comprehension of the physiological responses of sea cucumbers to trace elements and provides a theoretical basis for their use in aquaculture.
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Affiliation(s)
- Qi Ye
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Jiahui Xie
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Haoran Xiao
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Junhui Wang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Wanrong Tian
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Wenpei Wang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Jinyuan Zhang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Yaqing Chang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Luo Wang
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Donghong Yin
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China
| | - Jun Ding
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China.
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China.
| | - Bing Han
- Liaoning Provincial Key Laboratory of Northern Aquatic Germplasm Resources and Genetics and Breeding, Dalian Ocean University, Dalian, 116023, Liaoning, PR China.
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, 52 Heishijiao Rd., Dalian, 116023, Liaoning, PR China.
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Tagnères S, Santo PE, Radermecker J, Rinaldi D, Froment C, Provost Q, Bongers M, Capeille S, Watkins N, Marcoux J, Gleizes PE, Marcel V, Plisson-Chastang C, Lebaron S. SURF2 is a MDM2 antagonist in triggering the nucleolar stress response. Nat Commun 2024; 15:8404. [PMID: 39333141 PMCID: PMC11436901 DOI: 10.1038/s41467-024-52659-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 09/16/2024] [Indexed: 09/29/2024] Open
Abstract
Cancer cells rely on high ribosome production to sustain their proliferation rate. Many chemotherapies impede ribosome production which is perceived by cells as "nucleolar stress" (NS), triggering p53-dependent and independent pathways leading to cell cycle arrest and/or apoptosis. The 5S ribonucleoprotein (RNP) particle, a sub-ribosomal particle, is instrumental to NS response. Upon ribosome assembly defects, the 5S RNP accumulates as free form. This free form is able to sequester and inhibit MDM2, thus promoting p53 stabilization. To investigate how cancer cells can resist to NS, here we purify free 5S RNP and uncover an interaction partner, SURF2. Functional characterization of SURF2 shows that its depletion increases cellular sensitivity to NS, while its overexpression promotes their resistance to it. Consistently, SURF2 is overexpressed in many cancers and its expression level is an independent marker of prognosis for adrenocortical cancer. Our data demonstrate that SURF2 buffers free 5S RNP particles, and can modulate their activity, paving the way for the research of new molecules that can finely tune the response to nucleolar stress in the framework of cancer therapies.
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Affiliation(s)
- Sophie Tagnères
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Paulo Espirito Santo
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Julie Radermecker
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Dana Rinaldi
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Carine Froment
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
- Infrastructure Nationale de Protéomique, ProFI, Toulouse, France
| | - Quentin Provost
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Manon Bongers
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Solemne Capeille
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Nick Watkins
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UPS), Toulouse, France
- Infrastructure Nationale de Protéomique, ProFI, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Virginie Marcel
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Célia Plisson-Chastang
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), Team with an accreditation from the French "Ligue contre le Cancer" organism., University of Toulouse, CNRS, UPS, 118 route de Narbonne, Toulouse, Cedex, France.
- Institut national de la santé et de la recherche médicale (INSERM), Paris, France.
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Samanta P, Ghosh R, Pakhira S, Mondal M, Biswas S, Sarkar R, Bhowmik A, Saha P, Hajra S. Ribosome biogenesis and ribosomal proteins in cancer stem cells: a new therapeutic prospect. Mol Biol Rep 2024; 51:1016. [PMID: 39325314 DOI: 10.1007/s11033-024-09963-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 09/20/2024] [Indexed: 09/27/2024]
Abstract
Ribosome has been considered as the fundamental macromolecular machine involved in protein synthesis in both prokaryotic and eukaryotic cells. This protein synthesis machinery consists of several rRNAs and numerous proteins. All of these factors are synthesized, translocated and assembled in a tightly regulated process known as ribosome biogenesis. Any impairment in this process causes development of several diseases like cancer. According to growing evidences, cancer cells display alteration of several ribosomal proteins. Besides, most of them are considered as key molecules involved in ribosome biogenesis, suggesting a correlation between those proteins and formation of ribosomes. Albeit, defective ribosome biogenesis in several cancers has gained prime importance, regulation of this process in cancer stem cells (CSCs) are still unrecognized. In this article, we aim to summarize the alteration of ribosome biogenesis and ribosomal proteins in CSCs. Moreover, we want to highlight the relation of ribosome biogenesis with hypoxia and drug resistance in CSCs based on the existing evidences. Lastly, this review wants to pay attention about the promising anti-cancer drugs which have potential to inhibit ribosome biogenesis in cancer cells as well as CSCs.
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Affiliation(s)
- Priya Samanta
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Rituparna Ghosh
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Shampa Pakhira
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Mrinmoyee Mondal
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Souradeep Biswas
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Rupali Sarkar
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Arijit Bhowmik
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Prosenjit Saha
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India
| | - Subhadip Hajra
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute (CNCI), 37, S.P. Mukherjee Road, Kolkata, West Bengal, 700026, India.
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Saleem W, Carpentier N, Hinnekens C, Oh D, Van Vlierberghe S, Braeckmans K, Nauwynck H. Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus. Vet Res 2024; 55:113. [PMID: 39304917 DOI: 10.1186/s13567-024-01374-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/27/2024] [Indexed: 09/22/2024] Open
Abstract
Transmissible gastroenteritis virus (TGEV) causes high mortality in young piglets (< 3 days of age). With aging, the susceptibility/morbidity/mortality rates drop. We previously hypothesized that the age-related changes in the intestinal mucus could be responsible for this resistance. Hence, this study investigated the effect of porcine intestinal mucus from 3-day and 3-week-old pigs on the free mobility of the virulent TGEV Miller strain, and on the infection in swine testicle (ST) cells. Single particle tracking (SPT) revealed that TGEV had significantly higher diffusion coefficients in 3-day mucus compared to 3-week mucus. TGEV and charged and uncharged control nanoparticles diffused freely in 3-day mucus but were hindered by 3-week mucus in the diffusion model; TGEV mimicked the diffusion behavior of negatively charged carboxylated particles. Inoculation of ST cells with TGEV in the presence of 3-week mucus resulted in a significantly lower average number of infected cells (30.9 ± 11.9/5 fields) compared with 3-day mucus (84.6 ± 16.4/5 fields). These results show that 3-week mucus has a significant TGEV-blocking activity compared to 3-day mucus in free diffusion and infection of the underlying susceptible cells. Additionally, a label-free proteomics analysis revealed an increased expression of mucin 13, known for negatively regulating the tight junctions in intestinal epithelium, in 3-day-old pigs. In 3-week-old pigs, a higher expression of mucin 2, a type of secreted mucin which is known for inhibiting coronavirus infection, was observed. Concludingly, this study demonstrated a protective effect of 3-week mucus against viral infections.
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Affiliation(s)
- Waqar Saleem
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
| | - Nathan Carpentier
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Charlotte Hinnekens
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dayoung Oh
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Sandra Van Vlierberghe
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Hans Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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Xiong C, Ling H, Huang Y, Dong H, Xie B, Hao Q, Zhou X. AZD1775 synergizes with SLC7A11 inhibition to promote ferroptosis. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2589-1. [PMID: 39245684 DOI: 10.1007/s11427-023-2589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/11/2024] [Indexed: 09/10/2024]
Abstract
Tumor suppressor p53-mediated cell cycle arrest and DNA damage repair may exert cytoprotective effects against cancer therapies, including WEE1 inhibition. Considering that p53 activation can also lead to multiple types of cell death, the role of this tumor suppressor in WEE1 inhibitor-based therapies remains disputed. In this study, we reported that nucleolar stress-mediated p53 activation enhanced the WEE1 inhibitor AZD1775-induced ferroptosis to suppress lung cancer growth. Our findings showed that AZD1775 promoted ferroptosis by blocking cystine uptake, an action similar to that of Erastin. Meanwhile, inhibition of WEE1 by the WEE1 inhibitors or siRNAs induced compensatory upregulation of SLC7A11, which conferred resistance to ferroptosis. Mechanistically, AZD1775 prevented the enrichment of H3K9me3, a histone marker of transcriptional repression, on the SLC7A11 promoter by repressing the expression of the histone methyltransferase SETDB1, thereby enhancing NRF2-mediated SLC7A11 transcription. This finding was also validated using the H3K9me3 inhibitor BRD4770. Remarkably, we found that the nucleolar stress-inducing agent Actinomycin D (Act. D) inhibited SLC7A11 expression by activating p53, thus augmenting AZD1775-induced ferroptosis. Moreover, the combination of AZD1775 and Act. D synergistically suppressed wild-type p53-harboring lung cancer cell growth both in vitro and in vivo. Altogether, our study demonstrates that AZD1775 promotes ferroptosis by targeting cystine uptake but also mediates the adaptive activation of SLC7A11 through the WEE1-SETDB1 cascade and NRF2-induced transcription, and inhibition of SLC7A11 by Act. D boosts the anti-tumor efficacy of AZD1775 by enhancing ferroptosis in cancers with wild-type p53.
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Affiliation(s)
- Chen Xiong
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hong Ling
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Yingdan Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hanzhi Dong
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Bangxiang Xie
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
- Beijing Engineering Research Center for Precision Medicine and Transformation of Hepatitis and Liver Cancer, Beijing, 100069, China
| | - Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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8
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Fuentes P, Pelletier J, Gentilella A. Decoding ribosome complexity: role of ribosomal proteins in cancer and disease. NAR Cancer 2024; 6:zcae032. [PMID: 39045153 PMCID: PMC11263879 DOI: 10.1093/narcan/zcae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/31/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024] Open
Abstract
The ribosome is a remarkably complex machinery, at the interface with diverse cellular functions and processes. Evolutionarily conserved, yet intricately regulated, ribosomes play pivotal roles in decoding genetic information into the synthesis of proteins and in the generation of biomass critical for cellular physiological functions. Recent insights have revealed the existence of ribosome heterogeneity at multiple levels. Such heterogeneity extends to cancer, where aberrant ribosome biogenesis and function contribute to oncogenesis. This led to the emergence of the concept of 'onco-ribosomes', specific ribosomal variants with altered structural dynamics, contributing to cancer initiation and progression. Ribosomal proteins (RPs) are involved in many of these alterations, acting as critical factors for the translational reprogramming of cancer cells. In this review article, we highlight the roles of RPs in ribosome biogenesis, how mutations in RPs and their paralogues reshape the translational landscape, driving clonal evolution and therapeutic resistance. Furthermore, we present recent evidence providing new insights into post-translational modifications of RPs, such as ubiquitylation, UFMylation and phosphorylation, and how they regulate ribosome recycling, translational fidelity and cellular stress responses. Understanding the intricate interplay between ribosome complexity, heterogeneity and RP-mediated regulatory mechanisms in pathology offers profound insights into cancer biology and unveils novel therapeutic avenues targeting the translational machinery in cancer.
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Affiliation(s)
- Pedro Fuentes
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llpbregat, Barcelona, Spain
| | - Joffrey Pelletier
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llpbregat, Barcelona, Spain
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08908, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Gentilella
- Laboratory of Cancer Metabolism, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908, L'Hospitalet de Llpbregat, Barcelona, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, 08028, Barcelona, Spain
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9
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Abdollahi M, Castaño JD, Salem JB, Beaudry F. Anandamide Modulates Thermal Avoidance in Caenorhabditis elegans Through Vanilloid and Cannabinoid Receptor Interplay. Neurochem Res 2024; 49:2423-2439. [PMID: 38847909 DOI: 10.1007/s11064-024-04186-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 08/09/2024]
Abstract
Understanding the endocannabinoid system in C. elegans may offer insights into basic biological processes and potential therapeutic targets for managing pain and inflammation in human. It is well established that anandamide modulates pain perception by binding to cannabinoid and vanilloid receptors, regulating neurotransmitter release and neuronal activity. One objective of this study was to demonstrate the suitability of C. elegans as a model organism for assessing the antinociceptive properties of bioactive compounds and learning about the role of endocannabinoid system in C. elegans. The evaluation of the compound anandamide (AEA) revealed antinociceptive activity by impeding C. elegans nocifensive response to noxious heat. Proteomic and bioinformatic investigations uncovered several pathways activated by AEA. Enrichment analysis unveiled significant involvement of ion homeostasis pathways, which are crucial for maintaining neuronal function and synaptic transmission, suggesting AEA's impact on neurotransmitter release and synaptic plasticity. Additionally, pathways related to translation, protein synthesis, and mTORC1 signaling were enriched, highlighting potential mechanisms underlying AEA's antinociceptive effects. Thermal proteome profiling identified NPR-32 and NPR-19 as primary targets of AEA, along with OCR-2, Cathepsin B, Progranulin, Transthyretin, and ribosomal proteins. These findings suggest a complex interplay between AEA and various cellular processes implicated in nociceptive pathways and inflammation modulation. Further investigation into these interactions could provide valuable insights into the therapeutic potential of AEA and its targets for the management of pain-related conditions.
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Affiliation(s)
- Marzieh Abdollahi
- Canada Research Chair in Metrology of Bioactive Molecules and Target Discovery, Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
- Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, Québec, Canada
| | - Jesus D Castaño
- Canada Research Chair in Metrology of Bioactive Molecules and Target Discovery, Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
- Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, Québec, Canada
| | - Jennifer Ben Salem
- Canada Research Chair in Metrology of Bioactive Molecules and Target Discovery, Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada
- Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, Québec, Canada
| | - Francis Beaudry
- Canada Research Chair in Metrology of Bioactive Molecules and Target Discovery, Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, Saint-Hyacinthe, Québec, J2S 2M2, Canada.
- Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, Québec, Canada.
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10
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Huang YA, Wang X, Kim JC, Yao X, Sethi A, Strohm A, Doherty TA. PIP-seq identifies novel heterogeneous lung innate lymphocyte population activation after combustion product exposure. Sci Rep 2024; 14:20167. [PMID: 39215111 PMCID: PMC11364781 DOI: 10.1038/s41598-024-70880-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Innate lymphoid cells (ILCs) are a heterogeneous population that play diverse roles in airway inflammation after exposure to allergens and infections. However, how ILCs respond after exposure to environmental toxins is not well understood. Here we show a novel method for studying the heterogeneity of rare lung ILC populations by magnetic enrichment for lung ILCs followed by particle-templated instant partition sequencing (PIP-seq). Using this method, we were able to identify novel group 1 and group 2 ILC subsets that exist after exposure to both fungal allergen and burn pit-related constituents (BPC) that include dioxin, aromatic hydrocarbon, and particulate matter. Toxin exposure in combination with fungal allergen induced activation of specific ILC1/NK and ILC2 populations as well as promoted neutrophilic lung inflammation. Oxidative stress pathways and downregulation of specific ribosomal protein genes (Rpl41 and Rps19) implicated in anti-inflammatory responses were present after BPC exposure. Increased IFNγ expression and other pro-neutrophilic mediator transcripts were increased in BPC-stimulated lung innate lymphoid cells. Further, the addition of BPC induced Hspa8 (encodes HSC70) and aryl hydrocarbon transcription factor activity across multiple lung ILC subsets. Overall, using an airway disease model that develops after occupational and environmental exposures, we demonstrate an effective method to better understand heterogenous ILC subset activation.
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Affiliation(s)
- Yung-An Huang
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Xinyu Wang
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Jong-Chan Kim
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Xiang Yao
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Anshika Sethi
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Allyssa Strohm
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Taylor A Doherty
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA.
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA.
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Zhan S, Zhang L, Zhong T, Wang L, Guo J, Cao J, Li L, Zhang H. Evaluation of Reference Gene Stability in Goat Skeletal Muscle Satellite Cells during Proliferation and Differentiation Phases. Animals (Basel) 2024; 14:2479. [PMID: 39272264 PMCID: PMC11394193 DOI: 10.3390/ani14172479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
The process of skeletal muscle development is intricate and involves the regulation of a diverse array of genes. Accurate gene expression profiles are crucial for studying muscle development, making it essential to choose the right reference genes for real-time quantitative PCR (RT-qPCR). In the present study, eight candidate reference genes were identified from our previous transcriptome sequencing analysis of caprine skeletal muscle satellite cells (MuSCs), and two traditional reference genes (ACTB and GAPDH) were assessed. The quantitative levels of the candidate reference genes were determined through the RT-qPCR technique, while the stability of their expression was evaluated utilizing the GeNorm, NormFinder, BestKeeper, and RefFinder programs. Furthermore, the chosen reference genes were utilized for the normalization of the gene expression levels of PCNA and Myf5. It was determined that conventional reference genes, including ACTB and GAPDH, were not appropriate for normalizing target gene expression. Conversely, RPL14 and RPS15A, identified through RNA sequencing analysis, exhibited minimal variability and were identified as the optimal reference genes for normalizing gene expression during the proliferation and differentiation of goat MuSCs. Our research offers a validated panel of optimal reference genes for the detection of differentially expressed genes in goat muscle satellite cells using RT-qPCR.
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Affiliation(s)
- Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lufei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Tian Y, Liu X, Wang J, Zhang C, Yang W. Antitumor Effects and the Potential Mechanism of 10-HDA against SU-DHL-2 Cells. Pharmaceuticals (Basel) 2024; 17:1088. [PMID: 39204193 PMCID: PMC11357620 DOI: 10.3390/ph17081088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
10-hydroxy-2-decenoic acid (10-HDA), which is a unique bioactive fatty acid of royal jelly synthesized by nurse bees for larvae and adult queen bees, is recognized for its dual utility in medicinal and nutritional applications. Previous research has indicated that 10-HDA exerts antitumor effects on numerous tumor cell lines, including colon cancer cells, A549 human lung cancer cells, and human hepatoma cells. The present study extends this inquiry to lymphoma, specifically evaluating the impact of 10-HDA on the SU-DHL-2 cell line. Our findings revealed dose-dependent suppression of SU-DHL-2 cell survival, with an IC50 of 496.8 μg/mL at a density of 3 × 106 cells/well after 24 h. For normal liver LO2 cells and human fibroblasts (HSFs), the IC50 values were approximately 1000 μg/mL and over 1000 μg/mL, respectively. The results of label-free proteomics revealed 147 upregulated and 347 downregulated differentially expressed proteins that were significantly enriched in the complement and coagulation cascades pathway (adjusted p-value = 0.012), including the differentially expressed proteins prothrombin, plasminogen, plasminogen, carboxypeptidase B2, fibrinogen beta chain, fibrinogen gamma chain, and coagulation factor V. The top three hub proteins, ribosomal protein L5, tumor protein p53, and ribosomal protein L24, were identified via protein-protein interaction (PPI) analysis. This result showed that the complement and coagulation cascade pathways might play a key role in the antitumor process of 10-HDA, suggesting a potential therapeutic avenue for lymphoma treatment. However, the specificity of the effect of 10-HDA on SU-DHL-2 cells warrants further investigation.
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Affiliation(s)
- Yuanyuan Tian
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
- College of JunCao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoqing Liu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
| | - Jie Wang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
| | - Chuang Zhang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
| | - Wenchao Yang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
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13
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Khan MP, Sabini E, Beigel K, Lanzolla G, Laslow B, Wang D, Merceron C, Giaccia A, Long F, Taylor D, Schipani E. HIF1 activation safeguards cortical bone formation against impaired oxidative phosphorylation. JCI Insight 2024; 9:e182330. [PMID: 39088272 DOI: 10.1172/jci.insight.182330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024] Open
Abstract
Energy metabolism, through pathways such as oxidative phosphorylation (OxPhos) and glycolysis, plays a pivotal role in cellular differentiation and function. Our study investigates the impact of OxPhos disruption in cortical bone development by deleting mitochondrial transcription factor A (TFAM). TFAM controls OxPhos by regulating the transcription of mitochondrial genes. The cortical bone, constituting the long bones' rigid shell, is sheathed by the periosteum, a connective tissue layer populated with skeletal progenitors that spawn osteoblasts, the bone-forming cells. TFAM-deficient mice presented with thinner cortical bone, spontaneous midshaft fractures, and compromised periosteal cell bioenergetics, characterized by reduced ATP levels. Additionally, they exhibited an enlarged periosteal progenitor cell pool with impaired osteoblast differentiation. Increasing hypoxia-inducible factor 1a (HIF1) activity within periosteal cells substantially mitigated the detrimental effects induced by TFAM deletion. HIF1 is known to promote glycolysis in all cell types. Our findings underscore the indispensability of OxPhos for the proper accrual of cortical bone mass and indicate a compensatory mechanism between OxPhos and glycolysis in periosteal cells. The study opens new avenues for understanding the relationship between energy metabolism and skeletal health and suggests that modulating bioenergetic pathways may provide a therapeutic avenue for conditions characterized by bone fragility.
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Affiliation(s)
- Mohd P Khan
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elena Sabini
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Katherine Beigel
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Giulia Lanzolla
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Brittany Laslow
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dian Wang
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Christophe Merceron
- Department of Orthopaedic Surgery, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Amato Giaccia
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Fanxin Long
- Department of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ernestina Schipani
- Department of Orthopaedic Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
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14
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Fadaie M, Khalafiyan A, Ghafouri E, Ranjbarnejad T, Moein S. A Systems Biology Approach to the Pathogenesis of Celiac Disease: Identification of Potential Protective and Promoting Mechanisms. Adv Biomed Res 2024; 13:42. [PMID: 39224401 PMCID: PMC11368239 DOI: 10.4103/abr.abr_229_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/01/2024] [Accepted: 01/20/2024] [Indexed: 09/04/2024] Open
Abstract
Background Celiac disease (CeD) is an autoimmune enteropathy triggered by dietary gluten. Almost 90% of CeD patients have HLA-DQ2 or -DQ8 haplotypes. As a high proportion of first-degree relatives (FDRs) of CeD patients have the same haplotype, it is assumed that they are at a higher risk of disease development than the general population. Nevertheless, the prevalence of CeD among FDRs is considerably low (7.5%). Materials and Methods In order to figure out this discrepancy, a microarray dataset of intestinal mucosal biopsies of CeD patients, FDRs, and control groups was reanalyzed, and a protein-protein interaction network was constructed. Results Principal component analysis showed that CeD and FDR groups are far away in terms of gene expression. Comparing differentially expressed genes of both networks demonstrated inverse expression of some genes mainly related to cell cycle mechanisms. Moreover, analysis of the modular structures of up- and downregulated gene networks determined activation of protein degradation mechanisms and inhibition of ribosome-related protein synthesis in celiac patients with an upside-down pattern in FDRs. Conclusions The top-down systems biology approach determined some regulatory pathways with inverse function in CeD and FDR groups. These genes and molecular mechanisms could be a matter of investigation as potential druggable targets or prognostic markers in CeD.
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Affiliation(s)
- Mahmood Fadaie
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Ghafouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shiva Moein
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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15
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Du M, Liu Y, Cao J, Li X, Wang N, He Q, Zhang L, Zhao B, Dugarjaviin M. Food from Equids-Commercial Fermented Mare's Milk (Koumiss) Products: Protective Effects against Alcohol Intoxication. Foods 2024; 13:2344. [PMID: 39123538 PMCID: PMC11312395 DOI: 10.3390/foods13152344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Fermented mare's milk (koumiss), a traditional Central Asian dairy product derived from fermented mare's milk, is renowned for its unique sour taste and texture. It has long been consumed by nomadic tribes for its nutritional and medicinal benefits. This study aimed to comprehensively analyze the protective effects of koumiss against alcohol-induced harm across behavioral, hematological, gastrointestinal, hepatic, and reproductive dimensions using a mouse model. Optimal intoxicating doses of alcohol and koumiss doses were determined, and their effects were explored through sleep tests and blood indicator measurements. Pretreatment with koumiss delayed inebriation, accelerated sobering, and reduced mortality in mice, mitigating alcohol's impact on blood ethanol levels and various physiological parameters. Histopathological and molecular analyses further confirmed koumiss's protective role against alcohol-induced damage in the liver, stomach, small intestine, and reproductive system. Transcriptomic studies on reproductive damage indicated that koumiss exerts its benefits by influencing mitochondrial and ribosomal functions and also shows promise in mitigating alcohol's effects on the reproductive system. In summary, koumiss emerges as a potential natural agent for protection against alcohol-induced harm, opening avenues for future research in this field.
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Affiliation(s)
- Ming Du
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuanyi Liu
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jialong Cao
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xinyu Li
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Na Wang
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qianqian He
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lei Zhang
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bilig Zhao
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Manglai Dugarjaviin
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
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Fu M, Qiao Z, Zhou S, Han Y, Ling S, Peng C, Zhang W, Wu J. Five coexisting brominated flame retardants in a water-sediment-Vallisneria system: Bioaccumulation and effects on oxidative stress and photosynthesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173230. [PMID: 38750745 DOI: 10.1016/j.scitotenv.2024.173230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/18/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
The pollution of various brominated flame retardants (BFRs) is concurrence, while their environmental fate and toxicology in water-sediment-submerged plant systems remain unclear. In this study, Vallisneria natans plants were co-exposed to 2,3,4,5,6-pentabromotoluene (PBT), hexabromobenzene (HBB), 1,2-bis (2,4,6-tribromophenoxy) ethane (BTBPE), decabromodiphenyl ether (BDE209), and decabromodiphenyl ethane (DBDPE). The ∑BFRs concentration in the root was 2.15 times higher than that in the shoot. Vallisneria natans accumulated more BTBPE and HBB in 0.2, 1, and 5 mg/kg treatments, while they accumulated more DBDPE and BDE209 in 25 and 50 mg/kg treatments. The bioaccumulation factors in the shoot and root were 1.08-96.95 and 0.04-0.70, respectively. BFRs in sediments had a more pronounced effect on bioaccumulation levels than BFRs in water, and biotranslocation was another potential influence factor. The SOD activity, POD activity, and MDA content were significantly increased under co-exposure. The DBDPE separate exposure impacted the metabolism of substances and energy, inhibited mismatch repair, and disrupted ribosomal functions in Vallisneria natans. However, DBDPE enhanced their photosynthesis by upregulating the expression level of genes related to the light reaction. This study provides a broader understanding of the bioaccumulation and toxicity of BFRs in submerged plants, shedding light on the scientific management of products containing BFRs.
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Affiliation(s)
- Mengru Fu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhihua Qiao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shanqi Zhou
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanna Han
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siyuan Ling
- Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Cheng Peng
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Zhang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Jinhong Wu
- Shanghai Yaxin Urban Construction Co., Ltd., Shanghai 200436, China.
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17
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Costa GCA, Silva FAA, Torquato RJS, Silva Vaz I, Parizi LF, Tanaka AS. Evaluation of the biological function of ribosomal protein S18 from cattle tick Rhipicephalus microplus. Ticks Tick Borne Dis 2024; 15:102333. [PMID: 38522220 DOI: 10.1016/j.ttbdis.2024.102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 03/02/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
Rhipicephalus (Boophilus) microplus, also known as the cattle tick, causes severe parasitism and transmits different pathogens to vertebrate hosts, leading to massive economic losses. In the present study, we performed a functional characterization of a ribosomal protein from R. microplus to investigate its importance in blood feeding, egg production and viability. Ribosomal protein S18 (RPS18) is part of the 40S subunit, associated with 18S rRNA, and has been previously pointed to have a secondary role in different organisms. Rhipicephalus microplus RPS18 (RmRPS18) gene expression levels were modulated in female salivary glands during blood feeding. Moreover, mRNA levels in this tissue were 10 times higher than those in the midgut of fully engorged female ticks. Additionally, recombinant RmRPS18 was recognized by IgG antibodies from sera of cattle naturally or experimentally infested with ticks. RNAi-mediated knockdown of the RmRPS18 gene was performed in fully engorged females, leading to a significant (29 %) decrease in egg production. Additionally, egg hatching was completely impaired, suggesting that no viable eggs were produced by the RmRPS18-silenced group. Furthermore, antimicrobial assays revealed inhibitory activities against gram-negative Escherichia coli and gram-positive Staphylococcus aureus bacteria, affecting bacterial growth. Data presented here show the important role of RmRPS18 in tick physiology and suggest that RmRPS18 can be a potential target for the development of novel strategies for tick control.
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Affiliation(s)
- Gabriel C A Costa
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade de Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Fernando A A Silva
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade de Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Ricardo J S Torquato
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade de Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Itabajara Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), RJ, Brazil
| | - Luís F Parizi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil; Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil
| | - Aparecida S Tanaka
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade de Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), RJ, Brazil.
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18
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Etzel L, Apsley AT, Hastings WJ, Ye Q, Shalev I. Early life adversity is associated with differential gene expression in immune cells: A cluster-based analysis across an acute psychosocial stressor. Brain Behav Immun 2024; 119:724-733. [PMID: 38663776 PMCID: PMC11190835 DOI: 10.1016/j.bbi.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/19/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Elucidating mechanisms by which early-life adversity (ELA) contributes to increased disease risk is important for mitigating adverse health outcomes. Prior work has found differences in immune cell gene expression related to inflammation and mitochondrial activity. Using a within-person between-group experimental design, we investigated differences in gene expression clusters across acute psychosocial stress and no-stress conditions. Participants were young adults (N = 29, aged 18 - 25 years, 62 % female, 47 % with a history of ELA). Gene expression was assessed in peripheral blood mononuclear cells collected at 8 blood draws spanning two 5-hour sessions (stress vs. no-stress) separated by a week, 4 across each session (number of observations = 221). We applied two unsupervised gene clustering methods - latent profile analysis (LPA) and weighted gene co-expression analysis (WGCNA) - to cluster genes with similar expression patterns across participants. LPA identified 11 clusters, 7 of which were significantly associated with ELA-status. WGCNA identified 5 clusters, 3 of which were significantly associated with ELA-status. LPA- and WGCNA-identified clusters were correlated, and all clusters were highly preserved across sessions and time. There was no significant effect of acute stress on cluster gene expression, but there was a significant effect of time, and significant differences by ELA-status. ELA-associated clusters related to RNA splicing/processing, inflammation, leukocyte differentiation and division, and mitochondrial activity were differentially expressed across time: ELA-exposed individuals showed decreased expression of these clusters at 90-minutes while controls showed increased expression. Our findings replicate previous work in this area and highlight additional mechanisms by which ELA may contribute to disease risk.
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Affiliation(s)
- Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Waylon J Hastings
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA; Department of Psychiatry and Behavioral Science, Tulane University School of Medicine, New Orleans, LA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA.
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19
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Huang YA, Wang X, Kim JC, Yao X, Sethi A, Strohm A, Doherty TA. PIP-Seq identifies novel heterogeneous lung innate lymphocyte population activation after combustion product exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600420. [PMID: 38979234 PMCID: PMC11230265 DOI: 10.1101/2024.06.24.600420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Innate lymphoid cells (ILCs) are a heterogeneous population that play diverse roles in airway inflammation after exposure to allergens and infections. However, how ILCs respond after exposure to environmental toxins is not well understood. Here we show a novel method for studying the heterogeneity of rare lung ILC populations by magnetic enrichment for lung ILCs followed by particle-templated instant partition sequencing (PIP-seq). Using this method, we were able to identify novel group 1 and group 2 ILC subsets that exist after exposure to both fungal allergen and burn pit-related constituents (BPC) that include dioxin, aromatic hydrocarbon, and particulate matter. Toxin exposure in combination with fungal allergen induced activation of specific ILC1/NK and ILC2 populations as well as promoted neutrophilic lung inflammation. Oxidative stress pathways and downregulation of specific ribosomal protein genes ( Rpl41 and Rps19 ) implicated in anti-inflammatory responses were present after BPC exposure. Increased IFNγ expression and other pro-neutrophilic mediator transcripts were increased in BPC-stimulated lung innate lymphoid cells. Further, the addition of BPC induced Hspa8 (encodes HSC70) and aryl hydrocarbon transcription factor activity across multiple lung ILC subsets. Overall, using an airway disease model that develops after occupational and environmental exposures, we demonstrate an effective method to better understand heterogenous ILC subset activation.
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20
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Campos TL, Korhonen PK, Young ND, Wang T, Song J, Marhoefer R, Chang BCH, Selzer PM, Gasser RB. Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning. Int J Mol Sci 2024; 25:7015. [PMID: 39000124 PMCID: PMC11240989 DOI: 10.3390/ijms25137015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Over the years, comprehensive explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have contributed substantially to our understanding of complex biological processes and pathways in multicellular organisms generally. Extensive functional genomic-phenomic, genomic, transcriptomic, and proteomic data sets have enabled the discovery and characterisation of genes that are crucial for life, called 'essential genes'. Recently, we investigated the feasibility of inferring essential genes from such data sets using advanced bioinformatics and showed that a machine learning (ML)-based workflow could be used to extract or engineer features from DNA, RNA, protein, and/or cellular data/information to underpin the reliable prediction of essential genes both within and between C. elegans and D. melanogaster. As these are two distantly related species within the Ecdysozoa, we proposed that this ML approach would be particularly well suited for species that are within the same phylum or evolutionary clade. In the present study, we cross-predicted essential genes within the phylum Nematoda (evolutionary clade V)-between C. elegans and the pathogenic parasitic nematode H. contortus-and then ranked and prioritised H. contortus proteins encoded by these genes as intervention (e.g., drug) target candidates. Using strong, validated predictors, we inferred essential genes of H. contortus that are involved predominantly in crucial biological processes/pathways including ribosome biogenesis, translation, RNA binding/processing, and signalling and which are highly transcribed in the germline, somatic gonad precursors, sex myoblasts, vulva cell precursors, various nerve cells, glia, or hypodermis. The findings indicate that this in silico workflow provides a promising avenue to identify and prioritise panels/groups of drug target candidates in parasitic nematodes for experimental validation in vitro and/or in vivo.
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Affiliation(s)
- Túlio L Campos
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Core Facility, Aggeu Magalhães Institute (Fiocruz), Recife 50740-465, PE, Brazil
| | - Pasi K Korhonen
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tao Wang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, VIC 3800, Australia
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Clayton, VIC 3800, Australia
| | - Richard Marhoefer
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim am Rhein, Germany
| | - Bill C H Chang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul M Selzer
- Boehringer Ingelheim Animal Health, Binger Strasse 173, 55216 Ingelheim am Rhein, Germany
| | - Robin B Gasser
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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21
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Brignola C, Pecoraro A, Danisi C, Iaccarino N, Di Porzio A, Romano F, Carotenuto P, Russo G, Russo A. uL3 Regulates Redox Metabolism and Ferroptosis Sensitivity of p53-Deleted Colorectal Cancer Cells. Antioxidants (Basel) 2024; 13:757. [PMID: 39061826 PMCID: PMC11274089 DOI: 10.3390/antiox13070757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Despite advancements in therapeutic strategies, the development of drug resistance and metastasis remains a serious concern for the efficacy of chemotherapy against colorectal cancer (CRC). We have previously demonstrated that low expression of ribosomal protein uL3 positively correlates with chemoresistance in CRC patients. Here, we demonstrated that the loss of uL3 increased the metastatic capacity of CRC cells in chick embryos. Metabolomic analysis revealed large perturbations in amino acid and glutathione metabolism in resistant uL3-silenced CRC cells, indicating that uL3 silencing dramatically triggered redox metabolic reprogramming. RNA-Seq data revealed a notable dysregulation of 108 genes related to ferroptosis in CRC patients. Solute Carrier Family 7 Member 11 (SLC7A11) is one of the most dysregulated genes; its mRNA stability is negatively regulated by uL3, and its expression is inversely correlated with uL3 levels. Inhibition of SLC7A11 with erastin impaired resistant uL3-silenced CRC cell survival by inducing ferroptosis. Of interest, the combined treatment erastin plus uL3 enhanced the chemotherapeutic sensitivity of uL3-silenced CRC cells to erastin. The antimetastatic potential of the combined strategy was evaluated in chick embryos. Overall, our study sheds light on uL3-mediated chemoresistance and provides evidence of a novel therapeutic approach, erastin plus uL3, to induce ferroptosis, establishing individualized therapy by examining p53, uL3 and SLC7A11 profiles in tumors.
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Affiliation(s)
- Chiara Brignola
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Annalisa Pecoraro
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Camilla Danisi
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Francesca Romano
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Pietro Carotenuto
- TIGEM, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Naples, Italy;
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, Corso Umberto I, 40, 80138 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Annapina Russo
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
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22
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Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
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Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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23
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Li A, Xie J, Lv L, Zheng Z, Yang W, Zhuo W, Yang S, Cai D, Duan J, Liu P, Min J, Wei J. RPL9 acts as an oncogene by shuttling miRNAs through exosomes in human hepatocellular carcinoma cells. Int J Oncol 2024; 64:58. [PMID: 38639179 PMCID: PMC11087036 DOI: 10.3892/ijo.2024.5646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/05/2024] [Indexed: 04/20/2024] Open
Abstract
The exosomal pathway is an essential mechanism that regulates the abnormal content of microRNAs (miRNAs) in hepatocellular carcinoma (HCC). The directional transport of miRNAs requires the assistance of RNA‑binding proteins (RBPs). The present study found that RBPs participate in the regulation of miRNA content through the exosomal pathway in HCC cells. First, differential protein expression profiles in the serum exosomes of patients with HCC and benign liver disease were detected using mass spectrometry. The results revealed that ribosomal protein L9 (RPL9) was highly expressed in serum exosomes of patients with HCC. In addition, the downregulation of RPL9 markedly suppressed the proliferation, migration and invasion of HCC cells and reduced the biological activity of HCC‑derived exosomes. In addition, using miRNA microarrays, the changes in exosomal miRNA profiles in HCC cells caused by RPL9 knockdown were examined. miR‑24‑3p and miR‑185‑5p were most differentially expressed, as verified by reverse transcription‑quantitative PCR. Additionally, using RNA immunoprecipitation, it was found that RPL9 was directly bound to the two miRNAs and immunofluorescence assays confirmed that RPL9 was able to carry miRNAs into recipient cells via exosomes. Overexpression of miR‑24‑3p in cells increased the accumulation of miR‑24‑3p in exosomes and simultaneously upregulated RPL9. Excessive expression of miR‑24‑3p in exosomes also increased their bioactivity. Exosome‑mediated miRNA regulation and transfer require the involvement of RBPs. RPL9 functions as an oncogene, can directly bind to specific miRNAs and can be co‑transported to receptor cells through exosomes, thereby exerting its biological functions. These findings provide a novel approach for modulating miRNA profiles in HCC.
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Affiliation(s)
- Ang Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation and Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jiyan Xie
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036
| | - Lihong Lv
- Clinical Trial Institution of Pharmaceuticals and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Zhihua Zheng
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Weibang Yang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260
| | - Wenfeng Zhuo
- Department of Hepatobiliary Surgery, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong 528406, P.R. China
| | - Sijia Yang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Diankui Cai
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jinxin Duan
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Peiqing Liu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jun Min
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
| | - Jinxing Wei
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120
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24
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Jordan-Ward R, von Hippel FA, Sancho Santos ME, Wilson CA, Rodriguez Maldonado Z, Dillon D, Titus T, Gardell A, Salamova A, Postlethwait JH, Contreras E, Capozzi SL, Panuwet P, Parrocha C, Bremiller R, Guiguen Y, Gologergen J, Immingan T, Miller P, Carpenter D, Buck CL. Transcriptomic and developmental effects of persistent organic pollutants in sentinel fishes collected near an arctic formerly used defense site. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124283. [PMID: 38823546 DOI: 10.1016/j.envpol.2024.124283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Alaska contains over 600 formerly used defense (FUD) sites, many of which serve as point sources of pollution. These sites are often co-located with rural communities that depend upon traditional subsistence foods, especially lipid-rich animals that bioaccumulate and biomagnify persistent organic pollutants (POPs). Many POPs are carcinogenic and endocrine-disrupting compounds that are associated with adverse health outcomes. Therefore, elevated exposure to POPs from point sources of pollution may contribute to disproportionate incidence of disease in arctic communities. We investigated PCB concentrations and the health implications of POP exposure in sentinel fishes collected near the Northeast Cape FUD site on Sivuqaq (St. Lawrence Island), Alaska. Sivuqaq residents are almost exclusively Yupik and rely on subsistence foods. At the request of the Sivuqaq community, we examined differential gene expression and developmental pathologies associated with exposure to POPs originating at the Northeast Cape FUD site. We found significantly higher levels of PCBs in Alaska blackfish (Dallia pectoralis) collected from contaminated sites downstream of the FUD site compared to fish collected from upstream reference sites. We compared transcriptomic profiles and histopathologies of these same blackfish. Blackfish from contaminated sites overexpressed genes involved in ribosomal and FoxO signaling pathways compared to blackfish from reference sites. Contaminated blackfish also had significantly fewer thyroid follicles and smaller pigmented macrophage aggregates. Conversely, we found that ninespine stickleback (Pungitius pungitius) from contaminated sites exhibited thyroid follicle hyperplasia. Despite our previous research reporting transcriptomic and endocrine differences in stickleback from contaminated vs. reference sites, we did not find significant differences in kidney or gonadal histomorphologies. Our results demonstrate that contaminants from the Northeast Cape FUD site are associated with altered gene expression and thyroid development in native fishes. These results are consistent with our prior work demonstrating disruption of the thyroid hormone axis in Sivuqaq residents.
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Affiliation(s)
- Renee Jordan-Ward
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ, 86011, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave., P.O. Box 245210, Tucson, AZ, 85724, USA.
| | | | - Catherine A Wilson
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Zyled Rodriguez Maldonado
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ, 86011, USA
| | - Danielle Dillon
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ, 86011, USA
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Alison Gardell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA, 98402, USA
| | - Amina Salamova
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - John H Postlethwait
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Elise Contreras
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ, 86011, USA
| | - Staci L Capozzi
- O'Neill School of Public and Environmental Affairs, Indiana University, Bloomington, IN, 47405, USA
| | - Parinya Panuwet
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Chelsea Parrocha
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Ruth Bremiller
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR, 97403, USA
| | | | - Jesse Gologergen
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK, 99518, USA
| | - Tiffany Immingan
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK, 99518, USA
| | - Pamela Miller
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK, 99518, USA
| | - David Carpenter
- Institute for Health and the Environment, University at Albany, 5 University Place, Rensselaer, NY, 12144, USA
| | - C Loren Buck
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ, 86011, USA
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25
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Izadifar Z, Cotton J, Chen S, Horvath V, Stejskalova A, Gulati A, LoGrande NT, Budnik B, Shahriar S, Doherty ER, Xie Y, To T, Gilpin SE, Sesay AM, Goyal G, Lebrilla CB, Ingber DE. Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips. Nat Commun 2024; 15:4578. [PMID: 38811586 PMCID: PMC11137093 DOI: 10.1038/s41467-024-48910-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 03/22/2024] [Indexed: 05/31/2024] Open
Abstract
Modulation of the cervix by steroid hormones and commensal microbiome play a central role in the health of the female reproductive tract. Here we describe organ-on-a-chip (Organ Chip) models that recreate the human cervical epithelial-stromal interface with a functional epithelial barrier and production of mucus with biochemical and hormone-responsive properties similar to living cervix. When Cervix Chips are populated with optimal healthy versus dysbiotic microbial communities (dominated by Lactobacillus crispatus and Gardnerella vaginalis, respectively), significant differences in tissue innate immune responses, barrier function, cell viability, proteome, and mucus composition are observed that are similar to those seen in vivo. Thus, human Cervix Organ Chips represent physiologically relevant in vitro models to study cervix physiology and host-microbiome interactions, and hence may be used as a preclinical testbed for development of therapeutic interventions to enhance women's health.
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Affiliation(s)
- Zohreh Izadifar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
- Urology Department, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Justin Cotton
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Siyu Chen
- Department of Chemistry, University of California Davis, Davis, California, Davis, CA, 95616, USA
| | - Viktor Horvath
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Anna Stejskalova
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Aakanksha Gulati
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Nina T LoGrande
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Bogdan Budnik
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Sanjid Shahriar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Erin R Doherty
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Yixuan Xie
- Department of Chemistry, University of California Davis, Davis, California, Davis, CA, 95616, USA
| | - Tania To
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Sarah E Gilpin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Adama M Sesay
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Girija Goyal
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California, Davis, CA, 95616, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA.
- Vascular Biology Program, Boston Children's Hospital and Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, 02134, USA.
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26
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Cannon AS, Holloman BL, Wilson K, Miranda K, Nagarkatti PS, Nagarkatti M. 6-Formylindolo[3,2-b]carbazole, a potent ligand for the aryl hydrocarbon receptor, attenuates concanavalin-induced hepatitis by limiting T-cell activation and infiltration of proinflammatory CD11b+ Kupffer cells. J Leukoc Biol 2024; 115:1070-1083. [PMID: 38366630 PMCID: PMC11135611 DOI: 10.1093/jleuko/qiae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024] Open
Abstract
FICZ (6-formylindolo[3,2-b]carbazole) is a potent aryl hydrocarbon receptor agonist that has a poorly understood function in the regulation of inflammation. In this study, we investigated the effect of aryl hydrocarbon receptor activation by FICZ in a murine model of autoimmune hepatitis induced by concanavalin A. High-throughput sequencing techniques such as single-cell RNA sequencing and assay for transposase accessible chromatin sequencing were used to explore the mechanisms through which FICZ induces its effects. FICZ treatment attenuated concanavalin A-induced hepatitis, evidenced by decreased T-cell infiltration, decreased circulating alanine transaminase levels, and suppression of proinflammatory cytokines. Concanavalin A revealed an increase in natural killer T cells, T cells, and mature B cells upon concanavalin A injection while FICZ treatment reversed the presence of these subsets. Surprisingly, concanavalin A depleted a subset of CD55+ B cells, while FICZ partially protected this subset. The immune cells showed significant dysregulation in the gene expression profiles, including diverse expression of migratory markers such as CCL4, CCL5, and CXCL2 and critical regulatory markers such as Junb. Assay for transposase accessible chromatin sequencing showed more accessible chromatin in the CD3e promoter in the concanavalin A-only group as compared to the naive and concanavalin A-exposed, FICZ-treated group. While there was overall more accessible chromatin of the Adgre1 (F4/80) promoter in the FICZ-treated group, we observed less open chromatin in the Itgam (CD11b) promoter in Kupffer cells, supporting the ability of FICZ to reduce the infiltration of proinflammatory cytokine producing CD11b+ Kupffer cells. Taken together, these data demonstrate that aryl hydrocarbon receptor activation by FICZ suppresses liver injury through the limitation of CD3+ T-cell activation and CD11b+ Kupffer cell infiltration.
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Affiliation(s)
- Alkeiver S Cannon
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, 6439 Garners Ferry Road, Columbia, SC 29209, United States
| | - Bryan L Holloman
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, 6439 Garners Ferry Road, Columbia, SC 29209, United States
| | - Kiesha Wilson
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, 6439 Garners Ferry Road, Columbia, SC 29209, United States
| | - Kathryn Miranda
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, 6439 Garners Ferry Road, Columbia, SC 29209, United States
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, 6439 Garners Ferry Road, Columbia, SC 29209, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, 6439 Garners Ferry Road, Columbia, SC 29209, United States
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27
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Borges FS, Quilles JC, Lorenzon LB, Espada CR, Freitas-Castro F, Defina TPA, Holetz FB, Cruz AK. Leishmania Ribosomal Protein (RP) paralogous genes compensate each other's expression maintaining protein native levels. PLoS One 2024; 19:e0292152. [PMID: 38753846 PMCID: PMC11098316 DOI: 10.1371/journal.pone.0292152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
In the protozoan parasite Leishmania, most genes encoding for ribosomal proteins (RPs) are present as two or more copies in the genome. However, their untranslated regions (UTRs) are predominantly divergent and might be associated with a distinct regulation of the expression of paralogous genes. Herein, we investigated the expression profiles of two RPs (S16 and L13a) encoded by duplicated genes in Leishmania major. The genes encoding for the S16 protein possess identical coding sequences (CDSs) and divergent UTRs, whereas the CDSs of L13a diverge by two amino acids and by their UTRs. Using CRISPR/Cas9 genome editing, we generated knockout (Δ) and endogenously tagged transfectants for each paralog of L13a and S16 genes. Combining tagged and Δ cell lines we found evidence of differential expression of both RPS16 and RPL13a isoforms throughout parasite development, with one isoform consistently more abundant than its respective copy. In addition, compensatory expression was observed for each paralog upon deletion of the corresponding isoform, suggesting functional conservation between these proteins. This differential expression pattern relates to post-translational processes, given compensation occurs at the level of the protein, with no alterations detected at transcript level. Ribosomal profiles for RPL13a indicate a standard behavior for these paralogues suggestive of interaction with heavy RNA-protein complexes, as already reported for other RPs in trypanosomatids. We identified paralog-specific bound to their 3'UTRs which may be influential in regulating paralog expression. In support, we identified conserved cis-elements within the 3'UTRs of RPS16 and RPL13a; cis-elements exclusive to the UTR of the more abundant paralog or to the less abundant ones were identified.
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Affiliation(s)
- Francisca S. Borges
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - José C. Quilles
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Lucas B. Lorenzon
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Caroline R. Espada
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Felipe Freitas-Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Tânia P. A. Defina
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Fabíola B. Holetz
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
| | - Angela K. Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
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28
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LeDoux MS. Polymerase I as a Target for Treating Neurodegenerative Disorders. Biomedicines 2024; 12:1092. [PMID: 38791054 PMCID: PMC11118182 DOI: 10.3390/biomedicines12051092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Polymerase I (Pol I) is at the epicenter of ribosomal RNA (rRNA) synthesis. Pol I is a target for the treatment of cancer. Given the many cellular commonalities between cancer and neurodegeneration (i.e., different faces of the same coin), it seems rational to consider targeting Pol I or, more generally, rRNA synthesis for the treatment of disorders associated with the death of terminally differentiated neurons. Principally, ribosomes synthesize proteins, and, accordingly, Pol I can be considered the starting point for protein synthesis. Given that cellular accumulation of abnormal proteins such as α-synuclein and tau is an essential feature of neurodegenerative disorders such as Parkinson disease and fronto-temporal dementia, reduction of protein production is now considered a viable target for treatment of these and closely related neurodegenerative disorders. Abnormalities in polymerase I activity and rRNA production may also be associated with nuclear and nucleolar stress, DNA damage, and childhood-onset neuronal death, as is the case for the UBTF E210K neuroregression syndrome. Moreover, restraining the activity of Pol I may be a viable strategy to slow aging. Before starting down the road of Pol I inhibition for treating non-cancerous disorders of the nervous system, many questions must be answered. First, how much Pol I inhibition can neurons tolerate, and for how long? Should inhibition of Pol I be continuous or pulsed? Will cells compensate for Pol I inhibition by upregulating the number of active rDNAs? At present, we have no effective and safe disease modulatory treatments for Alzheimer disease, α-synucleinopathies, or tauopathies, and novel therapeutic targets and approaches must be explored.
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Affiliation(s)
- Mark S. LeDoux
- Department of Psychology and College of Health Sciences, University of Memphis, Memphis, TN 38152, USA; or
- Veracity Neuroscience LLC, Memphis, TN 38157, USA
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29
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Shlapakova PS, Dobrynina LA, Kalashnikova LA, Gubanova MV, Danilova MS, Gnedovskaya EV, Grigorenko AP, Gusev FE, Manakhov AD, Rogaev EI. Peripheral Blood Gene Expression Profiling Reveals Molecular Pathways Associated with Cervical Artery Dissection. Int J Mol Sci 2024; 25:5205. [PMID: 38791244 PMCID: PMC11121660 DOI: 10.3390/ijms25105205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Cervical artery dissection (CeAD) is the primary cause of ischemic stroke in young adults. Monogenic heritable connective tissue diseases account for fewer than 5% of cases of CeAD. The remaining sporadic cases have known risk factors. The clinical, radiological, and histological characteristics of systemic vasculopathy and undifferentiated connective tissue dysplasia are present in up to 70% of individuals with sporadic CeAD. Genome-wide association studies identified CeAD-associated genetic variants in the non-coding genomic regions that may impact the gene transcription and RNA processing. However, global gene expression profile analysis has not yet been carried out for CeAD patients. We conducted bulk RNA sequencing and differential gene expression analysis to investigate the expression profile of protein-coding genes in the peripheral blood of 19 CeAD patients and 18 healthy volunteers. This was followed by functional annotation, heatmap clustering, reports on gene-disease associations and protein-protein interactions, as well as gene set enrichment analysis. We found potential correlations between CeAD and the dysregulation of genes linked to nucleolar stress, senescence-associated secretory phenotype, mitochondrial malfunction, and epithelial-mesenchymal plasticity.
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Affiliation(s)
- Polina S. Shlapakova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Larisa A. Dobrynina
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Ludmila A. Kalashnikova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Mariia V. Gubanova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Maria S. Danilova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Elena V. Gnedovskaya
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Anastasia P. Grigorenko
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia (F.E.G.)
| | - Fedor E. Gusev
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia (F.E.G.)
- Department of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi 354340, Russia; (A.D.M.)
| | - Andrey D. Manakhov
- Department of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi 354340, Russia; (A.D.M.)
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow 119192, Russia
| | - Evgeny I. Rogaev
- Department of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi 354340, Russia; (A.D.M.)
- Department of Psychiatry, UMass Chan Medical School, 222 Maple Ave, Reed-Rose-Gordon Building, Shrewsbury, MA 01545, USA
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30
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Zhao L, Zhang T, Zhang K. Pharmacological effects of ginseng and ginsenosides on intestinal inflammation and the immune system. Front Immunol 2024; 15:1353614. [PMID: 38698858 PMCID: PMC11064651 DOI: 10.3389/fimmu.2024.1353614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
Intestinal inflammatory imbalance and immune dysfunction may lead to a spectrum of intestinal diseases, such as inflammatory bowel disease (IBD) and gastrointestinal tumors. As the king of herbs, ginseng has exerted a wide range of pharmacological effects in various diseases. Especially, it has been shown that ginseng and ginsenosides have strong immunomodulatory and anti-inflammatory abilities in intestinal system. In this review, we summarized how ginseng and various extracts influence intestinal inflammation and immune function, including regulating the immune balance, modulating the expression of inflammatory mediators and cytokines, promoting intestinal mucosal wound healing, preventing colitis-associated colorectal cancer, recovering gut microbiota and metabolism imbalance, alleviating antibiotic-induced diarrhea, and relieving the symptoms of irritable bowel syndrome. In addition, the specific experimental methods and key control mechanisms are also briefly described.
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Affiliation(s)
| | | | - Kai Zhang
- Department of General Surgery, The Second Hospital of Jilin University, Jilin University, Changchun, Jilin, China
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31
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Alenezi H, Parnell G, Schibeci S, Ozkan J, Willcox M, White AJR, Carnt N. Ocular surface immune transcriptome and tear cytokines in corneal infection patients. Front Cell Infect Microbiol 2024; 14:1346821. [PMID: 38694515 PMCID: PMC11061372 DOI: 10.3389/fcimb.2024.1346821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/19/2024] [Indexed: 05/04/2024] Open
Abstract
Background Microbial keratitis is one of the leading causes of blindness globally. An overactive immune response during an infection can exacerbate damage, causing corneal opacities and vision loss. This study aimed to identify the differentially expressed genes between corneal infection patients and healthy volunteers within the cornea and conjunctiva and elucidate the contributing pathways to these conditions' pathogenesis. Moreover, it compared the corneal and conjunctival transcriptomes in corneal-infected patients to cytokine levels in tears. Methods Corneal and conjunctival swabs were collected from seven corneal infection patients and three healthy controls under topical anesthesia. RNA from seven corneal infection patients and three healthy volunteers were analyzed by RNA sequencing (RNA-Seq). Tear proteins were extracted from Schirmer strips via acetone precipitation from 38 cases of corneal infection and 14 healthy controls. The cytokines and chemokines IL-1β, IL-6, CXCL8 (IL-8), CX3CL1, IL-10, IL-12 (p70), IL-17A, and IL-23 were measured using an antibody bead assay. Results A total of 512 genes were found to be differentially expressed in infected corneas compared to healthy corneas, with 508 being upregulated and four downregulated (fold-change (FC) <-2 or > 2 and adjusted p <0.01). For the conjunctiva, 477 were upregulated, and 3 were downregulated (FC <-3 or ≥ 3 and adjusted p <0.01). There was a significant overlap in cornea and conjunctiva gene expression in patients with corneal infections. The genes were predominantly associated with immune response, regulation of angiogenesis, and apoptotic signaling pathways. The most highly upregulated gene was CXCL8 (which codes for IL-8 protein). In patients with corneal infections, the concentration of IL-8 protein in tears was relatively higher in patients compared to healthy controls but did not show statistical significance. Conclusions During corneal infection, many genes were upregulated, with most of them being associated with immune response, regulation of angiogenesis, and apoptotic signaling. The findings may facilitate the development of treatments for corneal infections that can dampen specific aspects of the immune response to reduce scarring and preserve sight.
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Affiliation(s)
- Heba Alenezi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Grant Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Stephen Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Jerome Ozkan
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew J. R. White
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, The University of New South Wales, Sydney, NSW, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Institute of Ophthalmology, University College London, London, United Kingdom
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32
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Cai Z, Zhao X, Qian Y, Zhang K, Guo S, Kan Y, Wang Y, Ayra-Pardo C, Li D. Transcriptomic and Metatranscriptomic Analyses Provide New Insights into the Response of the Pea Aphid Acyrthosiphon pisum (Hemiptera: Aphididae) to Acetamiprid. INSECTS 2024; 15:274. [PMID: 38667404 PMCID: PMC11050337 DOI: 10.3390/insects15040274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Acetamiprid is a broad-spectrum neonicotinoid insecticide used in agriculture to control aphids. While recent studies have documented resistance to acetamiprid in several aphid species, the underlying mechanisms are still not fully understood. In this study, we analyzed the transcriptome and metatranscriptome of a laboratory strain of the pea aphid, Acyrthosiphon pisum (Harris, 1776), with reduced susceptibility to acetamiprid after nine generations of exposure to identify candidate genes and the microbiome involved in the adaptation process. Sequencing of the transcriptome of both selected (RS) and non-selected (SS) strains allowed the identification of 14,858 genes and 4938 new transcripts. Most of the differentially expressed genes were associated with catalytic activities and metabolic pathways involving carbon and fatty acids. Specifically, alcohol-forming fatty acyl-CoA reductase (FAR) and acyl-CoA synthetase (ACSF2), both involved in the synthesis of epidermal wax layer components, were significantly upregulated in RS, suggesting that adaptation to acetamiprid involves the synthesis of a thicker protective layer. Metatranscriptomic analyses revealed subtle shifts in the microbiome of RS. These results contribute to a deeper understanding of acetamiprid adaptation by the pea aphid and provide new insights for aphid control strategies.
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Affiliation(s)
- Zhiyan Cai
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Xuhui Zhao
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Yuxin Qian
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Kun Zhang
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Shigang Guo
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Yunchao Kan
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
- School of Life Science and Technology, Henan Institute of Science and Technology, 90 East of Hualan Avenue, Xinxiang 453003, China
| | - Yuqing Wang
- Scientific Research Center, Nanyang Medical College, Nanyang 473061, China;
| | - Camilo Ayra-Pardo
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, Avda. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Dandan Li
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
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Raposo de Magalhães C, Sandoval K, Kagan F, McCormack G, Schrama D, Carrilho R, Farinha AP, Cerqueira M, Rodrigues PM. Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration. PLoS One 2024; 19:e0300472. [PMID: 38517901 PMCID: PMC10959376 DOI: 10.1371/journal.pone.0300472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.
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Affiliation(s)
- Cláudia Raposo de Magalhães
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Grace McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | - Denise Schrama
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Raquel Carrilho
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Paula Farinha
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Escola Superior Agrária de Santarém, Santarém, Portugal
| | - Marco Cerqueira
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Pedro M. Rodrigues
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
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Söderman J, Almer S. Discerning Endoscopic Severity of Inflammatory Bowel Disease by Scoping the Peripheral Blood Transcriptome. GASTRO HEP ADVANCES 2024; 3:618-633. [PMID: 39165421 PMCID: PMC11330933 DOI: 10.1016/j.gastha.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/29/2024] [Indexed: 08/22/2024]
Abstract
Background and Aims Ulcerative colitis (UC) and Crohn's disease (CD) are chronic inflammatory bowel diseases (IBDs) with an incompletely understood etiology and pathogenesis. Identification of suitable drug targets and assessment of disease severity are crucial for optimal management. Methods Using RNA sequencing, we investigated differential gene expression in peripheral blood samples from IBD patients and non-inflamed controls, analyzed pathway enrichment, and identified genes whose expression correlated with endoscopic disease severity. Results Neutrophil degranulation emerged as the most significant pathway across all IBD sample types. Signaling by interleukins was prominent in patients with active intestinal inflammation but also enriched in CD and UC patients without intestinal inflammation. Nevertheless, genes correlated to endoscopic disease severity implicated the primary cilium in CD patients and translation and focal adhesion in UC patients. Moreover, several of these genes were located in genome-wide associated loci linked to IBD, cholesterol levels, blood cell counts, and levels of markers assessing liver and kidney function. These genes also suggested connections to intestinal epithelial barrier dysfunction, contemporary IBD drug treatment, and new actionable drug targets. A large number of genes associated with endoscopic disease severity corresponded to noncoding RNAs. Conclusion This study revealed biological pathways associated with IBD disease state and endoscopic disease severity, thus providing insights into the underlying mechanisms of IBD pathogenesis as well as identifying potential biomarkers and therapies. Peripheral blood might constitute a suitable noninvasive diagnostic sample type, in which gene expression profiles might serve as indicators of ongoing mucosal inflammation, and thus guide personalized treatment decisions.
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Affiliation(s)
- Jan Söderman
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Laboratory Medicine, Jönköping, Region Jönköping County, Sweden
| | - Sven Almer
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- IBD-Unit, Division of Gastroenterology, Karolinska University Hospital, Stockholm, Sweden
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Wu H, Xia L, Sun L, Li D, Liu X, Song H, Sheng J, Wang K, Feng Q. RPL35A drives ovarian cancer progression by promoting the binding of YY1 to CTCF promoter. J Cell Mol Med 2024; 28:e18115. [PMID: 38436544 PMCID: PMC10910871 DOI: 10.1111/jcmm.18115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 03/05/2024] Open
Abstract
Ovarian cancer is one of the most common gynaecological malignancies with poor prognosis and lack of effective treatment. The improvement of the situation of ovarian cancer urgently requires the exploration of its molecular mechanism to develop more effective molecular targeted drugs. In this study, the role of human ribosomal protein l35a (RPL35A) in ovarian cancer was explored in vitro and in vivo. Our data identified that RPL35A expression was abnormally elevated in ovarian cancer. Clinically, high expression of RPL35A predicted short survival and poor TNM staging in patients with ovarian cancer. Functionally, RPL35A knock down inhibited ovarian cancer cell proliferation and migration, enhanced apoptosis, while overexpression had the opposite effect. Mechanically, RPL35A promoted the direct binding of transcription factor YY1 to CTCF in ovarian cancer cells. Consistently, RPL35A regulated ovarian cancer progression depending on CTCF in vitro and in vivo. Furthermore, RPL35A affected the proliferation and apoptosis of ovarian cancer cells through PPAR signalling pathway. In conclusion, RPL35A drove ovarian cancer progression by promoting the binding of YY1 and CTCF promoter, and inhibiting this process may be an effective strategy for targeted therapy of this disease.
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Affiliation(s)
- Huijuan Wu
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Liangbin Xia
- Department of Obstetrics and GynecologyRenmin Hospital of Wuhan UniversityWuhanChina
| | - Lu Sun
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Dan Li
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Xiangyu Liu
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Hualin Song
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Jindong Sheng
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Ke Wang
- Department of Gynecological OncologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and TherapyTianjinChina
| | - Qinmei Feng
- Department of Gynecological OncologyShanxi Province People's HospitalShanxiChina
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Erickson EC, You I, Perry G, Dugourd A, Donovan KA, Crafter C, Johannes JW, Williamson S, Moss JI, Ros S, Ziegler RE, Barry ST, Fischer ES, Gray NS, Madsen RR, Toker A. Multiomic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation. Sci Signal 2024; 17:eadf2670. [PMID: 38412255 PMCID: PMC10949348 DOI: 10.1126/scisignal.adf2670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
More than 50% of human tumors display hyperactivation of the serine/threonine kinase AKT. Despite evidence of clinical efficacy, the therapeutic window of the current generation of AKT inhibitors could be improved. Here, we report the development of a second-generation AKT degrader, INY-05-040, which outperformed catalytic AKT inhibition with respect to cellular suppression of AKT-dependent phenotypes in breast cancer cell lines. A growth inhibition screen with 288 cancer cell lines confirmed that INY-05-040 had a substantially higher potency than our first-generation AKT degrader (INY-03-041), with both compounds outperforming catalytic AKT inhibition by GDC-0068. Using multiomic profiling and causal network integration in breast cancer cells, we demonstrated that the enhanced efficacy of INY-05-040 was associated with sustained suppression of AKT signaling, which was followed by induction of the stress mitogen-activated protein kinase (MAPK) c-Jun N-terminal kinase (JNK). Further integration of growth inhibition assays with publicly available transcriptomic, proteomic, and reverse phase protein array (RPPA) measurements established low basal JNK signaling as a biomarker for breast cancer sensitivity to AKT degradation. Together, our study presents a framework for mapping the network-wide signaling effects of therapeutically relevant compounds and identifies INY-05-040 as a potent pharmacological suppressor of AKT signaling.
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Affiliation(s)
- Emily C. Erickson
- Department of Pathology, Medicine and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally to this work
| | - Inchul You
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally to this work
| | - Grace Perry
- Department of Pathology, Medicine and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Aurelien Dugourd
- Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg 69120, Germany
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Claire Crafter
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Jeffrey W. Johannes
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA 02451, USA
| | - Stuart Williamson
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Jennifer I. Moss
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Susana Ros
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Robert E. Ziegler
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, MA 02451, USA
| | - Simon T. Barry
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ralitsa R. Madsen
- University College London Cancer Institute, Paul O’Gorman Building, University College London, London WC1E 6BT, UK
- Current: MRC-Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alex Toker
- Department of Pathology, Medicine and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Feng L, Wang G, Song Q, Feng X, Su J, Ji G, Li M. Proteomics revealed an association between ribosome-associated proteins and amyloid beta deposition in Alzheimer's disease. Metab Brain Dis 2024; 39:263-282. [PMID: 38019374 DOI: 10.1007/s11011-023-01330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Most scholars believe that amyloid-beta (Aβ) has the potential to induce apoptosis, stimulate an inflammatory cascade, promote oxidative stress and exacerbate the pathological progression of Alzheimer's disease (AD). Therefore, it is crucial to investigate the deposition of Aβ in AD. At approximately 6 months of age, APP/PS1 double transgenic mice gradually exhibit the development of plaques, as well as spatial and learning impairment. Notably, the hippocampus is specifically affected in the course of AD. Herein, 6-month-old APP/PS1 double transgenic mice were utilized, and the differentially expressed (DE) proteins in the hippocampus were identified and analyzed using 4D label-free quantitative proteomics technology and parallel reaction monitoring (PRM). Compared to wild-type mice, 29 proteins were upregulated and 25 proteins were downregulated in the AD group. Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the DE proteins were mainly involved in 'ribosomal large subunit biogenesis'. Molecular function (MF) analysis results were primarily associated with '5.8S rRNA binding' and 'structural constituent of ribosome'. In terms of cellular components (CC), the DE proteins were mainly found in 'polysomal ribosome', 'cytosolic large ribosomal subunit', 'cytosolic ribosome', and 'large ribosomal subunit', among others. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the results were mainly enriched in the 'Ribosome signaling pathway'. The key target proteins identified were ribosomal protein (Rp)l18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6. The PRM verification results were consistent with the findings of the 4D label-free quantitative proteomics analysis. Overall, these findings suggest that Rpl18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6 may have potential therapeutic value for the treatment of AD by targeting Aβ.
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Affiliation(s)
- Lina Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Guojun Wang
- Department of Neurosurgery, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Qile Song
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Xiaotong Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Jing Su
- Department of Geriatric Cardiovascular, The Affiliated Taian City Central Hospital of Qingdao University, Longtan Road, Taian, 271000, Shandong, China.
| | - Guangcheng Ji
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
| | - Mingquan Li
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
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Hsu CH, Liu CY, Lo KY. Mutations of ribosomal protein genes induce overexpression of catalase in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foae005. [PMID: 38271612 PMCID: PMC10855018 DOI: 10.1093/femsyr/foae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 01/27/2024] Open
Abstract
Ribosome assembly defects result in ribosomopathies, primarily caused by inadequate protein synthesis and induced oxidative stress. This study aimed to investigate the link between deleting one ribosomal protein gene (RPG) paralog and oxidative stress response. Our results indicated that RPG mutants exhibited higher oxidant sensitivity than the wild type (WT). The concentrations of H2O2 were increased in the RPG mutants. Catalase and superoxide dismutase (SOD) activities were generally higher at the stationary phase, with catalase showing particularly elevated activity in the RPG mutants. While both catalase genes, CTT1 and CTA1, consistently exhibited higher transcription in RPG mutants, Ctt1 primarily contributed to the increased catalase activity. Stress-response transcription factors Msn2, Msn4, and Hog1 played a role in regulating these processes. Previous studies have demonstrated that H2O2 can cleave 25S rRNA via the Fenton reaction, enhancing ribosomes' ability to translate mRNAs associated with oxidative stress-related genes. The cleavage of 25S rRNA was consistently more pronounced, and the translation efficiency of CTT1 and CTA1 mRNAs was altered in RPG mutants. Our results provide evidence that the mutations in RPGs increase H2O2 levels in vivo and elevate catalase expression through both transcriptional and translational controls.
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Affiliation(s)
- Ching-Hsiang Hsu
- Department of Agricultural Chemistry National Taiwan University Agricultural Chemistry Building No. 2, Rm. 233 No. 1, Sec. 4, Roosevelt Rd. Taipei 10617, Taiwan
| | - Ching-Yu Liu
- Department of Agricultural Chemistry National Taiwan University Agricultural Chemistry Building No. 2, Rm. 233 No. 1, Sec. 4, Roosevelt Rd. Taipei 10617, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry National Taiwan University Agricultural Chemistry Building No. 2, Rm. 233 No. 1, Sec. 4, Roosevelt Rd. Taipei 10617, Taiwan
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Codognoto VM, de Souza FF, Cataldi TR, Labate CA, de Camargo LS, Scott C, da Rosa Filho RR, de Carvalho NAT, Oba E. Uterine secretome: What do the proteins say about maternal-fetal communication in buffaloes? J Proteomics 2024; 290:105023. [PMID: 37838095 DOI: 10.1016/j.jprot.2023.105023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
The aim was to compare the UF proteomics of pregnant and non-pregnant buffalo during early pregnancy. Forty-four females were submitted to hormonal estrus synchronization and randomly divided into two groups: pregnant (n = 30) and non-pregnant (n = 14). The pregnant group was artificially inseminated and divided into a further two groups: P12 (n = 15) and P18 (n = 15). Conceptus and uterine fluid samples were collected during slaughter at, respectively, 12 and 18 days after insemination. Of all the inseminated females, only eight animals in each group were pregnant, which reduced the sample of the groups to P12 (n = 8) and P18 (n = 8). The non-pregnant group was also re-divided into two groups at the end of synchronization: NP12 (n = 7) and NP18 (n = 7). The UF samples were processed for proteomic analysis. The results were submitted to multivariate and univariate analysis. A total of 1068 proteins were found in the uterine fluid in both groups. Our results describe proteins involved in the conceptus elongation and maternal recognition of pregnancy, and their action was associated with cell growth, endometrial remodeling, and modulation of immune and antioxidant protection, mechanisms necessary for embryonic maintenance in the uterine environment. SIGNIFICANCE: Uterine fluid is a substance synthesized and secreted by the endometrium that plays essential roles during pregnancy in ruminants, contributing significantly to embryonic development. Understanding the functions that the proteins present in the UF perform during early pregnancy, a period marked by embryonic implantation, and maternal recognition of pregnancy is of fundamental importance to understanding the mechanisms necessary for the maintenance of pregnancy. The present study characterized and compared the UF proteome at the beginning of pregnancy in pregnant and non-pregnant buffaloes to correlate the functions of the proteins and the stage of development of the conceptus and unravel their processes in maternal recognition of pregnancy. The proteins found were involved in cell growth and endometrial remodeling, in addition to acting in the immunological protection of the conceptus and performing antioxidant actions necessary for establishing a pregnancy.
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Affiliation(s)
- Viviane Maria Codognoto
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, Universidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil
| | - Fabiana Ferreira de Souza
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, Universidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil
| | - Thais Regiani Cataldi
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Laíza Sartori de Camargo
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, Universidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil
| | - Caroline Scott
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, Universidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil
| | - Roberto Rodrigues da Rosa Filho
- Department of Animal Reproduction - School of Veterinary Medicine and Animal Science, University of São Paulo, campus São Paulo, São Paulo, Brazil
| | - Nélcio Antonio Tonizza de Carvalho
- Research and Development Unit of Registro / Diversified Animal Science Research Center / Institute of Animal Science, Registro, São Paulo, Brazil
| | - Eunice Oba
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, Universidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil.
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Jordan-Ward R, von Hippel FA, Wilson CA, Rodriguez Maldonado Z, Dillon D, Contreras E, Gardell A, Minicozzi MR, Titus T, Ungwiluk B, Miller P, Carpenter D, Postlethwait JH, Byrne S, Buck CL. Differential gene expression and developmental pathologies associated with persistent organic pollutants in sentinel fish in Troutman Lake, Sivuqaq, Alaska. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122765. [PMID: 37913975 DOI: 10.1016/j.envpol.2023.122765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/07/2023] [Accepted: 10/15/2023] [Indexed: 11/03/2023]
Abstract
Persistent organic pollutants (POPs) are lipophilic compounds that bioaccumulate in animals and biomagnify within food webs. Many POPs are endocrine disrupting compounds that impact vertebrate development. POPs accumulate in the Arctic via global distillation and thereby impact high trophic level vertebrates as well as people who live a subsistence lifestyle. The Arctic also contains thousands of point sources of pollution, such as formerly used defense (FUD) sites. Sivuqaq (St. Lawrence Island), Alaska was used by the U.S. military during the Cold War and FUD sites on the island remain point sources of POP contamination. We examined the effects of POP exposure on ninespine stickleback (Pungitius pungitius) collected from Troutman Lake in the village of Gambell as a model for human exposure and disease. During the Cold War, Troutman Lake was used as a dump site by the U.S. military. We found that PCB concentrations in stickleback exceeded the U.S. Environmental Protection Agency's guideline for unlimited consumption despite these fish being low trophic level organisms. We examined effects at three levels of biological organization: gene expression, endocrinology, and histomorphology. We found that ninespine stickleback from Troutman Lake exhibited suppressed gonadal development compared to threespine stickleback (Gasterosteus aculeatus) studied elsewhere. Troutman Lake stickleback also displayed two distinct hepatic phenotypes, one with lipid accumulation and one with glycogen-type vacuolation. We compared the transcriptomic profiles of these liver phenotypes using RNA sequencing and found significant upregulation of genes involved in ribosomal and metabolic pathways in the lipid accumulation group. Additionally, stickleback displaying liver lipid accumulation had significantly fewer thyroid follicles than the vacuolated phenotype. Our study and previous work highlight health concerns for people and wildlife due to pollution hotspots in the Arctic, and the need for health-protective remediation.
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Affiliation(s)
- Renee Jordan-Ward
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave., P.O. Box 245210, Tucson, AZ 85724, USA.
| | - Catherine A Wilson
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - Zyled Rodriguez Maldonado
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Danielle Dillon
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Elise Contreras
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Alison Gardell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA 98402, USA
| | - Michael R Minicozzi
- Department of Biological Sciences, Minnesota State University Mankato, 242 Trafton Science Center South, Mankato, MN, 56001, USA
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - Bobby Ungwiluk
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK 99518, USA
| | - Pamela Miller
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK 99518, USA
| | - David Carpenter
- Institute for Health and the Environment, University at Albany, 5 University Place, Rensselaer, NY 12144, USA
| | - John H Postlethwait
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - Samuel Byrne
- Middlebury College, Department of Biology and Global Health Program, 14 Old Chapel Rd, Middlebury, VT 05753, USA
| | - C Loren Buck
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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Aluksanasuwan S, Somsuan K, Ngoenkam J, Chutipongtanate S, Pongcharoen S. Potential association of HSPD1 with dysregulations in ribosome biogenesis and immune cell infiltration in lung adenocarcinoma: An integrated bioinformatic approach. Cancer Biomark 2024; 39:155-170. [PMID: 37694354 PMCID: PMC11091585 DOI: 10.3233/cbm-220442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/03/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a major histological subtype of lung cancer with a high mortality rate worldwide. Heat shock protein family D member 1 (HSPD1, also known as HSP60) is reported to be increased in tumor tissues of lung cancer patients compared with healthy control tissues. OBJECTIVE We aimed to investigate the roles of HSPD1 in prognosis, carcinogenesis, and immune infiltration in LUAD using an integrative bioinformatic analysis. METHODS HSPD1 expression in LUAD was investigated in several transcriptome-based and protein databases. Survival analysis was performed using the KM plotter and OSluca databases, while prognostic significance was independently confirmed through univariate and multivariate analyses. Integrative gene interaction network and enrichment analyses of HSPD1-correlated genes were performed to investigate the roles of HSPD1 in LUAD carcinogenesis. TIMER and TISIDB were used to analyze correlation between HSPD1 expression and immune cell infiltration. RESULTS The mRNA and protein expressions of HSPD1 were higher in LUAD compared with normal tissues. High HSPD1 expression was associated with male gender and LUAD with advanced stages. High HSPD1 expression was an independent prognostic factor associated with poor survival in LUAD patients. HSPD1-correlated genes with prognostic impact were mainly involved in aberrant ribosome biogenesis, while LUAD patients with high HSPD1 expression had low tumor infiltrations of activated and immature B cells and CD4+ T cells. CONCLUSIONS HSPD1 may play a role in the regulation of ribosome biogenesis and B cell-mediated immunity in LUAD. It could serve as a predictive biomarker for prognosis and immunotherapy response in LUAD.
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Affiliation(s)
- Siripat Aluksanasuwan
- School of Medicine, Mae Fah Luang University, Chiang Rai, Thailand
- Cancer and Immunology Research Unit (CIRU), Mae Fah Luang University, Chiang Rai, Thailand
| | - Keerakarn Somsuan
- School of Medicine, Mae Fah Luang University, Chiang Rai, Thailand
- Cancer and Immunology Research Unit (CIRU), Mae Fah Luang University, Chiang Rai, Thailand
| | - Jatuporn Ngoenkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Somchai Chutipongtanate
- MILCH and Novel Therapeutics Lab, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sutatip Pongcharoen
- Division of Immunology, Department of Medicine, Faculty of Medicine, Naresuan University, Phitsanulok, Thailand
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Jiang H, Li X, Li Y, Liu X, Zhang S, Li H, Zhang M, Wang L, Yu M, Qiao Z. Molecular and functional characterization of ribosome protein S24 in ovarian development of Macrobrachium nipponense. Int J Biol Macromol 2024; 254:127934. [PMID: 37939777 DOI: 10.1016/j.ijbiomac.2023.127934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/21/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
Ribosomal proteins (RPs) have mang extraribosomal functions including regulation of ovarian development in some organisms. In order to solve the problem of rapid ovarian maturation in Macrobrachium nipponense aquaculture, this study identified a RPS24 (MnRPS24) gene from M. nipponense, which encodes a protein of ββαβαααα folding structure type. MnRPS24 exhibited the greatest expressions in the female adult stage among the six growth stages, in the ovary among the nine tissues, and in the stage I ovary among the six ovarian development stages. The MnRPS24 protein located in the cytoplasm of oogonia, previtellogenic and early-vitellogenic oocytes, and the follicular cells surrounding the oocytes. The expression of the vitellogenin (MnVg), vitellogenin receptor (MnVgr), cell cycle protein B (MnCyclin B) and cell division cyclin 2 (MnCdc2) genes were increased by recombinant MnRPS24 protein incubation. Conversely, the expression of the Wee1 kinase (MnWee1) gene was decreased. MnRPS24 gene silencing downregulated the expression for MnVg, MnVgr, MnCyclin B and MnCdc2 and upregulated the expression for MnWee1. Furthermore, MnRPS24 gene silencing delayed the vitellogenesis of oocytes, halting the progression of ovarian development. The findings of this research demonstrate that MnRPS24 could potentially function as a stimulator in promoting the development of ovaries in M. nipponense.
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Affiliation(s)
- Hongxia Jiang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Xiao Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Yizheng Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xuewei Liu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Shuaishuai Zhang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Huanxin Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Meng Zhang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Lei Wang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Miao Yu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
| | - Zhigang Qiao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
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Jiang B, Yang J, He R, Wang D, Huang Y, Zhao G, Ning M, Zeng T, Li G. Integrated multi-omics analysis for lung adenocarcinoma in Xuanwei, China. Aging (Albany NY) 2023; 15:14263-14291. [PMID: 38095636 PMCID: PMC10756121 DOI: 10.18632/aging.205300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/02/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Xuanwei lung cancer (XWLC) is well-known for its high incidence and mortality. However, the molecular mechanism is still unclear. METHODS We performed a comprehensive transcriptomic, proteomic, and phosphoproteomic characterization of tumors and matched normal adjacent tissues from three XWLC patients with lung adenocarcinoma (LUAD). RESULTS Integrated transcriptome and proteome analysis revealed dysregulated molecules and pathways in tumors and identified enhanced metabolic-disease coupling. Non-coding RNAs were widely involved in post-transcriptional regulatory mechanisms to coordinate the progress of LUAD and partially explained the molecular differences between RNA and protein expression patterns. Phosphoproteome provided evidence support for new phosphate sites, reporting the potential roles of core kinase family members and key kinase pathways involved in metabolism, immunity, and homeostasis. In addition, by comparing with the previous LUAD researches, we emphasized the higher degree of oxidative phosphorylation in Xuanwei LUAD and pointed that VIPR1 deficiency aggravated metabolic dysfunction. CONCLUSION Our integrated multi-omics analysis provided a powerful resource for a systematic understanding of the molecular structure of XWLC and proposed therapeutic opportunities based on redox metabolism.
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Affiliation(s)
- Boyi Jiang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Jiapeng Yang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Rui He
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Dong Wang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Yunchao Huang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Guangqiang Zhao
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Mingjie Ning
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Teng Zeng
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
| | - Guangjian Li
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, Yunnan 650032, China
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Huertas-Abril PV, Jurado J, Prieto-Álamo MJ, García-Barrera T, Abril N. Proteomic analysis of the hepatic response to a pollutant mixture in mice. The protective action of selenium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166558. [PMID: 37633382 DOI: 10.1016/j.scitotenv.2023.166558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Metals and pharmaceuticals contaminate water and food worldwide, forming mixtures where they can interact to enhance their individual toxicity. Here we use a shotgun proteomic approach to evaluate the toxicity of a pollutant mixture (PM) of metals (As, Cd, Hg) and pharmaceuticals (diclofenac, flumequine) on mice liver proteostasis. These pollutants are abundant in the environment, accumulate in the food chain, and are toxic to humans primarily through oxidative damage. Thus, we also evaluated the putative antagonistic effect of low-dose dietary supplementation with the antioxidant trace element selenium. A total of 275 proteins were affected by PM treatment. Functional analyses revealed an increased abundance of proteins involved in the integrated stress response that promotes translation, the inflammatory response, carbohydrate and lipid metabolism, and the sustained expression of the antioxidative response mediated by NRF2. As a consequence, a reductive stress situation arises in the cell that inhibits the RICTOR pathway, thus activating the early stage of autophagy, impairing xenobiotic metabolism, and potentiating lipid biosynthesis and steatosis. PM exposure-induced hepato-proteostatic alterations were significantly reduced in Se supplemented mice, suggesting that the use of this trace element as a dietary supplement may at least partially ameliorate liver damage caused by exposure to environmental mixtures.
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Affiliation(s)
- Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Juan Jurado
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - María-José Prieto-Álamo
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
| | - Tamara García-Barrera
- Research Center of Natural Resources, Health, and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, Campus El Carmen, University of Huelva, Fuerzas Armadas Ave., 21007 Huelva, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain.
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Song J, Xu X, He S, Zhang H, Wang N, Bai Y, Li B, Zhang S. Identification of the therapeutic effect and molecular mechanism of Coptis chinensis Franch. and Magnolia officinalis var. biloba on chronic gastritis. JOURNAL OF ETHNOPHARMACOLOGY 2023; 317:116864. [PMID: 37393026 DOI: 10.1016/j.jep.2023.116864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicine (TCM) theory believes that clearing heat and promoting dampness is the main treatment method for chronic gastritis. Coptis chinensis Franch. has the effects of clearing heat, detoxifying, and anti-inflammatory; Magnolia officinalis var. biloba can be used to treat abdominal pain, cough, and asthma. Coptis chinensis Franch. and Magnolia officinalis var. biloba can regulate the balance of intestinal microbiota and inhibit inflammatory reactions. AIM This study will verify the therapeutic effect of Coptis chinensis Franch. and Magnolia officinalis var. biloba on chronic gastritis, and explore its mechanism through transcriptome sequencing. METHODS Firstly, a rat chronic gastritis model was established, and the anal temperature and body weight changes of the rats before and after modeling were observed. Next, H&E staining, TUNEL assay and ELISA assay were performed on rat gastric mucosal tissues. Subsequently, the key fractions of Coptis chinensis Franch. and Magnolia officinalis var. biloba were obtained by high performance liquid chromatography (HPLC), and a GES-1 cell inflammation model was constructed to select the optimal monomer. Finally, the mechanism of action of Coptis chinensis Franch. and Magnolia officinalis var. biloba was explored through RNA seq. RESULTS Compared with the control group, the rats in the administered group were in better condition, with higher anal temperature, reduced inflammatory response in gastric mucosal tissue and reduced apoptosis. The optimal fraction Coptisine was subsequently determined by HPLC and GES-1 cell model. RNA-seq analysis revealed that DEG was significantly enriched in ribosomes, NF-κB signaling pathway, etc. The key genes TPT1 and RPL37 were subsequently obtained. CONCLUSIONS This study verified the therapeutic effects of Coptis chinensis Franch. and Magnolia officinalis var. biloba on chronic gastritis by in vivo and in vitro experiments in rats, identified Coptisine as the optimal component, and obtained two potential target genes.
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Affiliation(s)
- Jin Song
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China
| | - Xiaolong Xu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China
| | - Shasha He
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China
| | - Huicun Zhang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China
| | - Ning Wang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China
| | - Yunjing Bai
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China
| | - Bo Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China.
| | - Shengsheng Zhang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China.
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Kour R, Kim J, Roy A, Richardson B, Cameron MJ, Knott JG, Mazumder B. Loss of function of ribosomal protein L13a blocks blastocyst formation and reveals a potential nuclear role in gene expression. FASEB J 2023; 37:e23275. [PMID: 37902531 PMCID: PMC10999073 DOI: 10.1096/fj.202301475r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023]
Abstract
Ribosomal proteins play diverse roles in development and disease. Most ribosomal proteins have canonical roles in protein synthesis, while some exhibit extra-ribosomal functions. Previous studies in our laboratory revealed that ribosomal protein L13a (RPL13a) is involved in the translational silencing of a cohort of inflammatory proteins in myeloid cells. This prompted us to investigate the role of RPL13a in embryonic development. Here we report that RPL13a is required for early development in mice. Crosses between Rpl13a+/- mice resulted in no Rpl13a-/- offspring. Closer examination revealed that Rpl13a-/- embryos were arrested at the morula stage during preimplantation development. RNA sequencing analysis of Rpl13a-/- morulae revealed widespread alterations in gene expression, including but not limited to several genes encoding proteins involved in the inflammatory response, embryogenesis, oocyte maturation, stemness, and pluripotency. Ex vivo analysis revealed that RPL13a was localized to the cytoplasm and nucleus between the two-cell and morula stages. RNAi-mediated depletion of RPL13a phenocopied Rpl13a-/- embryos and knockdown embryos exhibited increased expression of IL-7 and IL-17 and decreased expression of the lineage specifier genes Sox2, Pou5f1, and Cdx2. Lastly, a protein-protein interaction assay revealed that RPL13a is associated with chromatin, suggesting an extra ribosomal function in transcription. In summary, our data demonstrate that RPL13a is essential for the completion of preimplantation embryo development. The mechanistic basis of the absence of RPL13a-mediated embryonic lethality will be addressed in the future through follow-up studies on ribosome biogenesis, global protein synthesis, and identification of RPL13a target genes using chromatin immunoprecipitation and RNA-immunoprecipitation-based sequencing.
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Affiliation(s)
- Ravinder Kour
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Jaehwan Kim
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Antara Roy
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Brian Richardson
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark J. Cameron
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jason G. Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Barsanjit Mazumder
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
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Hu T, Guo D, Li B, Wang L, Liu H, Yin J, Jin T, Luan H, Sun L, Liu M, Zhi H, Li K. Soybean 40S Ribosomal Protein S8 (GmRPS8) Interacts with 6K1 Protein and Contributes to Soybean Susceptibility to Soybean Mosaic Virus. Viruses 2023; 15:2362. [PMID: 38140603 PMCID: PMC10748009 DOI: 10.3390/v15122362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Soybean mosaic virus (SMV), a member of Potyvirus, is the most destructive and widespread viral disease in soybean production. Our earlier studies identified a soybean 40S ribosomal protein S8 (GmRPS8) using the 6K1 protein of SMV as the bait to screen a soybean cDNA library. The present study aims to identify the interactions between GmRPS8 and SMV and characterize the role of GmRPS8 in SMV infection in soybean. Expression analysis showed higher SMV-induced GmRPS8 expression levels in a susceptible soybean cultivar when compared with a resistant cultivar, suggesting that GmRPS8 was involved in the response to SMV in soybean. Subcellular localization showed that GmRPS8 was localized in the nucleus. Moreover, the yeast two-hybrid (Y2H) experiments showed that GmRPS8 only interacted with 6K1 among the eleven proteins encoded by SMV. The interaction between GmRPS8 and 6K1 was further verified by a bimolecular fluorescence complementation (BiFC) assay, and the interaction was localized in the nucleus. Furthermore, knockdown of GmRPS8 by a virus-induced gene silencing (VIGS) system retarded the growth and development of soybeans and inhibited the accumulation of SMV in soybeans. Together, these results showed that GmRPS8 interacts with 6K1 and contributes to soybean susceptibility to SMV. Our findings provide new insights for understanding the role of GmRPS8 in the SMV infection cycle, which could help reveal potyviral replication mechanisms.
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Affiliation(s)
- Ting Hu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Dongquan Guo
- Jilin Academy of Agricultural Sciences, Changchun 130033, China;
| | - Bowen Li
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Liqun Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Hui Liu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Jinlong Yin
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Tongtong Jin
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Hexiang Luan
- Institute of Plant Genetic Engineering, College of Life Science, Qingdao Agricultural University, Qingdao 266109, China;
| | - Lei Sun
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Mengzhuo Liu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Haijian Zhi
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
| | - Kai Li
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture/Zhongshan Biological Breeding Laboratory (ZSBBL)/National Innovation Platform for Soybean Breeding and Industry-Education Integration/State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (T.H.); (B.L.); (L.W.); (H.L.); (J.Y.); (T.J.); (L.S.); (M.L.)
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49
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Ip WH, Tatham MH, Krohne S, Gruhne J, Melling M, Meyer T, Gornott B, Bertzbach LD, Hay RT, Rodriguez E, Dobner T. Adenovirus E1B-55K controls SUMO-dependent degradation of antiviral cellular restriction factors. J Virol 2023; 97:e0079123. [PMID: 37916833 PMCID: PMC10688335 DOI: 10.1128/jvi.00791-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Human adenoviruses (HAdVs) generally cause mild and self-limiting diseases of the upper respiratory and gastrointestinal tracts but pose a serious risk to immunocompromised patients and children. Moreover, they are widely used as vectors for vaccines and vector-based gene therapy approaches. It is therefore vital to thoroughly characterize HAdV gene products and especially HAdV virulence factors. Early region 1B 55 kDa protein (E1B-55K) is a multifunctional HAdV-encoded oncoprotein involved in various viral and cellular pathways that promote viral replication and cell transformation. We analyzed the E1B-55K dependency of SUMOylation, a post-translational protein modification, in infected cells using quantitative proteomics. We found that HAdV increases overall cellular SUMOylation and that this increased SUMOylation can target antiviral cellular pathways that impact HAdV replication. Moreover, we showed that E1B-55K orchestrates the SUMO-dependent degradation of certain cellular antiviral factors. These results once more emphasize the key role of E1B-55K in the regulation of viral and cellular proteins in productive HAdV infections.
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Affiliation(s)
- Wing-Hang Ip
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Michael H. Tatham
- Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Steewen Krohne
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Julia Gruhne
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Michael Melling
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Tina Meyer
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Britta Gornott
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Luca D. Bertzbach
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Ronald T. Hay
- Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Estefania Rodriguez
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Braunschweig, Germany
| | - Thomas Dobner
- Department of Viral Transformation, Leibniz Institute of Virology (LIV), Hamburg, Germany
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50
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Dong H, Liao Q, Xie B, Qiu YA, Peng Z, Deng J, Xiong J, Lu H, Hao Q, Zhou X. Nucleolar stress promotes and cooperates with ferroptosis to suppress cancer growth. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2684-2687. [PMID: 37574526 DOI: 10.1007/s11427-023-2386-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/06/2023] [Indexed: 08/15/2023]
Affiliation(s)
- Hanzhi Dong
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Quan Liao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Bangxiang Xie
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
- Beijing Engineering Research Center for Precision Medicine and Transformation of Hepatitis and Liver Cancer, Beijing, 100069, China
| | - Yu-An Qiu
- Department of Critical Care Medicine, Jiangxi Cancer Hospital, Jiangxi Cancer Center, Nanchang, 330029, China
| | - Zhiqiang Peng
- Department of Lymphohematology, Jiangxi Cancer Hospital, Jiangxi Cancer Center, Nanchang, 330029, China
| | - Jun Deng
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Jianping Xiong
- Department of Oncology, First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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