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Saito T, Espe M, Vikeså V, Bock C, Thomsen TH, Adam AC, Fernandes JMO, Skjaerven KH. One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic salmon. Epigenetics 2024; 19:2318517. [PMID: 38404006 PMCID: PMC10900267 DOI: 10.1080/15592294.2024.2318517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulphite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism.
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Affiliation(s)
- Takaya Saito
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | - Marit Espe
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | - Vibeke Vikeså
- Skretting AI, Aquaculture Innovation, Stavanger, Norway
| | - Christoph Bock
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Anne-Catrin Adam
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
| | | | - Kaja H Skjaerven
- Feed and Nutrition group, Institute of Marine Research, Bergen, Norway
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2
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Liu Q, Liao L. Identification of macrophage-related molecular subgroups and risk signature in colorectal cancer based on a bioinformatics analysis. Autoimmunity 2024; 57:2321908. [PMID: 38466182 DOI: 10.1080/08916934.2024.2321908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/17/2024] [Indexed: 03/12/2024]
Abstract
Macrophages play a crucial role in tumor initiation and progression, while macrophage-associated gene signature in colorectal cancer (CRC) patients has not been investigated. Our study aimed to identify macrophage-related molecular subgroups and develop a macrophage-related risk model to predict CRC prognosis. The mRNA expression profile and clinical information of CRC patients were obtained from TCGA and GEO databases. CRC patients from TCGA were divided into high and low macrophage subgroups based on the median macrophage score. The ESTIMATE and CIBERSORT algorithms were used to assess immune cell infiltration between subgroups. GSVA and GSEA analyses were performed to investigate differences in enriched pathways between subgroups. Univariate and LASSO Cox regression were used to build a prognostic risk model, which was further validated in the GSE39582 dataset. A high macrophage score subgroup was associated with poor prognosis, highly activated immune-related pathways and an immune-active microenvironment. A total of 547 differentially expressed macrophage-related genes (DEMRGs) were identified, among which seven genes (including RIMKLB, UST, PCOLCE2, ZNF829, TMEM59L, CILP2, DTNA) were identified by COX regression analyses and used to build a risk score model. The risk model shows good predictive and diagnostic values for CRC patients in both TCGA and GSE39852 datasets. Furthermore, multivariate Cox regression analysis showed that the risk score was an independent risk factor for overall survival in CRC patients. Our findings provided a novel insight into macrophage heterogeneity and its immunological role in CRC. This risk score model may serve as an effective prognostic tool and contribute to personalised clinical management of CRC patients.
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Affiliation(s)
- Qi Liu
- Department of General Surgery, Heyuan People's Hospital, Heyuan, China
| | - Li Liao
- Department of preventive health care, Heyuan People's Hospital, Heyuan, China
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3
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Jeremias G, Muñiz-González AB, Mendes Gonçalves FJ, Martínez-Guitarte JL, Asselman J, Luísa Pereira J. History of exposure to copper influences transgenerational gene expression responses in Daphnia magna. Epigenetics 2024; 19:2296275. [PMID: 38154067 PMCID: PMC10761054 DOI: 10.1080/15592294.2023.2296275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
The establishment of transgenerational effects following chemical exposure is a powerful phenomenon, capable of modulating ecosystem health beyond exposure periods. This study assessed the transgenerational effects occurring due to copper exposure in the invertebrate D. magna at the transcriptional level, while evaluating the role of exposure history on such responses. Thus, daphnids acclimated for several generations in a copper vs. clean medium were then exposed for one generation (F0) to this metal, and monitored for the following non-exposed generations (F1, F2 and F3). Organisms differing in exposure histories showed remarkably different transcriptional profiles at the F0, with naïve organisms being more profoundly affected. These trends were confirmed for F3 treatments, which presented different transcriptional patterns for genes involved in detoxification, oxidative stress, DNA damage repair, circadian clock functioning and epigenetic regulation. Furthermore, regardless of exposure history, a great number of histone modifier genes were always found transcriptionally altered, thus suggesting the involvement of histone modifications in the response of Daphnia to metal exposure. Lastly, remarkably distinct transgenerational transcriptional responses were found between naïve and non-naïve organisms, thereby highlighting the influence of exposure history on gene expression and confirming the capacity of metals to determine transgenerational transcriptional effects across non-exposed generations.
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Affiliation(s)
- Guilherme Jeremias
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Ana-Belén Muñiz-González
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | | | - José-Luis Martínez-Guitarte
- Biology & Toxicology Group, Department of Mathematics, Physics, and Fluids, National Distance Education University (UNED), Madrid, Spain
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Ostend, Belgium
| | - Joana Luísa Pereira
- CESAM - Centre for Environmental and Marine Studies & Department of Biology, University of Aveiro, Aveiro, Portugal
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Mortillo M, Kennedy EG, Hermetz KM, Burt AA, Marsit CJ. Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta. Epigenetics 2024; 19:2326869. [PMID: 38507502 PMCID: PMC10956631 DOI: 10.1080/15592294.2024.2326869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth G. Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karen M. Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Zhang J, Sun T, Zhang W, Chen L. Identification of acidic stress-responsive genes and acid tolerance engineering in Synechococcus elongatus PCC 7942. Appl Microbiol Biotechnol 2024; 108:115. [PMID: 38204133 PMCID: PMC10781874 DOI: 10.1007/s00253-023-12984-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. KEY POINTS: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China.
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Rahimian Y, Kheiri F, Faghani M. Evaluation the effect of dietary vitamin E, sesamin and thymoquinone bioactive compounds on immunological response, intestinal traits and MUC-2 gene expression in broiler Japanese quails ( Coturnix japonica). Anim Biotechnol 2024; 35:2259437. [PMID: 37729462 DOI: 10.1080/10495398.2023.2259437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The current study was performed to determine the effect of dietary vitamin E, sesamin and thymoquinone bioactive lignans derived from sesame and black seed on immunological response, intestinal traits and Mucin2 gene expression in broiler quails. Three hundred and fifty (one days-old) quails were allotted to seven dietary treatments with five replicates as an experimental randomized design study. Treatments were basal diet as a control, control +100 and +200 mg of vitamin E, sesamin and thymoquinone per each kg of diet respectively. At 35 d of age, two quails from each pen were chosen, weighted, slaughtered, eviscerated and lymphoid organ relative weights were measured. Anti-body titers against Newcastle disease (ND), Sheep red blood cell (SRBC), and infectious bronchitis virus (IBV) and Avian influenza (AI) vaccination were determined. The serum activities of alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST) and serum antioxidant activates such as superoxide dismutase (SOD),glutathione peroxidase(GPX), catalase (CAT) and total antioxidant capacity (TAC) were examined. The cell mediated immunity by dinitrochlorobenzene (DNCB) and phytohemagglutinin (PHA) challenges were assessed. The microflora populations of ileum, morphological traits of jejunum and mucin2 gene expression were analyzed. Data showed that the lymphoid organ (thymus, spleen and Bursa) relative weights and antibody titer against HI, AI, SRBC and IB vaccination were increased compared to the control (p ≤ 0.05). Serum activities of ALP, ALT and AST were decreased under influences of dietary treatments (p ≤ 0.05). The serum antioxidant activates of GPX,SOD,CAT and TAC were increased and Increasing in mean skin thickness after DNCB challenge and decrease wing web swelling response to PHA mitojen injection were observed (p ≤ 0.05). Salmonella enterica, E-coli and Coliforms colonies were decrease and Lactobacillus colonies increased instead (p ≤ 0.05). The villus height and surface, crypt depth and goblet cells density were increased compared to the control (p ≤ 0.05). The expression of MUC2 gene increased under influnces of vitamin E, sesamin and thymoquinone supplemented diets (p ≤ 0.05).
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Affiliation(s)
- Yaser Rahimian
- Department of Animal Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Farshid Kheiri
- Department of Animal Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mostafa Faghani
- Department of Animal Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Carlo AQ, Pathak D, Choudhary RK, Singh O, Bansal N. Analysis of OCT4 and PGP9.5 gene expression in prenatal and postnatal buffalo ( Bubalus bubalis) testes. Anim Biotechnol 2024; 35:2285509. [PMID: 38006579 DOI: 10.1080/10495398.2023.2285509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
This study aimed to investigate and characterize the spermatogonial stem cells (SSCs) in buffaloes at different stages of development, including prenatal, neonatal, prepubertal, and adult testes. We sought a comprehensive understanding of these cells through a combination of histological, immunohistochemical, and ultrastructural analyses. Specifically, we examined changes in the expression of two potential SSC markers, OCT4 and PGP9.5, using immunohistochemistry. Additionally, we conducted a real-time quantitative polymerase chain reaction (RT-qPCR) to assess the relative gene expression of OCT4 and PGP9.5. The relative expression of the OCT4 gene was down-regulated in the adult testes compared to its expression during prepubertal and neonatal life. The relative expression of the PGP9.5 gene was up-regulated in the neonatal testes and down-regulated in the prepubertal and adult testes. The spermatogonia were round, oval-to-ellipsoidal cells lying over the basement membrane (BM) with a round-to-oval nucleus. Based on the immunoexpression of the putative SSC markers, OCT4 and PGP9.5, we concluded that the proportion of stem cells was highest during the neonatal stage, followed by the prepubertal and prenatal stages. This finding sheds light on the dynamics of spermatogonial stem cells in buffalo testes at different developmental stages, providing valuable insights into these cells' regulation and potential applications.
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Affiliation(s)
- Ashritha Q Carlo
- Department of Veterinary Anatomy, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Devendra Pathak
- Department of Veterinary Anatomy, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Ratan K Choudhary
- Animal Stem Cells Lab, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Opinder Singh
- Department of Veterinary Anatomy, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Neelam Bansal
- Department of Veterinary Anatomy, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
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Qin M, Han S, Chen M, Li P, Wang Y, Niu W, Gao C, Wang H, Li Y. Biofilm formation of Hafnia paralvei induced by c-di-GMP through facilitating bcsB gene expression promotes spoilage of Yellow River carp (Cyprinus carpio). Food Microbiol 2024; 120:104482. [PMID: 38431313 DOI: 10.1016/j.fm.2024.104482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
Hafnia paralvei, a Gram-negative foodborne pathogen, is found ubiquitously in various aquatic animals and seafoods, which can form biofilm as a dominant virulence factor that contributes to its pathogenesis. However, the biofilm formation mechanism of H. paralvei and its effect on food spoilage has not been fully characterized. Here we show that biofilm formation, is regulated by c-di-GMP which mediated by bcsB, can increase the spoilage ability of H. paralvei. We found that GTP was added exogenously to enhance the synthesis of c-di-GMP, which further promoted biofilm formation. The gene dgcC, one of 11 genes encoding GGDEF domain-containing proteins in H. paralvei, was significantly upregulated with GTP as substrate. The upregulation of dgcC contributes to a significant increase of c-di-GMP and the formation of biofilm. In addition, the overexpression of dgcC induced upregulation of bcsB, a reported effector protein encoding gene, which was further demonstrated that overexpression of bcsB can encourage the synthesis of bacterial cellulose and biofilm formation. The effect of biofilm formation induced by c-di-GMP on spoilage of Yellow River carp (Cyprinus carpio) was evaluated by sensory evaluation, the total viable count, and the total volatile basic nitrogen, which showed that biofilm formation can significantly increase the spoilage ability of H. paralvei on C. carpio. Our findings provide the regulation of c-di-GMP on expression of bcsB, that can contribute to biofilm formation and spoilage ability of H. paralvei, which is favor to understanding the pathogenesis of Hafnia paralvei and its role in food spoilage.
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Affiliation(s)
- Mengyuan Qin
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Shuo Han
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Miaomiao Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Pengju Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Yuqi Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Wenfang Niu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Chao Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China
| | - Hailei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China; Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, 637141, Singapore
| | - Yi Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang, 453007, China.
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Liu Y, Han X, Han Y, Bi J, Wu Y, Xiang D, Zhang Y, Bi W, Xu M, Li J. Integrated transcriptomic analysis systematically reveals the heterogeneity and molecular characterization of cancer-associated fibroblasts in osteosarcoma. Gene 2024; 907:148286. [PMID: 38367852 DOI: 10.1016/j.gene.2024.148286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Osteosarcoma (OS), with a peak incidence during the adolescent growth spurt, is correlated with poor prognosis for its high malignancy. The tumor microenvironment (TME) is highly complicated, with frequent interactions between tumor and stromal cells. The cancer-associated fibroblasts (CAFs) in the TME have been considered to actively involve in the progression, metastasis, and drug resistance of OS. This study aimed to characterize cellular heterogeneity and molecular characterization in CAFs subtypes and explore the potential targeting therapeutic strategies to improve the prognosis of OS patients. METHODS The single-cell atlas of human OS tumor lesions were constructed from the GEO database. Then significant marker genes and potential biological functions for each CAFs subtype were identified and explored using the Seurat R package. Next, by performing the survival analyses and constructing the risk scores for CAFs subtypes, we aimed to identify and characterize the prognostic values of specific marker genes and different CAFs subtypes. Furthermore, we explored the therapeutic targets and innovative drugs targeting different CAFs subtypes based on the GDSC database. Finally, prognoses related CAFs subtypes were further validated through immunohistochemistry (IHC) on clinical OS specimens. RESULTS Overall, nine main cell clusters and five subtypes of CAFs were identified. The differentially expressed marker genes for each CAFs clusters were then identified. Moreover, through Gene Ontology (GO) enrichment analysis, we defined the CAFs_2 (upregulated CXCL14 and C3), which was closely related to leukocyte migration and chemotaxis, as inflammatory CAFs (iCAFs). Likewise, we defined the CAFs_4 (upregulated CD74, HLA-DRA and HLA-DRB1), which was closely related to antigen process and presentation, as antigen-presenting CAFs (apCAFs). Furthermore, Kaplan-Meier analyses showed that CAFs_2 and CAFs_4 were correlated with poor clinical prognosis of OS patients. Meanwhile, therapeutic drugs targeting CAFs_2 and CAFs_4, such as 17-AAG/Docetaxel/Bleomycin and PHA-793887/NG-25/KIN001-102, were also explored, respectively. Finally, IHC assay confirmed the abundant CAFs_2 and CAFs_4 subtypes infiltration in the OS microenvironment compared with adjacent tissues. CONCLUSION Our study revealed the diversity, complexity, and heterogeneity of CAFs in OS, and complemented the single-cell atlas in OS TME.
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Affiliation(s)
- Yuyang Liu
- Department of Neurosurgery, 920th Hospital of Joint Logistics Support Force, Kunming 650032, Yunnan, China; Chinese PLA Spinal Cord Injury Treatment Center, Kunming, Yunnan 650032, China
| | - Xinli Han
- School of Medicine, Nankai University, Tianjin 300074, China
| | - Yuchen Han
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China; Medical School of Chinese PLA, Beijing 100853, China
| | - Jingyou Bi
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China
| | - Yanan Wu
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China
| | - Dongquan Xiang
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China
| | - Yinglong Zhang
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China
| | - Wenzhi Bi
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China; School of Medicine, Nankai University, Tianjin 300074, China; Medical School of Chinese PLA, Beijing 100853, China
| | - Meng Xu
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China; Medical School of Chinese PLA, Beijing 100853, China.
| | - Jianxiong Li
- Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital, Beijing 100048, China.
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Rohani Z, Sazegar H, Rahimi E. Unlocking the potential of Escherichia coli K-12: A novel approach for malignancy reduction in colorectal cancer through gene expression modulation. Gene 2024; 906:148266. [PMID: 38342251 DOI: 10.1016/j.gene.2024.148266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
Studies have noted the association between Escherichia coli K-12 (E. coli K-12) and the reduction of malignancy in colorectal cancer (CRC). However, the molecular mechanisms underlying this relationship have not been thoroughly explored. The aim of this study was to identify the genes influenced by E. coli K-12 and their connection to CRC. We identified the genes affected by E. coli K-12 using the GSE50040 dataset. Additionally, we investigated the relationship between the expression of genes affected by E. coli K-12 and CRC using the cancer genome atlas data. The association between the expression of E. coli K-12-affected genes and patient prognosis was investigated using clinical data. Pathways related to CRC and E. coli K-12-related genes were analyzed using the Enrichr tool. Furthermore, we employed a protein-protein interaction (PPI) network to identify hub genes associated with both E. coli K-12 and CRC. To validate our findings, we conducted RT-qPCR analysis on CRC samples and adjacent normal tissue. The results of GSE50040 showed that E. coli K-12 could change the expression of many genes related to CRC in colorectal cell lines. The results showed that E. coli K-12 reduces the expression of several genes linked to the main pathways used by cancer cells, such as the metastasis, WNT, cell proliferation pathway, and mTORC1. It was demonstrated that elevated BGN, FJX1, and LZTS1 expression is linked to a bad prognosis in patients and that E. coli K-12 may be able to lower this expression. Also, based on the PPI network, genes such as KLF4 and CXCL3 were identified as hub genes related to genes affected by E. coli K-12. When KLF4 and CXCL3 expression levels in cancer samples were compared to nearby normal tissue, a significant change in these genes' expression levels was found in CRC. Our findings demonstrated the potential relationship between oncogene genes and genes impacted by E. coli K-12. Also, our findings demonstrated that E. coli K-12 may regulate the expression of genes linked to a high death rate. In summary, the results of this study suggest that E. coli K-12 can be regarded as a significant probiotic with the potential to mitigate the risk of CRC development.
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Affiliation(s)
- Zeinab Rohani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hossein Sazegar
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Ebrahim Rahimi
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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11
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Kadan-Jamal K, Jog A, Sophocleous M, Dotan T, Frumin P, Kuperberg Goshen T, Schuster S, Avni A, Shacham-Diamand Y. Sensing of gene expression in live cells using electrical impedance spectroscopy and DNA-functionalized gold nanoparticles. Biosens Bioelectron 2024; 252:116041. [PMID: 38401280 DOI: 10.1016/j.bios.2024.116041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 02/26/2024]
Abstract
A novel electrical impedance spectroscopy-based method for non-destructive sensing of gene expression in living cells is presented. The approach used takes advantage of the robustness and responsiveness of electrical impedance spectroscopy and the highly specific and selective nature of DNA hybridization. The technique uses electrical impedance spectroscopy and gold nanoparticles functionalized with single-stranded DNA complementary to an mRNA of interest to provide reliable, real-time, and quantifiable data on gene expression in live cells. The system was validated by demonstrating specific detection of the uidA mRNA, which codes for the β-glucuronidase (GUS) enzyme, in Solanum lycopersicum MsK8 cells. Gold nanoparticles were functionalized with single-stranded DNA oligonucleotides consisting of either a sequence complementary to uidA mRNA or an arbitrary sequence. The DNA-functionalized gold nanoparticles were mixed with cell suspensions, allowing the gold nanoparticles to penetrate into the cells. The impedance spectra of suspensions of cells with gold nanoparticles inserted within them were then studied. In suspensions of uidA-expressing cells and gold nanoparticles functionalized with the complementary single-stranded DNA oligonucleotide, the impedance magnitude in the frequency range of interest was significantly higher (146 %) in comparison to all other controls. Due to its highly selective nature, the methodology has the potential to be used as a precision agricultural sensing system for accurate and real-time detection of markers of stress, viral infection, disease, and normal physiological activities.
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Affiliation(s)
- Kian Kadan-Jamal
- Department of Materials Science and Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Aakash Jog
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel.
| | - Marios Sophocleous
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Research & Development Department, eBOS Technologies Ltd., Nicosia, Cyprus
| | - Tali Dotan
- Department of Materials Science and Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Polina Frumin
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Silvia Schuster
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yosi Shacham-Diamand
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel; Scojen Institute of Synthetic Biology, Reichmann University, Herzliya, Israel
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12
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Chen K, Zhang Y, Li C, Liu Y, Cao Q, Zhang X. Clinical value of molecular subtypes identification based on anoikis-related lncRNAs in castration-resistant prostate cancer. Cell Signal 2024; 117:111104. [PMID: 38373667 DOI: 10.1016/j.cellsig.2024.111104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/07/2023] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Anoikis is a distinctive type of apoptosis. It is involved in tumor progression and metastasis. But its function in castration-resistant prostate cancer (CRPC) remains veiled. We aimed to develop a prognostic indicator based on anoikis-related long non-coding RNAs (arlncRNAs) and to investigate their biological function in CRPC. MATERIAL AND METHOD Differentially expressed anoikis-related genes were extracted from two CRPC datasets, GSE51873, and GSE78201. Four lncRNAs associated with the anoikis-related genes were selected. A risk model based on these lncRNAs was developed and validated in The Cancer Genome Atlas (TCGA) and the Memorial Sloan-Kettering Cancer Center (MSKCC) prostate cancer cohorts. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, immune infiltration, immune checkpoints expression, and drug susceptibility were performed based on the model. To identify the biofunction of anoikis-related lncRNA, CCK-8 assays, colony formation assays, and flow cytometry were used. RESULT Twenty-nine anoikis-related genes were differentially expressed in the CRPC datasets. And 36 prognostic arlncRNAs were selected for the LASSO Cox analysis. Patients were subsequently classified into two subtypes by constructing an anoikis-related lncRNA based prognostic index (ARPI). The accuracy of this index was validated. KEGG enrichment analysis revealed that the high-ARPI group was enriched in cancer-related and immune-related pathways. Immune infiltration analysis has indicated a positive association between high-ARPI groups and increased immune infiltration. Fulvestrant, OSI-027, Lapatinib, Dabrafenib, and Palbociclib were identified as potential sensitive drugs for high-ARPI patients. In vitro experiments exhibited that silencing LINC01138 dampened the proliferation, migration and enzalutamide resistance in CRPC. Furthermore, it stimulated apoptosis and inhibited the eithelial-mesenchymal transition process. CONCLUSION Four arlncRNAs were identified and a risk model was established to predict the prognosis of patients with prostate cancer. Immune infiltration and drug susceptibility analysis revealed a potential therapeutic strategy for patients with castration-resistant prostate cancer.
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Affiliation(s)
- Kailei Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yunxuan Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chengyong Li
- Department of Urology, the Second Hospital of Shanxi Medical University, Taiyuan 030000, China
| | - Yuenan Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qi Cao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China..
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13
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Suthar JK, Vaidya A, Ravindran S. Size, Surface Properties, and Ion Release of Zinc Oxide Nanoparticles: Effects on Cytotoxicity, Dopaminergic Gene Expression, and Acetylcholinesterase Inhibition in Neuronal PC-12 Cells. Biol Trace Elem Res 2024; 202:2254-2271. [PMID: 37713055 DOI: 10.1007/s12011-023-03832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/25/2023] [Indexed: 09/16/2023]
Abstract
The extensive applications of zinc oxide nanoparticles (ZnO NPs) have resulted in a substantial risk of human exposure. However, the knowledge of the toxicity of these NPs in the nervous system is still limited. A comparative analysis of ZnO NPs of various sizes and NPs of the same size, with and without surface coating, and the potential role of released zinc ions is yet to be thoroughly explored. As a result, we have studied the cellular toxicity of two different-sized ZnO NPs, ZnO-22 (22 nm) and ZnO-43 (43 nm), and NPs with similar size but with polyvinylpyrrolidone coating (ZnO-P, 45 nm). The findings from our study suggested a time-, size-, and surface coating-dependent cytotoxicity in PC-12 cells at a concentration ≥ 10 μg/ml. ZnO NP treatment significantly elevated reactive oxygen and reactive nitrogen species, thereby increasing oxidative stress. The exposure of ZnO-22 and ZnO-43 significantly upregulated the expression of monoamine oxidase-A and downregulated the α-synuclein gene expression associated with the dopaminergic system. The interaction of NPs enzymes in the nervous system is also hazardous. Therefore, the inhibition activity of acetylcholinesterase enzyme was also studied for its interaction with these NPs, and the results indicated a dose-dependent inhibition of enzyme activity. Particle size, coating, and cellular interactions modulate ZnO NP's cytotoxicity; smaller sizes enhance cellular uptake and reactivity, while coating reduces cytotoxicity by limiting direct cell contact and potentially mitigating oxidative stress. Furthermore, the study of released zinc ions from the NPs suggested no significant contribution to the observed cytotoxicity compared to the NPs.
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Affiliation(s)
- Jitendra Kumar Suthar
- Symbiosis School of Biological Sciences, Faculty of Medical and Health Sciences, Symbiosis International (Deemed) University, Pune, India
| | - Anuradha Vaidya
- Symbiosis Centre for Stem Cell Research, Symbiosis School of Biological Sciences, Symbiosis International (Deemed) University, Pune, India
| | - Selvan Ravindran
- Symbiosis School of Biological Sciences, Faculty of Medical and Health Sciences, Symbiosis International (Deemed) University, Pune, India.
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14
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Sun M, Jing Y, Zhang T, Hu F, Chen Q, Liu G. Effect of salinity on the toxicokinetics, oxidative stress, and metallothionein gene expression in Meretrix meretrix exposed to cadmium. Comp Biochem Physiol C Toxicol Pharmacol 2024; 279:109863. [PMID: 38387688 DOI: 10.1016/j.cbpc.2024.109863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/29/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
To understand the effect of salinity on the toxicokinetics, oxidative stress, and detoxification of cadmium-exposed Meretrix meretrix, M. meretrix were acclimatized to different salinities (8, 14, 20, 26, and 32 ppt) for 14 d, exposed to 10 μg/L Cd for 7 d, followed by a 28-day depuration period. The internal Cd concentration was determined, and the activities of antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and glutathione-S-transferase (GST)), and the malondialdehyde (MDA) content were measured. The mRNA expression levels of antioxidant enzyme (Cu/Zn SOD, CAT) and detoxification-related genes metallothionein (MT) were analyzed. The mean concentrations of Cd in M. meretrix tissues were in the order gill > digestive gland > mantle > axe foot. The Cd uptake rate in the four tissues decreased with increasing salinity (range: 14-26 ppt). The Cd elimination half-lives were the highest at 8 ppt and 14 ppt salinity. Cadmium activated the four oxidative stress-related related enzymes in the gills. At the end of accumulation period, Cd exposure at 20 ppt salinity significantly increased the expression of Cu/Zn SOD. CAT expression was significantly inhibited at 20 ppt salinity, but was induced at 32 ppt. MT mRNA expression was only induced under Cd at 20 ppt salinity. At the end of depuration period, Cu/Zn SOD expression was inhibited at salinities of 8, 14, and 26 ppt. The results indicated that SOD, CAT, GST, MDA, Cu/Zn SOD, CAT, and MT were sensitive to cadmium in a water environment, and can be used as indicators of marine heavy metal pollution.
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Affiliation(s)
- Ming Sun
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China.
| | - Yuanyuan Jing
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Tianwen Zhang
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Fanguang Hu
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Qun Chen
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China
| | - Guangbin Liu
- Marine Science Research Institute of Shandong Province, Qingdao 266104, PR China.
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15
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El-Kossi DMMH, Ibrahim SS, Hassanin KMA, Hamad N, Rashed NA, Abdel-Wahab A. Ameliorative Effects of Zinc Oxide, in Either Conventional or Nanoformulation, Against Bisphenol A Toxicity on Reproductive Performance, Oxidative Status, Gene Expression and Histopathology in Adult Male Rats. Biol Trace Elem Res 2024; 202:2143-2157. [PMID: 37682394 PMCID: PMC10954980 DOI: 10.1007/s12011-023-03830-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023]
Abstract
Bisphenol A (BPA) is a widely used endocrine disruptor that represents a significant risk to male reproductive function. Zinc (Zn) is vital for appropriate development of testes and to guarantee optimal testicular function and spermatogenesis. Our goal was to investigate if zinc oxide (ZnO), either in conventional or nanoformulation, could safeguard adult male rats' reproductive performance against the damaging effects of BPA. Signaling expression of CYP11A1 and Nrf-2 in the testis, testicular oxidant-antioxidant status, Bax/Bcl-2 apoptotic ratio, and histological examination of various reproductive organs were all evaluated. Twenty-eight adult male albino rats were divided randomly into 4 groups (7 animals each) including the control, BPA, conventional zinc oxide (cZnO) + BPA, and zinc oxide nanoparticles (ZnO-NPs) + BPA groups. The study was extended for 2 successive months. Our findings revealed strong negative effects of BPA on sperm cell characteristics such as sperm motility, viability, concentration and abnormalities. Additionally, BPA reduced serum levels of testosterone, triiodothyronine (T3), and thyroxine (T4). Also, it evoked marked oxidative stress in the testes; elevating malondialdehyde (MDA) and reducing total antioxidant capacity (TAC). BPA significantly downregulated testicular mRNA relative expression levels of CYP11A1 and Nrf-2, compared to control. Testicular apoptosis was also prompted by increasing Bax/ Bcl-2 ratio in testicular tissue. Histopathological findings in the testes, epididymis, prostate gland, and seminal vesicle confirmed the detrimental effects of BPA. Interestingly, cZnO and ZnO-NPs significantly alleviated all negative effects of BPA, but ZnO-NPs performed better. In conclusion, our findings point to ZnO, specifically ZnO-NPs, as a viable treatment for BPA-induced testicular dysfunction.
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Affiliation(s)
- Dina M M H El-Kossi
- Physiology Department, Faculty of Veterinary Medicine, Minia University, El-Minia, 61519, Egypt
| | - Shawky S Ibrahim
- Physiology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Kamel M A Hassanin
- Biochemistry Department, Faculty of Veterinary Medicine, Minia University, El-Minia, 61519, Egypt
| | - Nashwa Hamad
- Department of Pathology and Clinical Pathology, Faculty of Veterinary Medicine, Assiut University, Assiut, 71515, Egypt
| | - Noha A Rashed
- Department of Human Anatomy and Embryology, Faculty of Medicine, Assiut University, Assiut, 71515, Egypt
| | - Ahmed Abdel-Wahab
- Physiology Department, Faculty of Veterinary Medicine, Minia University, El-Minia, 61519, Egypt.
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16
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Almeida OGG, Pereira MG, Bighetti-Trevisan RL, Santos ES, De Campos EG, Felis GE, Guimarães LHS, Polizeli MLTM, De Martinis BS, De Martinis ECP. Investigating luxS gene expression in lactobacilli along lab-scale cocoa fermentations. Food Microbiol 2024; 119:104429. [PMID: 38225038 DOI: 10.1016/j.fm.2023.104429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Previous metagenomic analyses have suggested that lactobacilli present potential for Quorum Sensing (QS) in cocoa fermentation, and in the present research, laboratory scale fermentations were carried out to monitor the expression of luxS, a universal marker of QS. For that, 96 h-fermentations were studied, as follows: F0 (non inoculated control), F1 (inoculated with yeasts, lactic acid bacteria, and acetic acid bacteria), F2 (inoculated with yeasts and acetic acid bacteria), F3 (inoculated with yeasts only). The parameters evaluated were: plate counting, quantification of key enzymes and analysis of volatile organic compounds associated with key sensory descriptors, using headspace gas chromatography-mass spectrometry (GC-MS). Furthermore, QS was estimated by the quantification of the expression of luxS genes by Reverse Transcriptase Real-Time PCR. The results demonstrated that microbial succession occurred in pilot scale fermentations, but no statistical differences for microbial enumeration and α-diversity index were observed among experiments and control. Moreover, it was not possible to make conclusive correlations of enzymatic profile and fermenting microbiota, likely due to the intrinsic activity of plant hydrolases. Regarding to the expression of luxS genes, in Lactiplantibacillus plantarum they were active along the fermentation, but for Limosilactobacillus fermentum, luxS was expressed only at early and middle phases. Correlation analysis of luxS expression and production of volatile metabolites evidenced a possible negative association of Lp. Plantarum with fermentation quality. In conclusion, these data corroborate former shotgun metagenomic analysis by demonstrating the expression of luxS by lactobacilli in pilot scale cocoa fermentation and evidence Lp. Plantarum is the main lactic acid bacteria related to its expression.
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Affiliation(s)
- O G G Almeida
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Brazil
| | - M G Pereira
- Universidade Do Estado de Minas Gerais, Unidade Passos, Brazil
| | - R L Bighetti-Trevisan
- Universidade de São Paulo, Faculdade de Odontologia de Ribeirão Preto, Departamento de Biologia Básica e Oral, Brazil
| | - E S Santos
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Brazil
| | - E G De Campos
- Appalachian State University, Department of Chemistry and Fermentation Sciences, Boone, NC, United States; Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil
| | - G E Felis
- University of Verona, Department of Biotechnology, Verona, Italy
| | - L H S Guimarães
- Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Brazil
| | - M L T M Polizeli
- Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Brazil
| | - B S De Martinis
- Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil
| | - E C P De Martinis
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Brazil.
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17
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Mandal K, Tomar SK, Kumar Santra M. Decoding the ubiquitin language: Orchestrating transcription initiation and gene expression through chromatin remodelers and histones. Gene 2024; 904:148218. [PMID: 38307220 DOI: 10.1016/j.gene.2024.148218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Eukaryotic transcription is a finely orchestrated process and it is controlled by transcription factors as well as epigenetic regulators. Transcription factors and epigenetic regulators undergo different types of posttranslational modifications including ubiquitination to control transcription process. Ubiquitination, traditionally associated with protein degradation, has emerged as a crucial contributor to the regulation of chromatin structure through ubiquitination of histone and chromatin remodelers. Ubiquitination introduces new layers of intricacy to the regulation of transcription initiation through controlling the equilibrium between euchromatin and heterochromatin states. Nucleosome, the fundamental units of chromatin, spacing in euchromatin and heterochromatin states are regulated by histone modification and chromatin remodeling complexes. Chromatin remodeling complexes actively sculpt the chromatin architecture and thereby influence the transcriptional states of genes. Therefore, understanding the dynamic behavior of nucleosome spacing is critical as it impacts various cellular functions through controlling gene expression profiles. In this comprehensive review, we discussed the intricate interplay between ubiquitination and transcription initiation, and illuminated the underlying molecular mechanisms that occur in a variety of biological contexts. This exploration sheds light on the complex regulatory networks that govern eukaryotic transcription, providing important insights into the fine orchestration of gene expression and chromatin dynamics.
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Affiliation(s)
- Kartik Mandal
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Shiva Kumar Tomar
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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18
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Luo X, Luan C, Zhou J, Ye Y, Zhang W, Jain R, Zhang E, Chen N. Glycolytic enzyme Enolase-1 regulates insulin gene expression in pancreatic β-cell. Biochem Biophys Res Commun 2024; 706:149735. [PMID: 38461647 DOI: 10.1016/j.bbrc.2024.149735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Enolase-1 (Eno1) plays a critical role in regulating glucose metabolism; however, its specific impact on pancreatic islet β-cells remains elusive. This study aimed to provide a preliminary exploration of Eno1 function in pancreatic islet β-cells. The findings revealed that the expression of ENO1 mRNA in type 2 diabetes donors was significantly increased and positively correlated with HbA1C and negatively correlated with insulin gene expression. A high level of Eno1 in human insulin-secreting rat INS-1832/13 cells with co-localization with intracellular insulin proteins was accordingly observed. Silencing of Eno1 using siRNA or inhibiting Eno1 protein activity with an Eno1 antagonist significantly reduced insulin secretion and insulin content in β-cells, while the proinsulin/insulin content ratio remained unchanged. This reduction in β-cells function was accompanied by a notable decrease in intracellular ATP and mitochondrial cytochrome C levels. Overall, our findings confirm that Eno1 regulates the insulin secretion process, particularly glucose metabolism and ATP production in the β-cells. The mechanism primarily involves its influence on insulin production, suggesting that Eno1 represents a potential target for β-cell protection and diabetes treatment.
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Affiliation(s)
- Xiumei Luo
- , Department of Endocrinology, Fudan University Zhongshan Hospital Xiamen Branch, No668. Jinhu Road, Xiamen, 361000, China
| | - Cheng Luan
- , Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Lund University, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Jingqi Zhou
- , Department of Endocrinology, Fudan University Zhongshan Hospital Xiamen Branch, No668. Jinhu Road, Xiamen, 361000, China
| | - Yingying Ye
- , Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Lund University, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Wei Zhang
- , Xiamen Key Laboratory of Cardiac Electrophysiology, Xiamen Institute of Cardiovascular Diseases, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Ruchi Jain
- , Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Lund University, Jan Waldenströms Gata 35, 20502, Malmö, Sweden
| | - Enming Zhang
- , Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Lund University, Jan Waldenströms Gata 35, 20502, Malmö, Sweden.
| | - Ning Chen
- , Department of Endocrinology, Fudan University Zhongshan Hospital Xiamen Branch, No668. Jinhu Road, Xiamen, 361000, China.
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19
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Montoya CA, Young W, Ryan L, Dunstan K, Peters J, Dewhurst H, Dekker J, Haggarty N, Dilger RN, Roy NC. The probiotic Lacticaseibacillus rhamnosus HN001 influences the architecture and gene expression of small intestine tissue in a piglet model. Br J Nutr 2024; 131:1289-1297. [PMID: 38053344 PMCID: PMC10950449 DOI: 10.1017/s0007114523002830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/25/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023]
Abstract
This study investigated the effects of Lacticaseibacillus rhamnosus HN001 supplementation on the architecture and gene expression in small intestinal tissues of piglets used as an animal model for infant humans. Twenty-four 10-d-old entire male piglets (4·3 (sd 0·59) kg body weight) were fed an infant formula (IF) (control) or IF supplemented with 1·3 × 105 (low dose) or 7·9 × 106 (high dose) colony-forming units HN001 per ml of reconstituted formula (n 8 piglets/treatment). After 24 d, piglets were euthanised. Samples were collected to analyse the histology and gene expression (RNAseq and qPCR) in the jejunal and ileal tissues, blood cytokine concentrations, and blood and faecal calprotectin concentrations. HN001 consumption altered (false discovery rate < 0·05) gene expression (RNAseq) in jejunal tissues but not in ileal tissues. The number of ileal goblet cells and crypt surface area increased quadratically (P < 0·05) as dietary HN001 levels increased, but no increase was observed in the jejunal tissues. Similarly, blood plasma concentrations of IL-10 and calprotectin increased linearly (P < 0·05) as dietary HN001 levels increased. In conclusion, supplementation of IF with HN001 affected the architecture and gene expression of small intestine tissue, blood cytokine concentration and frequencies, and blood calprotectin concentrations, indicating that HN001 modulated small intestinal tissue maturation and immunity in the piglet model.
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Affiliation(s)
- Carlos A. Montoya
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
- Riddet Institute, Massey University, Te Ohu Rangahau Kai Facility, Palmerston North4474, New Zealand
| | - Wayne Young
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
- Riddet Institute, Massey University, Te Ohu Rangahau Kai Facility, Palmerston North4474, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Fonterra Research and Development Centre, Dairy Farm Rd, Palmerston North, New Zealand
| | - Leigh Ryan
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - Kelly Dunstan
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - Jason Peters
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - Hilary Dewhurst
- Smart Foods & Bioproducts, AgResearch, Te Ohu Rangahau Kai Facility, Palmerston North, New Zealand
| | - James Dekker
- Fonterra Research and Development Centre, Dairy Farm Rd, Palmerston North, New Zealand
| | - Neill Haggarty
- Fonterra Research and Development Centre, Dairy Farm Rd, Palmerston North, New Zealand
| | - Ryan N. Dilger
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Nicole C. Roy
- Riddet Institute, Massey University, Te Ohu Rangahau Kai Facility, Palmerston North4474, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
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Mozafari Z, Shams-Ghahfarokhi M, Yahyazadeh M, Razzaghi-Abyaneh M. Effects of Tripleurospermum caucasicum, Salvia rosmarinus and Tanacetum fruticulosum essential oils on aflatoxin B 1 production and aflR gene expression in Aspergillus flavus. Int J Food Microbiol 2024; 415:110639. [PMID: 38417281 DOI: 10.1016/j.ijfoodmicro.2024.110639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Aflatoxin B1 (AFB1) is one of the most hazardous mycotoxins for humans and livestock that mainly produced by members of the genus Aspergillus in a variety of food commodities. In this study, the effect of S. rosmarinus, T. fruticulosum, and T. caucasicum essential oils (EOs) was studied on fungal growth, AFB1 production and aflR gene expression in toxigenic A. flavus IPI 247. The AFB1 producer A. flavus strain was cultured in YES medium in presence of various two-fold concentrations of the plant EOs (62.5-500 μg/mL) for 4 days at 28 °C. EO composition of plants was analyzed by Gas Chromatography/Mass Spectrometry (GC/MS). The amount of fungal growth, ergosterol content of fungal mycelia and AFB1 content of EO-treated and non-treated controls were measured. The expression of aflR gene was evaluated using Real-time PCR in the fungus exposed to minimum inhibitory concentration (MIC50) of EOs. The main constituents of the oils analyzed by GC/MS analysis were elemicin (33.80 %) and 2,3-dihydro farnesol (33.19 %) in T. caucasicum, 1,8-cineole (17.87 %), trans-caryophyllene (11.14 %), α and ẞ-pinene (10.92 and 8.83 %) in S. rosmarinus, and camphor (17.65 %), bornyl acetate (15.08 %), borneol (12.48 %) and camphene (11.72 %) in T. fruticulosum. The results showed that plant EOs at the concentration of 500 μg/mL suppressed significantly the fungal growth by 35.24-71.70 %, while mycelial ergosterol content and AFB1 production were inhibited meaningfully by 36.20-65.51 % and 20.61-89.16 %. T. caucasicum was the most effective plant, while T. fruticulosum showed the lowest effectiveness on fungal growth and AFB1 production. The expression of aflR in T. caucasicum and S. rosmarinus -treated fungus was significantly down-regulated by 2.85 and 2.12 folds, respectively, while it did not change in T. fruticulosum-treated A. flavus compared to non-treated controls. Our findings on the inhibitory activity of T. caucasicum and S. rosmarinus EOs toward A. flavus growth and AFB1 production could promise these plants as good candidates to control fungal contamination of agricultural crops and food commodities and subsequent contamination by AFB1. Down-regulation of aflR as the key regulatory gene in AF biosynthesis pathway warrants the use of these plants in AF control programs. Further studies to evaluate the inhibitory activity of studied plants EOs in food model systems are recommended.
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Affiliation(s)
- Zahra Mozafari
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran
| | - Masoomeh Shams-Ghahfarokhi
- Department of Mycology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-331, Iran.
| | - Mahdi Yahyazadeh
- Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization, Iran
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Song WJ, Cheon DH, Song H, Jung D, Chan Park H, Yeong Hwang J, Choi HJ, NamKoong C. Activation of ChAT+ neuron in dorsal motor vagus (DMV) increases blood glucose through the regulation of hepatic gene expression in mice. Brain Res 2024; 1829:148770. [PMID: 38266888 DOI: 10.1016/j.brainres.2024.148770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/26/2024]
Abstract
The brain and peripheral organs communicate through hormones and neural connections. Proper communication is required to maintain normal whole-body energy homeostasis. In addition to endocrine system, from the perspective of neural connections for metabolic homeostasis, the role of the sympathetic nervous system has been extensively studied, but understanding of the parasympathetic nervous system is limited. The liver plays a central role in glucose and lipid metabolism. This study aimed to clarify the innervation of parasympathetic nervous system in the liver and its functional roles in metabolic homeostasis. The liver-specific parasympathetic nervous system innervation (PNS) was shown by tissue clearing, immunofluorescence and transgenic mice at the three-dimensional histological level. The parasympathetic efferent signals were manipulated using a chemogenetic technique and the activation of ChAT+ parasympathetic neurons in dorsal motor vagus (DMV) results in the increased blood glucose through the elevated hepatic gluconeogenic and lipogenic gene expression in the liver. Thus, our study showed the evidence of ChAT+ parasympathetic neurons in the liver and its role for hepatic parasympathetic nervous signaling in glucose homeostasis through the regulation of hepatic gene expression.
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Affiliation(s)
- Woo-Jin Song
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Deok-Hyeon Cheon
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - HeeIn Song
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Daeun Jung
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hae Chan Park
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ju Yeong Hwang
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Jin Choi
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea; BK21Plus Biomedical Science Project Team, Seoul National University College of Medicine, Seoul, Republic of Korea; Wide River Institute of Immunology, Seoul National University College of Medicine, Hongchoen, Republic of Korea; Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Cherl NamKoong
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Division of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Core Research Laboratory, Medical Science Institute, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea.
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22
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Yu Y, Li X, Teng T, He Y, Jiang Y, Liu X, Zhou X, Luo Y, Xie P. Comparative analysis of the nucleus accumbens transcriptional features in multiple depressive animal models. Behav Brain Res 2024; 463:114890. [PMID: 38309372 DOI: 10.1016/j.bbr.2024.114890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
Chronic stress is deemed a significant clinical contributor to depression. The use of animal models of chronic stress can fully reveal the complex pathological mechanisms and their changing trends in the pathogenesis of depression, which is crucial for both disease prevention and therapy. It is also unknown how various forms of stress differ in their impact on animal physiology and behavior. The nucleus accumbens (NAc), an essential brain area for the pathophysiology of depression, and its underlying neural mechanisms remain unclear. Here, we systematically compared transcriptional signatures in the NAc of four chronic stress models in rats: chronic unpredictable mild stress (CUMS), chronic social defeat stress (CSDS), learned helplessness (LH), chronic restraint stress (CRS). The majority of differentially expressed genes (DEGs) were unique to a single depression model, while the rank-rank hypergeometric overlap analysis showed that the CSDS and CRS models had the greatest overlap, and the CRS and CUMS models had the least. Then, we performed pathway analysis of the differential genes and found that the neuroactive ligand-receptor interaction pathway was significantly enriched not only in the LH, CRS and CSDS stress models, but also significantly enriched in stress genes that were also altered in at least two stress models. Finally, we found three hub genes (Dcx, Tnc and Wdfy4) by constructing co-expression networks for stress genes. In summary, our research has the potential to offer fresh insights into the molecular mechanisms underlying depression induced by different types of stress, highlighting both their similarities and differences. It may provide valuable clues for understanding the pathogenesis of depression.
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Affiliation(s)
- Ying Yu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Li
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Teng Teng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuqian He
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuanliang Jiang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xueer Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xinyu Zhou
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Yong Luo
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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23
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Rodrigues Barreto I, Monteiro A, Paiva A, Fonseca AM. Relapsing-remitting multiple sclerosis patients exhibit differential natural killer functional subpopulations. Acta Neurol Belg 2024; 124:603-610. [PMID: 38441808 DOI: 10.1007/s13760-024-02488-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/22/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) and has been known as T-cell mediated. However, the contribution of multiple cell types, notably natural killer (NK) cells, has also been reported. AIM To quantify circulating total NK cells and its subpopulations, CD56 dim and bright, and to characterize the functional phenotype and IFN-γ and TNF-α production in relapsing-remitting patients treated with IFN-β and in apparently healthy controls. RESULTS CD56bright NK cells were found to be the least represented subpopulation. In relapse patients, the frequencies of IFN-γ-producing NK cells and their subpopulations were significantly decreased. In remission patients, CD56dim NK cells expressed high levels of HLA-DR and CD54. CONCLUSION These results suggest that remission RRMS patients, although in an inactive stage of MS, present circulating NK cells with an activation phenotype, supporting the idea that NK cells may be relevant mediators in the MS pathophysiology.
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Affiliation(s)
- Inês Rodrigues Barreto
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
| | - Andreia Monteiro
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
- Clinical Pathology Service, Centro Hospitalar Universitário da Cova da Beira (CHUCB), Covilhã, Portugal
| | - Artur Paiva
- Cytometry Operational Management Unit, Clinical Pathology Service, CHUC, Coimbra, Portugal
- iCBR - Coimbra Institute for Clinical and Biomedical Research, University of Coimbra, Coimbra, Portugal
- ESTESC-Coimbra Health School, Coimbra, Portugal
| | - Ana Mafalda Fonseca
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal.
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Harshaw K, Fahim A, Zi J, Chandrasekera PC, Chang X, Dixon B, MacIsaac HJ. Non-microcystin extracellular metabolites of Microcystis aeruginosa impair viability and reproductive gene expression in rainbow trout cell lines. Sci Total Environ 2024; 919:170747. [PMID: 38340819 DOI: 10.1016/j.scitotenv.2024.170747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Microcystis aeruginosa is a ubiquitous freshwater cyanobacterium best known for producing hepatotoxic microcystins; however, this common bloom-forming species also produces myriad biologically active and potentially deleterious other metabolites. Our understanding of the effects of these non-microcystin metabolites on fish is limited. In this study, we evaluated cytotoxicity of extracellular metabolites harvested from both microcystin-producing (MC+) and non-producing (MC-) strains of M. aeruginosa on rainbow trout (Oncorhynchus mykiss) cell lines derived from tissues of the brain, pituitary, heart, gonads, gills, skin, liver, and milt. We also examined the influence of M. aeruginosa exudates (MaE) on the expression of critical reproduction-related genes using the same cell lines. We found that exudates of the MC- M. aeruginosa strain significantly reduced viability in RTBrain, RTgill-W1, and RT-milt5 cell lines and induced significant cellular stress and/or injury in six of the eight cell lines-highlighting potential target tissues of cyanobacterial cytotoxic effects. Observed sublethal consequences of Microcystis bloom exposure occurred with both MC+ and MC- strains' exudates and significantly altered expression of developmental and sex steroidogenic genes. Collectively, our results emphasize the contributions of non-MC metabolites to toxicity of Microcystis-dominated algal blooms and the need to integrate the full diversity of M. aeruginosa compounds-beyond microcystins-into ecotoxicological risk assessments.
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Affiliation(s)
- Keira Harshaw
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Ambreen Fahim
- Canadian Centre for Alternatives to Animal Methods, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Jinmei Zi
- Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, College of Agronomy and Life Sciences, Kunming University, Kunming 650214, China
| | | | - Xuexiu Chang
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada; Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, College of Agronomy and Life Sciences, Kunming University, Kunming 650214, China
| | - Brian Dixon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Hugh J MacIsaac
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
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25
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Barnard ME, Wang X, Petrick JL, Zirpoli GR, Jones D, Johnson WE, Palmer JR. Psychosocial stressors and breast cancer gene expression in the Black Women's Health Study. Breast Cancer Res Treat 2024; 204:327-340. [PMID: 38127176 DOI: 10.1007/s10549-023-07182-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Prior studies indicate that the physiologic response to stress can affect gene expression. We evaluated differential gene expression in breast cancers collected from Black women with high versus low exposure to psychosocial stressors. METHODS We analyzed tumor RNA sequencing data from 417 Black Women's Health Study breast cancer cases with data on early life trauma and neighborhood disadvantage. We conducted age-adjusted differential gene expression analyses and pathway analyses. We also evaluated Conserved Transcriptional Response to Adversity (CTRA) contrast scores, relative fractions of immune cell types, T cell exhaustion, and adrenergic signaling. Analyses were run separately for estrogen receptor positive (ER+; n = 299) and ER- (n = 118) cases. RESULTS Among ER+ cases, the top differentially expressed pathways by stress exposure were related to RNA and protein metabolism. Among ER- cases, they were related to developmental biology, signal transduction, metabolism, and the immune system. Targeted analyses indicated greater immune pathway enrichment with stress exposure for ER- cases, and possible relevance of adrenergic signaling for ER+ cases. CTRA contrast scores did not differ by stress exposure, but in analyses of the CTRA components, ER- breast cancer cases with high neighborhood disadvantage had higher pro-inflammatory gene expression (p = 0.039) and higher antibody gene expression (p = 0.006) compared to those with low neighborhood disadvantage. CONCLUSION There are multiple pathways through which psychosocial stress exposure may influence breast tumor biology. Given the present findings on inflammation and immune response in ER- tumors, further research to identify stress-induced changes in the etiology and progression of ER- breast cancer is warranted.
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Affiliation(s)
- Mollie E Barnard
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Xutao Wang
- Division of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Jessica L Petrick
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA
| | - Dennis Jones
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, 72 E. Concord St., Boston, MA, 02118, USA.
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26
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Colvin KL, Wolter-Warmerdam K, Hickey F, Yeager ME. Altered peripheral blood leukocyte subpopulations, function, and gene expression in children with Down syndrome: implications for respiratory tract infection. Eur J Med Genet 2024; 68:104922. [PMID: 38325643 DOI: 10.1016/j.ejmg.2024.104922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 12/12/2023] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVES We tested the hypothesis that aberrant expression of Hsa21-encoded interferon genes in peripheral blood immune cells would correlate to immune cell dysfunction in children with Down syndrome (DS). STUDY DESIGN We performed flow cytometry to quantify peripheral blood leukocyte subtypes and measured their ability to migrate and phagocytose. In matched samples, we measured gene expression levels for constituents of interferon signaling pathways. We screened 49 children, of which 29 were individuals with DS. RESULTS We show that the percentages of two peripheral blood myeloid cell subtypes (alternatively-activated macrophages and low-density granulocytes) in children with DS differed significantly from typical children, children with DS circulate a very different pattern of cytokines vs. typical individuals, and higher expression levels of type III interferon receptor Interleukin-10Rb in individuals with DS correlated with reduced migratory and phagocytic capacity of macrophages. CONCLUSIONS Increased susceptibility to severe and chronic infection in children with DS may result from inappropriate numbers and subtypes of immune cells that are phenotypically and functionally altered due to trisomy 21 associated interferonopathy.
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Affiliation(s)
- Kelley L Colvin
- Department of Bioengineering, University of Colorado Denver, Aurora, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Denver, Aurora, USA
| | | | - Francis Hickey
- Anna and John J. Sie Center for Down Syndrome, Children's Hospital Colorado, Aurora, USA; Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
| | - Michael E Yeager
- Department of Bioengineering, University of Colorado Denver, Aurora, USA; Linda Crnic Institute for Down Syndrome, University of Colorado Denver, Aurora, USA.
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27
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Ren J, Gao Q, Zhou X, Chen L, Guo W, Feng K, Huang T, Cai YD. Identification of key gene expression associated with quality of life after recovery from COVID-19. Med Biol Eng Comput 2024; 62:1031-1048. [PMID: 38123886 DOI: 10.1007/s11517-023-02988-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Post-acute sequelae of COVID-19 (PASC) is a persistent complication of severe acute respiratory syndrome coronavirus 2 infection that includes symptoms, such as fatigue, cognitive impairment, and respiratory distress. These symptoms severely affect the quality of life of patients after their recovery from COVID-19. In this study, a group of machine learning algorithms analyzed the whole blood RNA-seq data from patients with different PASC levels. The purpose of this analysis was to identify the gene markers associated with PASC and the special expression patterns for different PASC levels. By comparing the quality of life of patients after the acute phase of COVID-19 and before the disease, samples in the dataset were divided into three groups, namely, "Better," "The Same," and "Worse." Each patient was represented by the expression levels of 58,929 genes. The machine learning-based workflow included six feature-ranking algorithms, incremental feature selection (IFS), and four classification algorithms. The feature ranking algorithms were in charge of assessing feature importance, whereas IFS with classification algorithms were used to extract essential genes and to construct efficient classifiers and classification rules. The expression of top genes in the results was associated with the immune response to viral infection, which is supported by the published literature. For example, patients with low CCDC18 expression and high CPED1 expression had good quality of life, whereas those with low CDC16 expression had poor quality of life.
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Affiliation(s)
- JingXin Ren
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Qian Gao
- Department of Pharmacy, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - XianChao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200030, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, 510507, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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Hussein S, Soliman NA, Dahmy SIE, Khamis T, Sameh R, Mostafa FM. Effectiveness of cannabidiol (CBD) on histopathological changes and gene expression in hepatocellular carcinoma (HCC) model in male rats: the role of Hedgehog (Hh) signaling pathway. Histochem Cell Biol 2024; 161:337-343. [PMID: 38296878 DOI: 10.1007/s00418-023-02262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2023] [Indexed: 02/02/2024]
Abstract
The third most prevalent malignancy to cause mortality is hepatocellular carcinoma (HCC). The Hedgehog (Hh) signaling pathway is activated by binding to the transmembrane receptor Patched-1 (PTCH-1), which depresses the transmembrane G protein-coupled receptor Smoothened (SMO). This study was performed to examine the preventative and therapeutic effects of cannabidiol in adult rats exposed to diethyl nitrosamine (DENA)-induced HCC.A total of 50 male rats were divided into five groups of 10 rats each. Group I was the control group. Group II received intraperitoneal (IP) injections of DENA for 14 weeks. Group III included rats that received cannabidiol (CBD) orally (3-30 mg/kg) for 2 weeks and DENA injections for 14 weeks. Group IV rats received oral CBD for 2 weeks before 14 weeks of DENA injections. Group V included rats that received CBD orally for 2 weeks after their last injection of DENA. Measurements were made for alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma glutamyl transferase (GGT), superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA), and alpha fetoprotein (AFP). Following total RNA extraction, Smo, Hhip, Ptch-1, and Gli-1 expressions were measured using quantitative real-time polymerase chain reaction (qRT-PCR). A histopathological analysis of liver tissues was performed.The liver enzymes, oxidant-antioxidant state, morphological, and molecular parameters of the adult male rat model of DENA-induced HCC showed a beneficial improvement after CBD administration. In conclusion, by focusing on the Hh signaling system, administration of CBD showed a beneficial improvement in the liver enzymes, oxidant-antioxidant status, morphological, and molecular parameters in the DENA-induced HCC in adult male rats.
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Affiliation(s)
- Samia Hussein
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Zagazig University, Zagazig, Egypt.
| | - Nabil A Soliman
- Department of Zoology, Faculty of Science, Zagazig University, Sharkia, Egypt
| | - Samih I El Dahmy
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Sharkia, Egypt
| | - Tarek Khamis
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt
| | - Reham Sameh
- Department of Pathology, Faculty of Medicine, Zagazig University, Sharkia, Egypt
| | - Fatma M Mostafa
- Department of Zoology, Faculty of Science, Zagazig University, Sharkia, Egypt
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Song P, Yakufujiang Y, Zhou J, Gu S, Wang W, Huo Z. Identification of important genes related to anoikis in acute myocardial infarction. J Cell Mol Med 2024; 28:e18264. [PMID: 38526027 PMCID: PMC10962123 DOI: 10.1111/jcmm.18264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
Acute myocardial infarction (AMI) increasingly precipitates severe heart failure, with diagnoses now extending to progressively younger demographics. The focus of this study was to pinpoint critical genes linked to both AMI and anoikis, thereby unveiling potential novel biomarkers for AMI detection and intervention. Differential analysis was performed to identify significant differences in expression, and gene functionality was explored. Weighted gene coexpression network analysis (WGCNA) was used to construct gene coexpression networks. Immunoinfiltration analysis quantified immune cell abundance. Protein-protein interaction (PPI) analysis identified the proteins that interact with theanoikis. MCODE identified key functional modules. Drug enrichment analysis identified relevant compounds explored in the DsigDB. Through WGCNA, 13 key genes associated with anoikis and differentially expressed genes were identified. GO and KEGG pathway enrichment revealed the regulation of apoptotic signalling pathways and negative regulation of anoikis. PPI network analysis was also conducted, and 10 hub genes, such as IL1B, ZAP70, LCK, FASLG, CD4, LRP1, CDH2, MERTK, APOE and VTN were identified. IL1B were correlated with macrophages, mast cells, neutrophils and Tcells in MI, and the most common predicted medications were roxithromycin, NSC267099 and alsterpaullone. This study identified key genes associated with AMI and anoikis, highlighting their role in immune infiltration, diagnosis and medication prediction. These findings provide valuable insights into potential biomarkers and therapeutic targets for AMI.
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Affiliation(s)
- Puwei Song
- Department of Thoracic‐Cardiovascular Surgery, Shanghai Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yasen Yakufujiang
- Department of Thoracic‐Cardiovascular Surgery, Shanghai Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Jianghui Zhou
- Department of Thoracic‐Cardiovascular Surgery, Shanghai Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Shaorui Gu
- Department of Thoracic‐Cardiovascular Surgery, Shanghai Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Wenli Wang
- Department of Thoracic‐Cardiovascular Surgery, Shanghai Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Zhengyuan Huo
- Department of Thoracic‐Cardiovascular Surgery, Shanghai Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
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Hamzaoui K, Louhaichi S, Salhi M, Sassi FH, Laathar A, Hamzaoui A. IL-38 in Behçet's disease: Gene expression in bronchoalveolar lavage from patients having pulmonary involvement. Immunol Lett 2024; 266:106840. [PMID: 38307260 DOI: 10.1016/j.imlet.2024.106840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024]
Abstract
The etiological complexity of Behçet disease (BD), an immune-mediated rare form of vasculitis characterized by multi-organ involvement, is still elusive due to an incomplete understanding of the synergy between genetic susceptibility, environmental triggers, and an abnormal immune response. The diagnosis of BD relies on clinical symptoms. Lung inflammatory disorders are severe conditions of patients with BD, here we focus on the expression of biomarkers in BD patients with pulmonary manifestations. Aiming to identify additional discriminating biomarker patterns, we measured and compared protein and gene expression of IL-38 and a broad panel of selected genes in bronchoalveolar cells of patients suffering from BD with and without pulmonary involvement compared to controls. ELISA and RT-PCR analysis were applied. The first principal analysis highlighted decreased IL-38 level in BD patients compared to Rheumatoid Arthritis (RA) patients and controls: BD patients expressed lower IL-38 levels, particularly in cases with pulmonary involvement. The area under the curve (AUC) of the receiver-operating characteristic curve showed that IL-38 may be an eventual biomarker for BD. Co-cultured recombinant IL-38 and stimulated memory PBMCs of active BD, were able to suppress IL-17 and NLRP3 inflammasome and ameliorate the secretion of IL-10 and TGFβ. Transcription factors of the IL-1 family (IL-1β, IL-18, IL-32, IL-33 and IL-37) along with IFN-γ, IL-17, RORγt, Foxp3, TGFβ, IL-10 and NLRP3 inflammasome were the parameters that are the main contributor to the segregation between BD with and without lung involvement. Our results indicate that IL-38 might be involved in the pathogenesis of BD and the combined gene expression in BAL suggests distinct mechanisms governing the inflammatory disorders in the lung.
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Affiliation(s)
- Kamel Hamzaoui
- University of Tunis El Manar, Tunis, Tunisia; Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Department of Respiratory Diseases, Pavillon B, Hospital A. Mami, Ariana, Tunisia.
| | - Sabrine Louhaichi
- University of Tunis El Manar, Tunis, Tunisia; Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Department of Respiratory Diseases, Pavillon B, Hospital A. Mami, Ariana, Tunisia; Department of Lung Diseases, Abderrahmane Mami Hospital of Pneumology, Ariana, Tunisia
| | - Mariem Salhi
- University of Tunis El Manar, Tunis, Tunisia; Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Department of Respiratory Diseases, Pavillon B, Hospital A. Mami, Ariana, Tunisia
| | - Fayçal Haj Sassi
- University of Tunis El Manar, Tunis, Tunisia; Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Department of Respiratory Diseases, Pavillon B, Hospital A. Mami, Ariana, Tunisia
| | - Ahmed Laathar
- University of Tunis El Manar, Tunis, Tunisia; Department of Rheumatology, Mongi Slim Hospital, La Marsa, Tunisia
| | - Agnes Hamzaoui
- University of Tunis El Manar, Tunis, Tunisia; Research Laboratory 19SP02 "Chronic Pulmonary Pathologies: From Genome to Management", Department of Respiratory Diseases, Pavillon B, Hospital A. Mami, Ariana, Tunisia; Department of Lung Diseases, Abderrahmane Mami Hospital of Pneumology, Ariana, Tunisia
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Rezaei S, Timani KA, He JJ. Metformin Treatment Leads to Increased HIV Transcription and Gene Expression through Increased CREB Phosphorylation and Recruitment to the HIV LTR Promoter. Aging Dis 2024; 15:831-850. [PMID: 37450926 PMCID: PMC10917544 DOI: 10.14336/ad.2023.0705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Antiretroviral therapy has effectively suppressed HIV infection and replication and prolonged the lifespan of HIV-infected individuals. In the meantime, various complications including type 2 diabetes associated with the long-term antiviral therapy have shown steady increases. Metformin has been the front-line anti-hyperglycemic drug of choice and the most widely prescribed medication for the treatment of type 2 diabetes. However, little is known about the effects of Metformin on HIV infection and replication. In this study, we showed that Metformin treatment enhanced HIV gene expression and transcription in HIV-transfected 293T and HIV-infected Jurkat and human PBMC. Moreover, we demonstrated that Metformin treatment resulted in increased CREB expression and phosphorylation, and TBP expression. Furthermore, we showed that Metformin treatment increased the recruitment of phosphorylated CREB and TBP to the HIV LTR promoter. Lastly, we showed that inhibition of CREB phosphorylation/activation significantly abrogated Metformin-enhanced HIV gene expression. Taken together, these results demonstrated that Metformin treatment increased HIV transcription, gene expression, and production through increased CREB phosphorylation and recruitment to the HIV LTR promoter. These findings may help design the clinical management plan and HIV cure strategy of using Metformin to treat type 2 diabetes, a comorbidity with an increasing prevalence, in people living with HIV.
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Affiliation(s)
- Sahar Rezaei
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Khalid A Timani
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Johnny J He
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
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Lou X, Wu Y, Huang Z, Zhang W, Xiao X, Wu J, Li J, Fang Z. Biofilm formation and associated gene expression changes in Cronobacter from cereal related samples in China. Food Microbiol 2024; 118:104409. [PMID: 38049271 DOI: 10.1016/j.fm.2023.104409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Cronobacter is an important foodborne pathogen that can cause severe neonatal meningitis, necrotizing enterocolitis, and bacteremia. Currently, there is limited knowledge of biofilm formation in Cronobacter. In the present study, biofilm formation ability and associated gene expression changes in Cronobacter from cereal related samples was carried out systematically. Our results from 307 Cronobacter isolates analyzed for 48 h showed strong biofilm-forming ability in 14 strains (4.6%), moderate in 47 strains (15.3%), weak in 142 strains (46.2%), and no such ability in the remaining 104 strains (33.9%). Further studies on five strains with strong biofilm-forming ability showed that maximum biofilm formation in Cronobacter occurred after 24 h of cultivation, reaching a peak around 48 h-72 h, reducing gradually thereafter. Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed that differentially expressed genes (DEGs) involved in flagellar assembly, oxidative phosphorylation, ribosome, photosynthesis, O-Antigen nucleotide sugar biosynthesis, citrate cycle (tricarboxylic acid cycle, TCA) and bacterial chemotaxis were enriched in biofilm forming cells. The genes involved these enrichment pathways were mostly downregulated when compared to planktonic cells. Several transcriptional regulator genes such as csrA and bolA, and the cell surface composition regulator gene glgS were significantly upregulated. 12 of 13 (92.3%) selected genes was found to be in agreement with the RNA-Seq of planktonic and biofilm cells by Quantitative real-time PCR analysis, thus increasing confidence in our data. Our research lays a sound theoretical basis for further studies on mechanisms regulating biofilm formation and provides a foundation for development of new food safety measures, clinical disease prevention and control.
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Affiliation(s)
- Xiuqin Lou
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, China
| | - Yue Wu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, China
| | - Zhenzhou Huang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, China
| | - Wei Zhang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, China
| | - Xiao Xiao
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, China
| | - Jun Wu
- Lin'an Center for Disease Control and Prevention, Hangzhou, 311399, China
| | - Jun Li
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, China.
| | - Zhiguo Fang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China.
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Molina-López J, Herrera-Quintana L, Vázquez-Lorente H, Planells E. Evolution of Vitamin D Status and Vitamin D Receptor Gene Expression Among Professional Handball Athletes During a Competitive Period. Relationship with Body Composition, Calcium, Magnesium and Phosphorous. Biol Trace Elem Res 2024; 202:1345-1355. [PMID: 37410265 PMCID: PMC10859345 DOI: 10.1007/s12011-023-03760-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
INTRODUCTION A generalized risk of vitamin D deficiency exists worldwide affecting also professional and elite athletes. This study assesses the evolution of vitamin D status and vitamin D receptor (VDR) gene expression and their relationship with body composition, calcium (Ca), magnesium (Mg) and phosphorous (P) among professional handball athletes during a competitive period. METHODS A total of 26 male subjects were recruited: 13 professional handball athletes and 13 non-athlete controls. An observational follow-up study was conducted in 2 time points over a 16-week period. Nutritional intake, body composition, and routinary biochemical parameters were measured via 24-hours recall, bioimpedance and enzyme immunoassay, respectively. Ca and Mg were measured by flame atomic absorption spectrophotometry and P was determined with the colorimetric method of Fiske-Subbarow. 25-hydroxyvitamin-D (25(OH)D) levels and its forms (i.e., 25(OH)D3 and 25(OH)D2) were measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS), whereas VDR gene expression was measured by quantitative real time-polymerase chain reaction (qRT-PCR). RESULTS A total of 54% of the athletes showed deficient vitamin D status. Moreover, a prevalence of insufficient vitamin D status in handball players affected 46% at baseline, reaching 61% after 16 weeks. Vitamin D showed no evolution during the competitive period and no differences between groups were observed (all p ≥ 0.05). Handball players increased the VDR expression, enhanced body composition, Ca and Mg levels at 16-weeks follow-up (all p < 0.05). VDR gene expression was positively related with body mass and body mass index at follow-up in athletes (all p ≤ 0.038; r ≥ 0.579) and with Ca at baseline in controls (p = 0.026; r = 0.648). Finally, 25(OH)D2 form was directly associated with P in athletes at 16 weeks of study (p = 0.034; r = 0.588). CONCLUSION Players of indoor team sports such as handball would be a population at risk of vitamin D deficiency. The 16-weeks competition improved VDR gene expression, body composition, Ca and Mg levels. The associations observed between VDR gene expression and the variables of the study evidenced the importance of this receptor as a marker involved in health status in handball athletes despite vitamin D - although in a deficient status -, Ca, Mg and P showed no remarkable changes during the competition period.
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Affiliation(s)
- Jorge Molina-López
- Faculty of Education, Psychology and Sports Sciences, University of Huelva, Huelva, 21007, Spain
- Department of Physiology, School of Pharmacy. Institute of Nutrition and Food Technology "José Mataix", University of Granada, Granada, 18071, Spain
| | - Lourdes Herrera-Quintana
- Department of Physiology, School of Pharmacy. Institute of Nutrition and Food Technology "José Mataix", University of Granada, Granada, 18071, Spain
| | - Héctor Vázquez-Lorente
- Department of Physiology, School of Pharmacy. Institute of Nutrition and Food Technology "José Mataix", University of Granada, Granada, 18071, Spain.
| | - Elena Planells
- Department of Physiology, School of Pharmacy. Institute of Nutrition and Food Technology "José Mataix", University of Granada, Granada, 18071, Spain
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Zheng X, Chen J, Nie R, Miao H, Chen Z, He J, Xie Y, Zhang H. Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens. Anim Genet 2024; 55:249-256. [PMID: 38194424 DOI: 10.1111/age.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
The genetic foundation of chicken body plumage color has been extensively studied. However, little attention has been paid to the inheritance patterns and molecular mechanisms underlying the formation of distal feather colors (tail and wingtip). Differences in these colors are common; for example, the Chinese Huiyang Beard chicken has black tail feathers, but yellow body plumage. Here, the hybrid offspring of Huiyang Beard and White Leghorn chickens were used to study the inheritance patterns of tail-feather color. The expression levels of pigment genes in differently colored feather follicles were analyzed using quantitative real-time PCR. The results showed that genetic regulation of tail-feather color was independent of body-plumage color. The Dominant White locus inhibited eumelanin synthesis in tail feathers without affecting the formation of yellow body plumage, whereas the Silver locus had the opposite effect. The expression of agouti signaling protein (ASIP) gene class 1 transcripts was significantly lower in black tail-feather follicles than in yellow body follicles, whereas tyrosinase-related protein 1 (TYRP1) gene expression was significantly higher in black tail feathers. These differentially expressed genes were confirmed to exert an effect on eumelanin and pheomelanin formation in feathers, thus influencing the regulation of chicken tail-feather color. In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.
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Affiliation(s)
- Xiaotong Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Jianfei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huanhuan Miao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ziwei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jiaheng He
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yinku Xie
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Baandrup L, Sand FL, Aalborg GL, Nøttrup TJ, Fiehn AMK, Kjaer SK. PD-L1 expression in vulvar cancer: a systematic review and meta-analysis. Histopathology 2024; 84:742-752. [PMID: 38084642 DOI: 10.1111/his.15112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/11/2023] [Accepted: 11/18/2023] [Indexed: 03/06/2024]
Abstract
Programmed cell death ligand-1 (PD-L1) expression in cancer may predict clinical response to immunotherapeutic treatment with PD-1/PD-L1 inhibitors. Within the vulvar cancer field, PD-L1 expression has only been assessed by a few studies. We conducted a meta-analysis to examine the prevalence of PD-L1 positivity in vulvar cancer. PubMed, Embase, and Cochrane were searched for articles reporting on PD-L1 expression in vulvar cancer. Study selection and data extraction were performed independently by two authors. We extracted data on PD-L1 prevalence in vulvar cancer according to combined positive score (CPS) and tumour proportion score (TPS). Cutoff values for positivity were ≥1 or ≥10 for CPS and ≥1% and ≥5% for TPS. Random-effects models were used to estimate pooled PD-L1 prevalence, with 95% confidence intervals (CIs). Tests of between-study heterogeneity were evaluated by the I2 statistics. Sources of heterogeneity were explored by subgroup analyses and meta-regression. In total, 19 studies were included. Pooled PD-L1 prevalence in vulvar cancer was 83.4% (95% CI: 70.8-91.3; I2 = 80.0) and 53.9% (95% CI: 37.4-69.6; I2 = 93.0) according to CPS and TPS, respectively. Based on TPS, human papillomavirus (HPV)-associated vulvar squamous cell carcinomas (SCC) showed a lower PD-L1 prevalence (39.9%; 95% CI: 13.3-74.2) compared with HPV-independent SCC (62.6%; 95% CI: 33.7-84.6), but meta-regression showed no significant variation in PD-L1 prevalence by HPV status. PD-L1 prevalence was similar in advanced (44.9%; 95% CI: 29.8-61.1) and localized vulvar cancer (56.7%; 95% CI: 18.9-76.7). In conclusion, PD-L1 expression in vulvar cancer is frequent but between-study heterogeneity was high. Based on a subgroup of heterogenous studies, we found no strong variation in PD-L1 prevalence according to HPV status and stage.
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Affiliation(s)
- Louise Baandrup
- Unit of Virus, Lifestyle and Genes, Danish Cancer Institute, Copenhagen, Denmark
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Freja Laerke Sand
- Unit of Virus, Lifestyle and Genes, Danish Cancer Institute, Copenhagen, Denmark
| | | | - Trine J Nøttrup
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Marie K Fiehn
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Susanne K Kjaer
- Unit of Virus, Lifestyle and Genes, Danish Cancer Institute, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Abundis EM, Hernandez-Landero F, Escobar-Calderon G, Gomez-Crisostomo N, Contreras-Paredes A, de la Cruz-Hernandez E. Gene expression of cardiovascular risk markers in mononuclear cells of pregnant woman in relation to plasma leptin and homocysteine levels: A cross sectional study. Int J Gynaecol Obstet 2024; 165:350-360. [PMID: 38126620 DOI: 10.1002/ijgo.15302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE To investigate the relationship between anthropometric, biochemical, and hematologic parameters and serum leptin and homocysteine (Hcy) levels. Also, to determine the effect of leptin and Hcy on expression of genes associated with cardiovascular disease susceptibility (APOA1, LRP1, COX-1, and COX-2) in mononuclear cells of healthy pregnant women. METHODS Between August 2018 and January 2020, a cross-sectional study was conducted on 161 healthy pregnant women in Tabasco, southeastern Mexico. The study population was classified by trimester, according to gestational pregnancy. Anthropometric, biochemical (leptin and homocysteine), and hematologic data were obtained under fasting conditions. APOA1, LRP1, COX-1, and COX-2 expression in mononuclear cells was evaluated using RT-qPCR. RESULTS Red cell indices (hemoglobin, hematocrit, and erythrocytes) were negatively and positively correlated with leptin and Hcy levels, respectively, in the first- and second-trimester groups. Increased leptin levels and low red cell indices were significantly associated with BMI <25.0 in the second-trimester group; however, no significant differences were observed in Hcy levels. Increased leptin and Hcy levels were significantly associated with high lipid indicators in the first- and third-trimester groups, respectively. High APOA1 and COX-2 expression was significantly associated with reduced leptin and increased Hcy levels in the second- and third-trimester groups. CONCLUSION Increased leptin and Hcy levels during pregnancy, mainly associated with modifications in erythrocytes and lipid indices, may lead to early modification of genes related to lipid metabolism (APOA1) and proinflammatory response (COX-2) and, thereby, increase cardiovascular disease risk.
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Affiliation(s)
- Eduardo Martínez Abundis
- Laboratorio de investigacion en Enfermedades Metabolicas e Infecciosas, Division Academica Multidisciplinaria de Comalcalco, Universidad Juarez Autonoma de Tabasco, Comalcalco, Tabasco, Mexico
| | - Fernanda Hernandez-Landero
- Laboratorio de investigacion en Enfermedades Metabolicas e Infecciosas, Division Academica Multidisciplinaria de Comalcalco, Universidad Juarez Autonoma de Tabasco, Comalcalco, Tabasco, Mexico
| | - Grecia Escobar-Calderon
- Laboratorio de investigacion en Enfermedades Metabolicas e Infecciosas, Division Academica Multidisciplinaria de Comalcalco, Universidad Juarez Autonoma de Tabasco, Comalcalco, Tabasco, Mexico
| | - Nancy Gomez-Crisostomo
- Laboratorio de investigacion en Enfermedades Metabolicas e Infecciosas, Division Academica Multidisciplinaria de Comalcalco, Universidad Juarez Autonoma de Tabasco, Comalcalco, Tabasco, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Erick de la Cruz-Hernandez
- Laboratorio de investigacion en Enfermedades Metabolicas e Infecciosas, Division Academica Multidisciplinaria de Comalcalco, Universidad Juarez Autonoma de Tabasco, Comalcalco, Tabasco, Mexico
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Xu W, Li S, Bock R, Zhang J. A heat-inducible expression system for external control of gene expression in plastids. Plant Biotechnol J 2024; 22:960-969. [PMID: 38059318 PMCID: PMC10955493 DOI: 10.1111/pbi.14238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/17/2023] [Accepted: 11/04/2023] [Indexed: 12/08/2023]
Abstract
Inducible expression systems can overcome the trade-off between high-level transgene expression and its pleiotropic effects on plant growth. In addition, they can facilitate the expression of biochemical pathways that produce toxic metabolites. Although a few inducible expression systems for the control of transgene expression in plastids have been developed, they all depend on chemical inducers and/or nuclear transgenes. Here we report a temperature-inducible expression system for plastids that is based on the bacteriophage λ leftward and rightward promoters (pL/pR) and the temperature-sensitive repressor cI857. We show that the expression of green fluorescent protein (GFP) in plastids can be efficiently repressed by cI857 under normal growth conditions, and becomes induced over time upon exposure to elevated temperatures in a light-dependent process. We further demonstrate that by introducing into plastids an expression system based on the bacteriophage T7 RNA polymerase, the temperature-dependent accumulation of GFP increased further and was ~24 times higher than expression driven by the pL/pR promoter alone, reaching ~0.48% of the total soluble protein. In conclusion, our heat-inducible expression system provides a new tool for the external control of plastid (trans) gene expression that is cost-effective and does not depend on chemical inducers.
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Affiliation(s)
- Wenbo Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Shengchun Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Ralph Bock
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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Richards SM, Gubser Keller C, Kreutzer R, Greiner G, Ley S, Doelemeyer A, Dubost V, Flandre T, Kirkland S, Carbone W, Pandya R, Knehr J, Roma G, Schuierer S, Bouchez L, Seuwen K, Aebi A, Westhead D, Hintzen G, Jurisic G, Hossain I, Neri M, Manevski N, Balavenkatraman KK, Moulin P, Begrich A, Bertschi B, Huber R, Bouwmeester T, Driver VR, von Schwabedissen M, Schaefer D, Wettstein B, Wettstein R, Ruffner H. Molecular characterization of chronic cutaneous wounds reveals subregion- and wound type-specific differential gene expression. Int Wound J 2024; 21:e14447. [PMID: 38149752 PMCID: PMC10958103 DOI: 10.1111/iwj.14447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 12/28/2023] Open
Abstract
A limited understanding of the pathology underlying chronic wounds has hindered the development of effective diagnostic markers and pharmaceutical interventions. This study aimed to elucidate the molecular composition of various common chronic ulcer types to facilitate drug discovery strategies. We conducted a comprehensive analysis of leg ulcers (LUs), encompassing venous and arterial ulcers, foot ulcers (FUs), pressure ulcers (PUs), and compared them with surgical wound healing complications (WHCs). To explore the pathophysiological mechanisms and identify similarities or differences within wounds, we dissected wounds into distinct subregions, including the wound bed, border, and peri-wound areas, and compared them against intact skin. By correlating histopathology, RNA sequencing (RNA-Seq), and immunohistochemistry (IHC), we identified unique genes, pathways, and cell type abundance patterns in each wound type and subregion. These correlations aim to aid clinicians in selecting targeted treatment options and informing the design of future preclinical and clinical studies in wound healing. Notably, specific genes, such as PITX1 and UPP1, exhibited exclusive upregulation in LUs and FUs, potentially offering significant benefits to specialists in limb preservation and clinical treatment decisions. In contrast, comparisons between different wound subregions, regardless of wound type, revealed distinct expression profiles. The pleiotropic chemokine-like ligand GPR15L (C10orf99) and transmembrane serine proteases TMPRSS11A/D were significantly upregulated in wound border subregions. Interestingly, WHCs exhibited a nearly identical transcriptome to PUs, indicating clinical relevance. Histological examination revealed blood vessel occlusions with impaired angiogenesis in chronic wounds, alongside elevated expression of genes and immunoreactive markers related to blood vessel and lymphatic epithelial cells in wound bed subregions. Additionally, inflammatory and epithelial markers indicated heightened inflammatory responses in wound bed and border subregions and reduced wound bed epithelialization. In summary, chronic wounds from diverse anatomical sites share common aspects of wound pathophysiology but also exhibit distinct molecular differences. These unique molecular characteristics present promising opportunities for drug discovery and treatment, particularly for patients suffering from chronic wounds. The identified diagnostic markers hold the potential to enhance preclinical and clinical trials in the field of wound healing.
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Affiliation(s)
| | | | - Robert Kreutzer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Department of PathologyAnaPath Services GmbHLiestalSwitzerland
| | | | - Svenja Ley
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Arno Doelemeyer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Valerie Dubost
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Thierry Flandre
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Susan Kirkland
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Harvantis Pharma Consulting LtdLondonUK
| | - Walter Carbone
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Research and Development CoordinatorELI TechGroup Corso SvizzeraTorinoItaly
| | - Rishika Pandya
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Judith Knehr
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Guglielmo Roma
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Discovery Data ScienceGSK VaccinesSienaItaly
| | - Sven Schuierer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Laure Bouchez
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Therapeutics Department, Executive in ResidenceGeneral InceptionBaselSwitzerland
| | - Klaus Seuwen
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Alexandra Aebi
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - David Westhead
- Leeds Institute of Data AnalyticsUniversity of LeedsLeedsUK
| | - Gabriele Hintzen
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Translational ScienceAffimed GmbHMannheimGermany
| | - Giorgia Jurisic
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Imtiaz Hossain
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Marilisa Neri
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Nenad Manevski
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Translational PKPD and Clinical Pharmacology, Pharmaceutical Sciences, pREDF. Hoffmann‐La Roche AGBaselSwitzerland
| | | | - Pierre Moulin
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Annette Begrich
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | | | - Roland Huber
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | | | - Vickie R. Driver
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- INOVA HealthcareWound Healing and Hyperbaric CentersFalls ChurchVirginiaUSA
| | | | - Dirk Schaefer
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Barbara Wettstein
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Reto Wettstein
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Heinz Ruffner
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
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Grayck MR, McCarthy WC, Solar M, Golden E, Balasubramaniyan N, Zheng L, Sherlock LG, Wright CJ. GSK3β/NF-κB -dependent transcriptional regulation of homeostatic hepatocyte Tnf production. Am J Physiol Gastrointest Liver Physiol 2024; 326:G374-G384. [PMID: 38193163 DOI: 10.1152/ajpgi.00229.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024]
Abstract
Maintenance of hepatocyte homeostasis plays an important role in mediating the pathogenesis of many diseases. A growing body of literature has established a critical role played by tumor necrosis factor-α (TNFα) in maintaining hepatocyte homeostasis; however, the transcriptional mechanisms underlying constitutive Tnf expression are unknown. Whole liver fractions and primary hepatocytes from adult control C57BL/6 mice and the murine hepatocyte cell line AML12 were assessed for constitutive Tnf expression. Impacts of glycogen synthase kinase-3 β (GSK3β) and nuclear factor κB (NF-κB) inhibition on constitutive Tnf expression were assessed in AML12 cells. Finally, AML12 cell proliferation following GSK3β and NF-κB inhibition was evaluated. Constitutive Tnf gene expression is present in whole liver, primary hepatocytes, and cultured AML12 hepatocytes. Cytokine-induced Tnf gene expression is regulated by NF-κB activation. Pharmacological inhibition of GSK3β resulted in a time- and dose-dependent inhibition of Tnf gene expression. GSK3β inhibition decreased nuclear levels of the NF-κB subunits p65 and p50. We determined that NF-κB transcription factor subunit p65 binds to consensus sequence elements present in the murine TNFα promoter and inhibition of GSK3β decreases binding and subsequent Tnf expression. Finally, AML12 cell growth was significantly reduced following GSK3β and NF-κB inhibition. These results demonstrate that GSK3β and NF-κB are essential for mediating Tnf expression and constitutive hepatocyte cell growth. These findings add to a growing body of literature on TNFα mediated hepatocyte homeostasis and identify novel molecular mechanisms involved in mediating response to various disease states in the liver.NEW & NOTEWORTHY Maintenance of hepatocyte homeostasis plays an important role in controlling the pathogenesis of many diseases. Our findings add to a growing body of literature on tumor necrosis factor-α (TNFα)-mediated hepatocyte homeostasis and identify novel molecular mechanisms involved in regulating this response.
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Affiliation(s)
- Maya R Grayck
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - William C McCarthy
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Mack Solar
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Emma Golden
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Natarajan Balasubramaniyan
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Lijun Zheng
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Laura G Sherlock
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
| | - Clyde J Wright
- Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States
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Dafne VJ, Manuel MA, Rocio CV. Chronobiotics, satiety signaling, and clock gene expression interplay. J Nutr Biochem 2024; 126:109564. [PMID: 38176625 DOI: 10.1016/j.jnutbio.2023.109564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/21/2023] [Accepted: 12/31/2023] [Indexed: 01/06/2024]
Abstract
The biological clock regulates the way our body works throughout the day, including releasing hormones and food intake. Disruption of the biological clock (chronodisruption) may deregulate satiety, which is strictly regulated by hormones and neurotransmitters, leading to health problems like obesity. Nowadays, using bioactive compounds as a coadjutant for several pathologies is a common practice. Phenolic compounds and short-chain fatty acids, called "chronobiotics," can modulate diverse mechanisms along the body to exert beneficial effects, including satiety regulation and circadian clock resynchronization; however, the evidence of the interplay between those processes is limited. This review compiles the evidence of natural chronobiotics, mainly polyphenols and short-chain fatty acids that affect the circadian clock mechanism and process modifications in genes or proteins resulting in a signaling chain that modulates satiety hormones or hunger pathways.
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Affiliation(s)
- Velásquez-Jiménez Dafne
- Research and Graduate Studies in Food Science, School of Chemistry, Autonomous University of Queretaro, Queretaro, Mexico
| | - Miranda-Anaya Manuel
- Multidisciplinary Unit for Teaching and Research (UMDI), School of Sciences, Autonomous National University of Mexico, Queretaro, Mexico
| | - Campos-Vega Rocio
- Research and Graduate Studies in Food Science, School of Chemistry, Autonomous University of Queretaro, Queretaro, Mexico.
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Horikawa I, Nagai H, Taniguchi M, Chen G, Shinohara M, Suzuki T, Ishii S, Katayama Y, Kitaoka S, Furuyashiki T. Chronic stress alters lipid mediator profiles associated with immune-related gene expressions and cell compositions in mouse bone marrow and spleen. J Pharmacol Sci 2024; 154:279-293. [PMID: 38485346 DOI: 10.1016/j.jphs.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
Despite the importance of lipid mediators in stress and depression and their link to inflammation, the influence of stress on these mediators and their role in inflammation is not fully understood. This study used RNA-seq, LC-MS/MS, and flow cytometry analyses in a mouse model subjected to chronic social defeat stress to explore the effects of acute and chronic stress on lipid mediators, gene expression, and cell population in the bone marrow and spleen. In the bone marrow, chronic stress induced a sustained transition from lymphoid to myeloid cells, accompanied by corresponding changes in gene expression. This change was associated with decreased levels of 15-deoxy-d12,14-prostaglandin J2, a lipid mediator that inhibits inflammation. In the spleen, chronic stress also induced a lymphoid-to-myeloid transition, albeit transiently, alongside gene expression changes indicative of extramedullary hematopoiesis. These changes were linked to lower levels of 12-HEPE and resolvins, both critical for inhibiting and resolving inflammation. Our findings highlight the significant role of anti-inflammatory and pro-resolving lipid mediators in the immune responses induced by chronic stress in the bone marrow and spleen. This study paves the way for understanding how these lipid mediators contribute to the immune mechanisms of stress and depression.
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Affiliation(s)
- Io Horikawa
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan; Japan Agency for Medical Research and Development, Tokyo, 100-0004, Japan
| | - Hirotaka Nagai
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan; Japan Agency for Medical Research and Development, Tokyo, 100-0004, Japan.
| | - Masayuki Taniguchi
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan; Japan Agency for Medical Research and Development, Tokyo, 100-0004, Japan
| | - Guowei Chen
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan; Japan Agency for Medical Research and Development, Tokyo, 100-0004, Japan
| | - Masakazu Shinohara
- Division of Molecular Epidemiology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan; The Integrated Center for Mass Spectrometry, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Tomohide Suzuki
- Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, 650-0017, Japan
| | - Shinichi Ishii
- Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, 650-0017, Japan
| | - Yoshio Katayama
- Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, 650-0017, Japan
| | - Shiho Kitaoka
- Department of Pharmacology, School of Medicine, Hyogo Medical University, Nishinomiya, 663-8501, Japan
| | - Tomoyuki Furuyashiki
- Division of Pharmacology, Graduate School of Medicine, Kobe University, Kobe, 650-0017, Japan; Japan Agency for Medical Research and Development, Tokyo, 100-0004, Japan.
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Johnson JR, Griffitt RJ. Environmentally relevant concentrations of aqueous atorvastatin produce alterations in cholesterol biosynthesis and gene expression patterns in Xenopus laevis. Aquat Toxicol 2024; 269:106856. [PMID: 38401338 DOI: 10.1016/j.aquatox.2024.106856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
Numerous studies report active pharmaceutical compounds detected in both wastewater effluent and surface waters. Exposure to statin drugs in general, and atorvastatin in particular, is likely to be a concern. We hypothesized that chronic exposure to low concentrations of atorvastatin in water would result in an adverse effect on production of steroids regulating growth and development of the model amphibian Xenopus laevis. The FETAX assay was used to evaluate the effects of a range of doses of atorvastatin on developing embryos. A 60 day metamorphosis assay assessed the effects of aqueous atorvastatin exposure at environmentally concentrations on metamorphosing tadpoles. A 60 day chronic flow-through exposure evaluated the effects of chronic low concentrations of atorvastatin on adults. The purpose of the FETAX assay was to confirm that atorvastatin can reduce circulating cholesterol in X. laevis with a similar manner to that expected in humans. The results of the 60-day flow-through exposure on metamorphosing tadpoles showed significant evidence of altered cholesterol biosynthesis. The dose-dependent increase in cyp19a1 expression also indicated that the steroidogenesis pathway was affected. The RNAseq analysis confirmed that exposure to environmentally relevant concentrations of atorvastatin does cause significant alterations to global transcriptional profiles in a manner consistent with dysregulation of the cholesterol biosynthesis pathway, both through the downregulation of many genes involved in that pathway, but also in the impacts to other, related pathways. The qPCR data for both adult males and adult females indicated only slight changes in expression with the exception that hmgcr was significantly downregulated in males, and cyp3a4 expression was significantly downregulated in females. The data we present here indicated that chronic exposure to environmentally relevant concentrations of atorvastatin does have the potential to impact early life stage frogs, particularly by altering expression of genes involved in critical molecular pathways.
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Affiliation(s)
- J R Johnson
- Department of Coastal Sciences, University of Southern Mississippi, Hattiesburg, MS 39407, USA
| | - R J Griffitt
- Department of Coastal Sciences, University of Southern Mississippi, Hattiesburg, MS 39407, USA.
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Clairet C, Gay EJ, Porquier A, Blaise F, Marais CL, Balesdent MH, Rouxel T, Soyer JL, Fudal I. Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-player game. New Phytol 2024; 242:247-261. [PMID: 38358035 DOI: 10.1111/nph.19581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Effector genes, encoding molecules involved in disease establishment, are concertedly expressed throughout the lifecycle of plant-pathogenic fungi. However, little is known about how effector gene expression is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in their regulation was recently investigated, notably establishing that the repressive histone modification H3K9me3, deposited by KMT1, was involved in several fungal species including Leptosphaeria maculans. Nevertheless, previous data suggest that a second regulatory layer, probably involving a specific transcription factor (TF), might be required. In L. maculans, a Dothideomycete causing stem canker of oilseed rape, we identified the ortholog of Pf2, a TF belonging to the Zn2Cys6 fungal-specific family, and described as essential for pathogenicity and effector gene expression. We investigated its role together with KMT1, by inactivating and over-expressing LmPf2 in a wild-type strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis and we found a major effect of LmPf2 on the induction of effector gene expression once KMT1 repression is lifted. Our results show, for the first time, a dual control of effector gene expression.
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Affiliation(s)
- Colin Clairet
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Antoine Porquier
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
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Wang X, Yu C, Sun Y, Liu Y, Tang S, Sun Y, Zhou Y. Three-dimensional morphology scoring of hepatocellular carcinoma stratifies prognosis and immune infiltration. Comput Biol Med 2024; 172:108253. [PMID: 38484698 DOI: 10.1016/j.compbiomed.2024.108253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/18/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND The morphological attributes could serve as pivotal indicators precipitating early recurrence and dismal overall survival in hepatocellular carcinoma (HCC), and quantifying morphological features may better stratify the prognosis of HCC. OBJECTIVE To develop a radiomics approach based on 3D tumor morphology features for predicting the prognosis of HCC and identifying differentially expressed genes related to morphology to guide HCC treatment. MATERIALS AND METHODS Retrospective study of 357 HCC patients. Radiomic features were extracted from MRI tumor regions; 14 morphology-related features predicted early HCC recurrence and patient stratification via LASSO-Cox modeling. Overall survival (OS) and recurrence-free survival (RFS) were analyzed. RNA sequencing from the Cancer Imaging Archive (TCIA) examined drug sensitivity and stratified HCC using morphological immunity genes, validating recurrence and prognosis. RESULTS Patients were split into training (n = 225), test (n = 132), and 50 TCIA dataset cohorts. Two features (Maximum2DdiameterColumn, Sphericity) in Cox regression stratified patients into high/low-risk Morphological Radiological Score (Morph-RS) groups. Significant OS and RFS were seen across all sets. Differentially expressed genes focused on T cell receptor signaling; low-risk group had higher T cells (P = 0.039), B cells (P = 0.041), NK cells (P = 0.018). SN-38, GSK2126458 might treat high-risk morphology. Morphology-immune genes stratified HCC, showing significant RFS/OS differences. CONCLUSION Tumor Morph-RS effectively stratifies HCC patients' recurrence and prognosis. Limited immune infiltration seen in Morph-RS high-risk groups signifies the potential of employing tumor morphology as a potent visual biomarker for diagnosing and managing HCC.
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Affiliation(s)
- Xinxin Wang
- Department of Radiology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Can Yu
- Department of Radiology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Sun
- Beidahuang Industry Group General Hospital, Harbin, China
| | - Yixin Liu
- Basic Medicine College, Harbin Medical University, Harbin, China
| | - Shuli Tang
- Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yige Sun
- Department of Radiology, Harbin Medical University Cancer Hospital, Harbin, China; Genomics Research Center (Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.
| | - Yang Zhou
- Department of Radiology, Harbin Medical University Cancer Hospital, Harbin, China.
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45
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Parker J, Marten SM, Ó Corcora TC, Rajkov J, Dubin A, Roth O. The effects of primary and secondary bacterial exposure on the seahorse (Hippocampus erectus) immune response. Dev Comp Immunol 2024; 153:105136. [PMID: 38185263 DOI: 10.1016/j.dci.2024.105136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
Evolutionary adaptations in the Syngnathidae teleost family (seahorses, pipefish and seadragons) culminated in an array of spectacular morphologies, key immune gene losses, and the enigmatic male pregnancy. In seahorses, genome modifications associated with immunoglobulins, complement, and major histocompatibility complex (MHC II) pathway components raise questions concerning their immunological efficiency and the evolution of compensatory measures that may act in their place. In this investigation heat-killed bacteria (Vibrio aestuarianus and Tenacibaculum maritimum) were used in a two-phased experiment to assess the immune response dynamics of Hippocampus erectus. Gill transcriptomes from double and single-exposed individuals were analysed in order to determine the differentially expressed genes contributing to immune system responses towards immune priming. Double-exposed individuals exhibited a greater adaptive immune response when compared with single-exposed individuals, while single-exposed individuals, particularly with V. aestuarianus replicates, associated more with the innate branch of the immune system. T. maritimum double-exposed replicates exhibited the strongest immune reaction, likely due to their immunological naivety towards the bacterium, while there are also potential signs of innate trained immunity. MHC II upregulated expression was identified in selected V. aestuarianus-exposed seahorses, in the absence of other pathway constituents suggesting a possible alternative or non-classical MHC II immune function in seahorses. Gene Ontology (GO) enrichment analysis highlighted prominent angiogenesis activity following secondary exposure, which could be linked to an adaptive immune process in seahorses. This investigation highlights the prominent role of T-cell mediated adaptive immune responses in seahorses when exposed to sequential foreign bacteria exposures. If classical MHC II pathway function has been lost, innate trained immunity in syngnathids could be a potential compensatory mechanism.
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Affiliation(s)
- Jamie Parker
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany.
| | - Silke-Mareike Marten
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
| | - Tadhg C Ó Corcora
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany
| | - Jelena Rajkov
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
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Alkhawaldeh O, Jarrar Y, Gharaibeh M, Abudahab S, Abulebdah D, Jarrar B. Alterations in the gene expression of SARS-COV-2 entry receptors and enzymes in lungs and hearts of controlled and uncontrolled diabetic mice. Fundam Clin Pharmacol 2024; 38:328-340. [PMID: 37950353 DOI: 10.1111/fcp.12964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND The entry of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the host cell is carried out by specific receptors and enzymes, including human angiotensin-converting enzyme 2 receptor (ACE2), transmembrane serine protease 2 (TMPRSS2), and cathepsin-L (CTSL). COVID-19 patients with comorbidities, such as diabetes mellitus (DM), are more prone to severe symptoms and have a higher risk of mortality. AIMS The present study aimed to investigate the impact of controlled and uncontrolled type 1 DM (T1DM) on the gene expression of mouse Ace2, Tmprss2, and Ctsl and correlate it with the pathological alterations in the lungs and the heart of DM mice. METHODS Balb/c mice were administered a single dose of 240 mg/kg streptozocin to induce T1DM. The blood glucose level was measured to confirm the induction of DM. Normalization of blood glucose levels in T1DM mice was achieved using 0.1 mL/kg Mixtard® insulin therapy. The mice's lungs and hearts were harvested, and the mRNA was extracted and converted to cDNA. The gene expression of Ace2, Tmprss2, Ctsl, Cyp4a11, and Adrb1 genes, which play a role in the homeostasis of lungs and hearts, were measured using quantitative real-time polymerase chain reaction (RT-PCR). The pathological alterations in the hearts and lungs induced by T1DM were evaluated using the relative heart and lung weights, in addition to the pathohistological examination. RESULTS After inducing T1DM for 14 days, we observed a significant reduction in the total weight of uncontrolled DM (UDM) mice (P < 0.05). Pathohistological examination of UDM lung tissues revealed thickening of the alveolar walls with narrowing of the surface of the alveolar sacs. Additionally, we found that UDM mice exhibited downregulation of Ace2 gene expression (P < 0.05) in their lungs, while both UDM and control DM (CDM) mice showed upregulation of Ctsl gene expression in their hearts (P < 0.05). Notably, Cyp4a12 gene expression was significantly downregulated (P < 0.05) in UDM mice but returned to normal levels in CDM mice. CONCLUSIONS We conclude from this study that T1DM downregulates Ace2 receptor and Cyp4a12 gene expression, which is correlated with the thickening of alveolar walls and narrowing of the surface of alveolar sacs in the lungs. Insulin administration for controlling T1DM ameliorated these pathological alterations. These results can help increase our understanding of the impact of controlled and uncontrolled T1DM on the lungs and may explain, at least in part, why DM patients with COVID-19 experience exacerbation of symptoms.
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Affiliation(s)
- Ohood Alkhawaldeh
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman, Jordan
| | - Yazun Jarrar
- Department of Basic Medical Sciences, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Munir Gharaibeh
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman, Jordan
| | - Sara Abudahab
- Deparment of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Dina Abulebdah
- Department of Pharmaceutical Science, College of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Bashir Jarrar
- Nanobiology Unit, Department of Biology, College of Science, Jerash University, Jerash, Jordan
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Salvador-Martín S, Rubbini G, Vellosillo P, Zapata-Cobo P, Velasco M, Palomino LM, Clemente S, Segarra O, Moreno-Álvarez A, Fernández-Lorenzo A, Pérez-Moneo B, Montraveta M, Sánchez C, Tolín M, Loverdos I, Fobelo MJ, Navas-López VM, Magallares L, García-Romero R, Torres-Peral R, Rodríguez A, Bossacoma F, Merino-Bohórquez V, Salcedo E, Álvarez R, Dopazo A, Sanjurjo-Sáez M, López-Fernández LA. Blood gene expression biomarkers of response to anti-TNF drugs in pediatric inflammatory bowel diseases before initiation of treatment. Biomed Pharmacother 2024; 173:116299. [PMID: 38401525 DOI: 10.1016/j.biopha.2024.116299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND/AIMS Changes in gene expression profiles among individuals with inflammatory bowel diseases (IBDs) could potentially influence the responsiveness to anti-TNF treatment. The aim of this study was to identify genes that could serve as predictors of early response to anti-TNF therapies in pediatric IBD patients prior to the initiation of treatment. METHODS We conducted a prospective, longitudinal, and multicenter study, enrolling 24 pediatric IBD patients aged less than 18 years who were initiating treatment with either infliximab or adalimumab. RNA-seq from blood samples was analyzed using the DESeq2 library by comparing responders and non-responders to anti-TNF drugs. RESULTS Bioinformatic analyses unveiled 102 differentially expressed genes, with 99 genes exhibiting higher expression in responders compared to non-responders prior to the initiation of anti-TNF therapy. Functional enrichment analyses highlighted defense response to Gram-negative bacteria (FDR = 2.3 ×10-7) as the most significant biological processes, and hemoglobin binding (FDR = 0.002), as the most significant molecular function. Gene Set Enrichment Analysis (GSEA) revealed notable enrichment in transcriptional misregulation in cancer (FDR = 0.016). Notably, 13 genes (CEACAM8, CEACAM6, CILP2, COL17A1, OLFM4, INHBA, LCN2, LTF, MMP8, DEFA4, PRTN3, AZU1, and ELANE) were selected for validation, and a consistent trend of increased expression in responders prior to drug administration was observed for most of these genes, with findings for 4 of them being statistically significant (CEACAM8, LCN2, LTF2, and PRTN3). CONCLUSIONS We identified 102 differentially expressed genes involved in the response to anti-TNF drugs in children with IBDs and validated CEACAM8, LCN2, LTF2, and PRTN3. Genes participating in defense response to Gram-negative bacterium, serine-type endopeptidase activity, and transcriptional misregulation in cancer are good candidates for anticipating the response to anti-TNF drugs in children with IBDs.
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Affiliation(s)
- Sara Salvador-Martín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Gianluca Rubbini
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Perceval Vellosillo
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Unidad de Investigación Materno Infantil Fundación Familia Alonso (UDIMIFFA), Spain.
| | - Paula Zapata-Cobo
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Marta Velasco
- Hospital Universitario Infantil Niño Jesús, Madrid, Spain.
| | | | | | | | | | | | | | | | - Cesar Sánchez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Mar Tolín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | | | - María José Fobelo
- Hospital Universitario Virgen de Valme, Universidad de Sevilla, Sevilla, Spain.
| | | | | | | | | | | | - Ferrán Bossacoma
- Servicio de Gastroenterología, Hepatología y Nutrición Pediátrica, Hospital Sant Joan de Dèu, Barcelona, Spain.
| | | | | | - Rebeca Álvarez
- Genomics Unit, Spanish National Center for Cardiovascular Disease (CNIC), Madrid 28029, Spain.
| | - Ana Dopazo
- Genomics Unit, Spanish National Center for Cardiovascular Disease (CNIC), Madrid 28029, Spain.
| | - María Sanjurjo-Sáez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Luis A López-Fernández
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
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Karisola P, Nikkola V, Joronen H, Ylianttila L, Grönroos M, Partonen T, Snellman E, Alenius H. Narrow-band UVB radiation triggers diverse changes in the gene expression and induces the accumulation of M1 macrophages in human skin. J Photochem Photobiol B 2024; 253:112887. [PMID: 38460430 DOI: 10.1016/j.jphotobiol.2024.112887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND The underlying molecular mechanisms that determine the biological effects of UVB radiation exposure on human skin are still only partially comprehended. OBJECTIVES Our goal is to examine the human skin transcriptome and related molecular mechanisms following a single exposure to UVB in the morning versus evening. METHODS We exposed 20 volunteer females to four-fold standard erythema doses (SED4) of narrow-band UVB (309-313 nm) in the morning or evening and studied skin transcriptome 24 h after the exposure. We performed enrichment analyses of gene pathways, predicted changes in skin cell composition using cellular deconvolution, and correlated cell proportions with gene expression. RESULTS In the skin transcriptome, UVB exposure yielded 1384 differentially expressed genes (DEGs) in the morning and 1295 DEGs in the evening, of which the most statistically significant DEGs enhanced proteasome and spliceosome pathways. Unexposed control samples showed difference by 321 DEGs in the morning vs evening, which was related to differences in genes associated with the circadian rhythm. After the UVB exposure, the fraction of proinflammatory M1 macrophages was significantly increased at both timepoints, and this increase was positively correlated with pathways on Myc targets and mTORC1 signaling. In the evening, the skin clinical erythema was more severe and had stronger positive correlation with the number of M1 macrophages than in the morning after UVB exposure. The fractions of myeloid and plasmacytoid dendritic cells and CD8 T cells were significantly decreased in the morning but not in the evening. CONCLUSIONS NB-UVB-exposure causes changes in skin transcriptome, inhibiting cell division, and promoting proteasome activity and repair responses, both in the morning and in the evening. Inflammatory M1 macrophages may drive the UV-induced skin responses by exacerbating inflammation and erythema. These findings highlight how the same UVB exposure influences skin responses differently in morning versus evening and presents a possible explanation to the differences in gene expression in the skin after UVB irradiation at these two timepoints.
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Affiliation(s)
- Piia Karisola
- Faculty of Medicine, Human Microbiome Research Program, University of Helsinki, Finland.
| | - Veera Nikkola
- Tampere University, Faculty of Medicine and Health Technology, Department of Dermatology and Venereology, Tampere, Finland
| | - Heli Joronen
- Tampere University, Faculty of Medicine and Health Technology, Department of Dermatology and Venereology, Tampere, Finland; Päijät-Häme Social and Health Care Group, Department of Dermatology and Allergology, Lahti, Finland.
| | - Lasse Ylianttila
- Radiation and Nuclear Safety Authority (STUK), Helsinki, Finland.
| | - Mari Grönroos
- Päijät-Häme Social and Health Care Group, Department of Dermatology and Allergology, Lahti, Finland.
| | - Timo Partonen
- Finnish Institute for Health and Welfare, Department of Public Health and Welfare, Finland.
| | - Erna Snellman
- Tampere University, Faculty of Medicine and Health Technology, Department of Dermatology and Venereology, Tampere, Finland.
| | - Harri Alenius
- Faculty of Medicine, Human Microbiome Research Program, University of Helsinki, Finland; Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden.
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Cai M, Ji Y, Zhao Q, Xue H, Sun Z, Wang H, Zhang Y, Chen Y, Zhao Y, Zhang Y, Lei M, Wang C, Zhuo C, Liu N, Liu H, Liu F. Homotopic functional connectivity disruptions in schizophrenia and their associated gene expression. Neuroimage 2024; 289:120551. [PMID: 38382862 DOI: 10.1016/j.neuroimage.2024.120551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/23/2024] Open
Abstract
It has been revealed that abnormal voxel-mirrored homotopic connectivity (VMHC) is present in patients with schizophrenia, yet there are inconsistencies in the relevant findings. Moreover, little is known about their association with brain gene expression profiles. In this study, transcription-neuroimaging association analyses using gene expression data from Allen Human Brain Atlas and case-control VMHC differences from both the discovery (meta-analysis, including 9 studies with a total of 386 patients and 357 controls) and replication (separate group-level comparisons within two datasets, including a total of 258 patients and 287 controls) phases were performed to identify genes associated with VMHC alterations. Enrichment analyses were conducted to characterize the biological functions and specific expression of identified genes, and Neurosynth decoding analysis was performed to examine the correlation between cognitive-related processes and VMHC alterations in schizophrenia. In the discovery and replication phases, patients with schizophrenia exhibited consistent VMHC changes compared to controls, which were correlated with a series of cognitive-related processes; meta-regression analysis revealed that illness duration was negatively correlated with VMHC abnormalities in the cerebellum and postcentral/precentral gyrus. The abnormal VMHC patterns were stably correlated with 1287 genes enriched for fundamental biological processes like regulation of cell communication, nervous system development, and cell communication. In addition, these genes were overexpressed in astrocytes and immune cells, enriched in extensive cortical regions and wide developmental time windows. The present findings may contribute to a more comprehensive understanding of the molecular mechanisms underlying VMHC alterations in patients with schizophrenia.
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Affiliation(s)
- Mengjing Cai
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yuan Ji
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiyu Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hui Xue
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Zuhao Sun
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - He Wang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yijing Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yayuan Chen
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yao Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yujie Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Minghuan Lei
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chunyang Wang
- Department of Scientific Research, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chuanjun Zhuo
- Laboratory of Psychiatric-Neuroimaging-Genetic and Co-morbidity (PGNP_Lab), Tianjin Anding Hospital, Nankai University Affiliated Tianjin Anding Hospital, Tianjin Mental Health Center of Tianjin Medical University, Tianjin, 300222, China
| | - Nana Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Huaigui Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
| | - Feng Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin 300052, China.
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50
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Arai H, Yang Y, Baca Y, Millstein J, Denda T, Ou FS, Innocenti F, Takeda H, Kubota Y, Doi A, Horie Y, Umemoto K, Izawa N, Wang J, Battaglin F, Jayachandran P, Algaze S, Soni S, Zhang W, Goldberg RM, Hall MJ, Scott AJ, Hwang JJ, Lou E, Weinberg BA, Marshall J, Goel S, Xiu J, Michael Korn W, Venook AP, Sunakawa Y, Lenz HJ. Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer. Eur J Cancer 2024; 201:113914. [PMID: 38359495 DOI: 10.1016/j.ejca.2024.113914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND CDC37 is a key determinant of client kinase recruitment to the HSP90 chaperoning system. We hypothesized that kinase-specific dependency on CDC37 alters the efficacy of targeted therapies for metastatic colorectal cancer (mCRC). MATERIAL AND METHODS Two independent mCRC cohorts were analyzed to compare the survival outcomes between CDC37-high and CDC37-low patients (stratified by the median cutoff values): the CALGB/SWOG 80405 trial (226 and 207 patients receiving first-line bevacizumab- and cetuximab-containing chemotherapies, respectively) and Japanese retrospective (50 refractory patients receiving regorafenib) cohorts. A dataset of specimens submitted to a commercial CLIA-certified laboratory was utilized to characterize molecular profiles of CDC37-high (top quartile, N = 5055) and CDC37-low (bottom quartile, N = 5055) CRCs. RESULTS In the bevacizumab-treated group, CDC37-high patients showed significantly better progression-free survival (PFS) (median 13.3 vs 9.6 months, hazard ratio [HR] 0.59, 95% confidence interval [CI] 0.44-0.79, p < 0.01) than CDC37-low patients. In the cetuximab-treated group, CDC37-high and CDC37-low patients had similar outcomes. In the regorafenib-treated group, CDC37-high patients showed significantly better overall survival (median 11.3 vs 6.0 months, HR 0.24, 95% CI 0.11-0.54, p < 0.01) and PFS (median 3.5 vs 1.9 months, HR 0.51, 95% CI 0.28-0.94, p = 0.03). Comprehensive molecular profiling revealed that CDC37-high CRCs were associated with higher VEGFA, FLT1, and KDR expressions and activated hypoxia signature. CONCLUSIONS CDC37-high mCRC patients derived more benefit from anti-VEGF therapies, including bevacizumab and regorafenib, but not from cetuximab. Molecular profiles suggested that such tumors were dependent on angiogenesis-relating pathways.
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Affiliation(s)
- Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yan Yang
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yasmine Baca
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tadamichi Denda
- Department of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Federico Innocenti
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yohei Kubota
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ayako Doi
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshiki Horie
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kumiko Umemoto
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Izawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Priya Jayachandran
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra Algaze
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Aaron James Scott
- Department of Medicine, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Jimmy J Hwang
- Department of Solid Tumor Oncology, GI Medical Oncology, Levine Cancer Institute, Charlotte, NC, USA
| | - Emil Lou
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - John Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Sanjay Goel
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Joanne Xiu
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - W Michael Korn
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Alan P Venook
- University of California, San Francisco, San Francisco, CA, USA
| | - Yu Sunakawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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