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Drozdova P, Gurkov A, Saranchina A, Vlasevskaya A, Zolotovskaya E, Indosova E, Timofeyev M, Borvinskaya E. Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers. Appl Microbiol Biotechnol 2024; 108:121. [PMID: 38229303 DOI: 10.1007/s00253-023-12863-z] [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: 06/07/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 01/18/2024]
Abstract
The model yeast, Saccharomyces cerevisiae, is a popular object for both fundamental and applied research, including the development of biosensors and industrial production of pharmaceutical compounds. However, despite multiple studies exploring S. cerevisiae transcriptional response to various substances, this response is unknown for some substances produced in yeast, such as D-lactic acid (DLA). Here, we explore the transcriptional response of the BY4742 strain to a wide range of DLA concentrations (from 0.05 to 45 mM), and compare it to the response to 45 mM L-lactic acid (LLA). We recorded a response to 5 and 45 mM DLA (125 and 113 differentially expressed genes (DEGs), respectively; > 50% shared) and a less pronounced response to 45 mM LLA (63 DEGs; > 30% shared with at least one DLA treatment). Our data did not reveal natural yeast promoters quantitatively sensing DLA but provide the first description of the transcriptome-wide response to DLA and enrich our understanding of the LLA response. Some DLA-activated genes were indeed related to lactate metabolism, as well as iron uptake and cell wall structure. Additional analyses showed that at least some of these genes were activated only by acidic form of DLA but not its salt, revealing the role of pH. The list of LLA-responsive genes was similar to those published previously and also included iron uptake and cell wall genes, as well as genes responding to other weak acids. These data might be instrumental for optimization of lactate production in yeast and yeast co-cultivation with lactic acid bacteria. KEY POINTS: • We present the first dataset on yeast transcriptional response to DLA. • Differential gene expression was correlated with yeast growth inhibition. • The transcriptome response to DLA was richer in comparison to LLA.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation.
- Baikal Research Centre, Rabochaya Str. 5V, Irkutsk, 664011, Russian Federation.
| | - Anton Gurkov
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
- Baikal Research Centre, Rabochaya Str. 5V, Irkutsk, 664011, Russian Federation
| | | | | | - Elena Zolotovskaya
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | - Elizaveta Indosova
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
| | - Maxim Timofeyev
- Irkutsk State University, Karl-Marx Str. 1, Irkutsk, 664025, Russian Federation
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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in Small Tail Han sheep with FecB++ genotype. Anim Biotechnol 2024; 35:2254568. [PMID: 37694839 DOI: 10.1080/10495398.2023.2254568] [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: 09/12/2023]
Abstract
The thyroid gland is an important endocrine gland in animals, which mainly secretes thyroid hormones and acts on various organs of the body. Long-chain non-coding RNA (lncRNA) plays an important role in animal reproduction. However, there is still a lack of understanding of their expression patterns and potential roles in the thyroid of Small Tail Han (STH) sheep. In this study, RNA-seq was used to examine the transcriptome expression patterns of lncRNAs and mRNAs in the follicular phase (ww_FT) and luteal phase (ww_LT) in FecB++ genotype STH Sheep. A total of 17,217 lncRNAs and 39,112 mRNAs were identified including 96 differentially expressed lncRNAs (DELs) and 1054 differentially expressed mRNAs (DEGs). Functional analysis of genes with significant differences in expression level showed that these genes could be enriched in Ras signalling pathway, hedgehog (HH) signalling pathway, ATP-binding cassette (ABC) transporters and other signalling pathways related to animal reproduction. In addition, through correlation analysis for lncRNA-mRNA co-expression and network construction, we found that LNC_009115 and LNC_005796 trans target NIK-related kinase (NRK) and poly(A)-specific ribonuclease (PARN). LNC_007189 and LNC_002045 trans target progesterone-induced blocking factor 1 (PIBF1), LNC_009013 trans targets small mothers against decapentaplegic (SMAD1) are related to animal reproduction. These genes add new resources for elucidating the regulatory mechanisms of reproduction in sheep with different reproductive cycles of the FecB++ genotype STH sheep.
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Affiliation(s)
- Cheng Chang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Seo YJ, Lim C, Lim B, Kim JM. Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum. Anim Biotechnol 2024; 35:2331179. [PMID: 38519440 DOI: 10.1080/10495398.2024.2331179] [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: 03/24/2024]
Abstract
Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.
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Affiliation(s)
- Young-Jun Seo
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Chiwoong Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Republic of Korea
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Zhang W, Li C, Lv Y, Wei S, Hu Y. Synergistic antifungal mechanism of cinnamaldehyde and nonanal against Aspergillus flavus and its application in food preservation. Food Microbiol 2024; 121:104524. [PMID: 38637086 DOI: 10.1016/j.fm.2024.104524] [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: 12/27/2023] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/20/2024]
Abstract
Aspergillus flavus colonization on agricultural products during preharvest and postharvest results in tremendous economic losses. Inspired by the synergistic antifungal effects of essential oils, the aims of this study were to explore the mechanism of combined cinnamaldehyde and nonanal (SCAN) against A. flavus and to evaluate the antifungal activity of SCAN loading into diatomite (DM). Shriveled mycelia were observed by scanning electron microscopy, especially in the SCAN treatment group. Calcofluor white staining, transmission electron microscopy, dichloro-dihydro-fluorescein diacetate staining and the inhibition of key enzymes in tricarboxylic acid cycle indicated that the antifungal mechanism of SCAN against A. flavus was related to the cell wall damage, reactive oxygen species accumulation and energy metabolism interruption. RNA sequencing revealed that some genes involved in antioxidation were upregulated, whereas genes responsible for cell wall biosynthesis, oxidative stress, cell cycle and spore development were significantly downregulated, supporting the occurrence of cellular apoptosis. In addition, compared with the control group, conidia production in 1.5 mg/mL DM/cinnamaldehyde, DM/nonanal and DM/SCAN groups were decreased by 27.16%, 48.22% and 76.66%, respectively, and the aflatoxin B1 (AFB1) contents decreased by 2.00%, 73.02% and 84.15%, respectively. These finding suggest that DM/SCAN complex has potential uses in food preservation.
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Affiliation(s)
- Wei Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Cuixiang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China; Food Laboratory of Zhongyuan, Luohe, 462300, Henan, China.
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Alsegehy S, Southey BR, Hernandez AG, Rund LA, Antonson AM, Nowak RA, Johnson RW, Rodriguez-Zas SL. Epigenetic disruptions in the offspring hypothalamus in response to maternal infection. Gene 2024; 910:148329. [PMID: 38431234 DOI: 10.1016/j.gene.2024.148329] [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: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
DNA methylation is an epigenetic modification that can alter gene expression, and the incidence can vary across developmental stages, inflammatory conditions, and sexes. The effects of viral maternal viral infection and sex on the DNA methylation patterns were studied in the hypothalamus of a pig model of immune activation during development. DNA methylation at single-base resolution in regions of high CpG density was measured on 24 individual hypothalamus samples using reduced representation bisulfite sequencing. Differential over- and under-methylated sites were identified and annotated to proximal genes and corresponding biological processes. A total of 120 sites were differentially methylated (FDR-adjusted p-value < 0.05) between maternal infection or sex groups. Among the 66 sites differentially methylated between groups exposed to inflammatory signals and control, most sites were over-methylated in the challenged group and included sites in the promoter regions of genes SIRT3 and NRBP1. Among the 54 differentially methylated sites between females and males, most sites were over-methylated in females and included sites in the promoter region of genes TNC and EIF4G1. The analysis of the genes proximal to the differentially methylated sites suggested that biological processes potentially impacted include immune response, neuron migration and ensheathment, peptide signaling, adaptive thermogenesis, and tissue development. These results suggest that translational studies should consider that the prolonged effect of maternal infection during gestation may be enacted through epigenetic regulatory mechanisms that may differ between sexes.
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Affiliation(s)
- Samah Alsegehy
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauretta A Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adrienne M Antonson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rodney W Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sandra L Rodriguez-Zas
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
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6
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Azeez BS, Kim DY, Na JK. Transcriptome dataset for comparative analysis of differentially expressed genes between wild type and transgenic potato plants overexpressing Nuclear Factor Y subunit A7. Data Brief 2024; 54:110349. [PMID: 38586149 PMCID: PMC10997943 DOI: 10.1016/j.dib.2024.110349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
Nuclear Factor Y (NF-Y) is divided into three different types of subunits, A, B, and C. NF-Ys play crucial roles in plants for controlling gene expression associated with various developmental processes and abiotic stresses, but it is mostly unknown the downstream genes regulated by NF-Ys in plant. One of the potato NF-Y genes, StNF-YA7, increased potato's drought tolerance when overexpressed under the control of constitutive CaMV 35S promoter. Therefore, it was of interest what genes are regulated by the increased expression level of StNF-YA7. To investigate the downstream genes of StNF-YA7, the transcriptome sequencing was carried out for four potato lines, including Solanum tuberosum L 'Superior' as wild type (WT), empty vector control (VC), and two StNF-YA7 overexpressor lines (designated to StNF-YA7 #19 & #26). The RNA sequencing data was produced by the Illumina NovaSeq 6000 sequencing system. The number of total raw reads obtained from the RNA sequencing was 36.7 million for WT, 36.2 for VC, 29.3 for StNF-YA7 #19, and 29.5 million for StNF-YA7 #26, respectively. The length of total raw reads for each sample was between 5.92 Gb (StNF-YA7 #19) and 7.42 Gb (WT), and after filtering raw quality reads, the total length was between 5.81 Gb (StNF-YA7 #19) and 7.29 Gb (WT). Each filtered clear read set of four transcriptomes was mapped on the potato reference genome, SolTub_3.0, and the percentage of mapped reads ranged from 89.8 % (VC) to 90.3 % (WT). GC contents range between 43.01 % (StNF-YA7 #19) and 42.44 % (StNF-YA7 #26). Q20 quality score ranges between 98.63 % (StNF-YA7 #26) and 98.74 % (VC).
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Affiliation(s)
- Bimpe Suliyat Azeez
- Department of Agriculture and Industries, Graduate School, Kangwon National University, Chuncheon 24341, South Korea
| | - Dool-Yi Kim
- National Institute of Crop Science, RDA, Wanju 55365, South Korea
| | - Jong-Kuk Na
- Department of Agriculture and Industries, Graduate School, Kangwon National University, Chuncheon 24341, South Korea
- Department of SmartFarm and Agriculural Industries, Kangwon National University, Chuncheon, Kangwon 24341, South Korea
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Song J, Huang F, Ma K, Ding R, Tan K, Lv D, Soyano K, Zhao K. Bifenthrin induces changes in clinical poisoning symptoms, oxidative stress, DNA damage, histological characteristics, and transcriptome in Chinese giant salamander (Andrias davidianus) larvae. Sci Total Environ 2024; 927:172041. [PMID: 38554955 DOI: 10.1016/j.scitotenv.2024.172041] [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: 12/05/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Bifenthrin (BF) is a broad-spectrum insecticide that has gained widespread use due to its high effectiveness. However, there is limited research on the potential toxic effects of bifenthrin pollution on amphibians. This study aimed to investigate the 50 % lethal concentration (LC50) and safety concentration of Chinese giant salamanders (CGS) exposed to BF (at 0, 6.25,12.5,25 and 50 μg/L BF) for 96 h. Subsequently, CGS were exposed to BF (at 0, 0.04, and 4 μg/L BF) for one week to investigate its toxic effects. Clinical poisoning symptoms, liver pathology, oxidative stress factors, DNA damage, and transcriptome differences were observed and analyzed. The results indicate that exposure to BF at 4 μg/L significantly decreased the adenosine-triphosphate (ATP), superoxide dismutase (SOD), glutathione (GSH), and catalase (CAT) contents in the brain, liver, and kidney of CGS. Additionally, the study found that the malondialdehyde (MDA), reactive oxygen species (ROS), and 8-hydroxydeoxyguanosine (8-OHdG) contents were increased. The liver tissue exhibited significant inflammatory reactions and structural malformations. RNA-seq analysis of the liver showed that BF caused abnormal antioxidant indices of CGS. This affected molecular function genes such as catalytic activity, ATP-dependent activity, metabolic processes, signaling and immune system processes, behavior, and detoxification, which were significantly upregulated, resulting in the differential genes significantly enriched in the calcium signaling pathway, PPARα signaling pathway and NF-kB signaling pathway. The results suggest that BF induces the abnormal production of free radicals, which overwhelms the body's self-defense system, leading to varying degrees of oxidative stress. This can result in oxidative damage, DNA damage, abnormal lipid metabolism, autoimmune diseases, clinical poisoning symptoms, and tissue inflammation. This work provides a theoretical basis for the rational application of bifenthrin and environmental risk assessment, as well as scientific guidance for the conservation of amphibian populations.
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Affiliation(s)
- Jing Song
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China; The Belt and Road Model International Science and Technology Cooperation Base for Biodiversity Conservation and Utilization in Basins of Anhui Province, Anqing Normal University, Anqing 246133, Anhui, China; Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki 851-2213, Japan
| | - Fengyun Huang
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China; The Belt and Road Model International Science and Technology Cooperation Base for Biodiversity Conservation and Utilization in Basins of Anhui Province, Anqing Normal University, Anqing 246133, Anhui, China
| | - Kun Ma
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China; The Belt and Road Model International Science and Technology Cooperation Base for Biodiversity Conservation and Utilization in Basins of Anhui Province, Anqing Normal University, Anqing 246133, Anhui, China
| | - Rui Ding
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China; The Belt and Road Model International Science and Technology Cooperation Base for Biodiversity Conservation and Utilization in Basins of Anhui Province, Anqing Normal University, Anqing 246133, Anhui, China
| | - Kai Tan
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China; The Belt and Road Model International Science and Technology Cooperation Base for Biodiversity Conservation and Utilization in Basins of Anhui Province, Anqing Normal University, Anqing 246133, Anhui, China
| | - Dan Lv
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China
| | - Kiyoshi Soyano
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Institute for East China Sea Research, Organization for Marine Science and Technology, Nagasaki University, Nagasaki 851-2213, Japan
| | - Kai Zhao
- College of Life Science, Anqing Normal University, Anqing 246133, Anhui, China; The Belt and Road Model International Science and Technology Cooperation Base for Biodiversity Conservation and Utilization in Basins of Anhui Province, Anqing Normal University, Anqing 246133, Anhui, China
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Tian X, Zhao Z, Zhao J, Su D, He B, Shi C, Shi Y. Transcriptomic analysis to identify genes associated with hypothalamus vulnerability in aging mice with cognitive decline. Behav Brain Res 2024; 465:114943. [PMID: 38452974 DOI: 10.1016/j.bbr.2024.114943] [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: 11/17/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
The normal aging process is accompanied by cognitive decline, and previous studies have indicated the crucial role of the hypothalamus in regulating both aging and cognition. However, the precise molecular mechanism underlying this relationship remains unclear. Therefore, this present study aimed to identify potential predictors of cognitive decline associated with aging specifically within the hypothalamus. To achieve this, we employed Morris water maze (MWM) testing to assess learning and memory differences between young and aged mice. Additionally, transcriptome sequencing was conducted on the hypothalamus of young and aged mice to identify potential genes. Subsequently, GO and KEGG analyses were performed to investigate the functions of differentially expressed genes (DEGs) and their associated biological pathways. Finally, the results obtained from sequencing analysis were further validated using qRT-PCR. Notably, MWM testing revealed a significant decrease in spatial learning and memory ability among aged mice. According to KEGG analysis, the DEGs primarily encompassed various biochemical signaling pathways related to immune system (e.g., C3; C4b; Ccl2; Ccl7; Cebpb; Clec7a; Col3a1; Cxcl10; Cxcl2; Fosb; Fosl1; Gbp5; H2-Ab1; Hspa1a; Hspa1b; Icam1; Il1b; Itga5; Itgax; Lilrb4a; Plaur; Ptprc; Serpine1; Tnfrsf10b; Tnfsf10), neurodegenerative disease (e.g., Atp2a1; Creb5; Fzd10; Hspa1a; Hspa1b; Il1b; Kcnj10; Nxf3; Slc6a3; Tubb6; Uba1y; Wnt9b), nervous system function (e.g., Chrna4; Chrna6; Creb5; Slc6a3),and aging (e.g., Creb5; Hspa1a; Hspa1b) among others. These identified genes may serve as potential predictors for cognitive function in elderly individuals and will provide a crucial foundation for further exploration into the underlying molecular mechanisms.
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Affiliation(s)
- Xiaofeng Tian
- Department of clinical laboratory, the Third Affiliated Hospital of Zhengzhou University. Zhengzhou, China
| | - Zhixing Zhao
- Department of clinical laboratory, the Third Affiliated Hospital of Zhengzhou University. Zhengzhou, China
| | - Jing Zhao
- Department of clinical laboratory, the Third Affiliated Hospital of Zhengzhou University. Zhengzhou, China
| | - Dongmei Su
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Beijing, China
| | - Bin He
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Beijing, China
| | - Cuige Shi
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Beijing, China.
| | - Ying Shi
- Department of clinical laboratory, the Third Affiliated Hospital of Zhengzhou University. Zhengzhou, China.
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Pereira S, Castellani LN, Kowalchuk C, Alganem K, Zhang X, Ryan WG, Singh R, Wu S, Au E, Asgariroozbehani R, Agarwal SM, Giacca A, Mccullumsmith RE, Hahn MK. Olanzapine's effects on hypothalamic transcriptomics and kinase activity. Psychoneuroendocrinology 2024; 163:106987. [PMID: 38340539 PMCID: PMC10947847 DOI: 10.1016/j.psyneuen.2024.106987] [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: 09/21/2023] [Revised: 01/12/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Olanzapine is a second-generation antipsychotic that disrupts metabolism and is associated with an increased risk of type 2 diabetes. The hypothalamus is a key region in the control of whole-body metabolic homeostasis. The objective of the current study was to determine how acute peripheral olanzapine administration affects transcription and serine/threonine kinase activity in the hypothalamus. Hypothalamus samples from rats were collected following the pancreatic euglycemic clamp, thereby allowing us to study endpoints under steady state conditions for plasma glucose and insulin. Olanzapine stimulated pathways associated with inflammation, but diminished pathways associated with the capacity to combat endoplasmic reticulum stress and G protein-coupled receptor activity. These pathways represent potential targets to reduce the incidence of type 2 diabetes in patients taking antipsychotics.
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Affiliation(s)
- Sandra Pereira
- Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Physiology, University of Toronto, Toronto, ON, Canada
| | | | | | - Khaled Alganem
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | - Xiaolu Zhang
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - William G Ryan
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
| | | | - Sally Wu
- Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Emily Au
- Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Pharmacology, University of Toronto, Toronto, ON, Canada
| | - Roshanak Asgariroozbehani
- Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Sri Mahavir Agarwal
- Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Banting & Best Diabetes Centre, Toronto, ON, Canada
| | - Adria Giacca
- Department of Physiology, University of Toronto, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada; Banting & Best Diabetes Centre, Toronto, ON, Canada
| | - Robert E Mccullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH, USA; ProMedica, Neuroscience Institute, Toledo, OH, USA
| | - Margaret K Hahn
- Centre for Addiction and Mental Health, Toronto, ON, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada; Department of Pharmacology, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Banting & Best Diabetes Centre, Toronto, ON, Canada.
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10
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Zhang Z, Jin P, Guo Z, Tu Z, Yang H, Hu M, Li Q, Liu X, Li W, Hou S. Integrated Analysis of Chromatin and Transcriptomic Profiling Identifies PU.1 as a Core Regulatory Factor in Microglial Activation Induced by Chronic Cerebral Hypoperfusion. Mol Neurobiol 2024; 61:2569-2589. [PMID: 37917300 DOI: 10.1007/s12035-023-03734-9] [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: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
In addition to causing white matter lesions, chronic cerebral hypoperfusion (CCH) can also cause damage to gray matter, but the underlying molecular mechanisms remain largely unknown. In order to obtain a better understanding of the relationship between gene expression and transcriptional regulation alterations, novel upstream regulators could be identified using integration analysis of the transcriptome and epigenetic approaches. Here, a bilateral common carotid artery stenosis (BCAS) model was established for inducing CCH in mice. The spatial cognitive function of mice was evaluated, and changes in cortical microglia morphology were observed. RNA-sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were performed on isolated mouse cortical brain tissue. Then, a systematic joint analysis of BCAS hypoperfusion-induced cortex-specific RNA-seq and ATAC-seq was conducted in order to assess the extent of the correlation between the two, and PU.1 was found to be greatly enriched through motif analysis and transcription factor annotation. Also, the core regulatory factor PU.1 induced by BCAS hypoperfusion was shown to be colocalized with microglia. Based on the above analysis, PU.1 plays a key regulatory role in microglial activation induced by CCH. And the transcriptome and epigenomic data presented in this study can help identify potential targets for future research exploring chronic hypoperfusion-induced brain injury.
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Affiliation(s)
- Zengyu Zhang
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengpeng Jin
- Department of Chronic Disease Management, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Zimin Guo
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhilan Tu
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Hualan Yang
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Mengting Hu
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Qinghua Li
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Xingdang Liu
- Department of Nuclear Medicine, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Weiwei Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, China.
| | - Shuangxing Hou
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China.
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11
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Al Tabosh T, Liu H, Koça D, Al Tarrass M, Tu L, Giraud S, Delagrange L, Beaudoin M, Rivière S, Grobost V, Rondeau-Lutz M, Dupuis O, Ricard N, Tillet E, Machillot P, Salomon A, Picart C, Battail C, Dupuis-Girod S, Guignabert C, Desroches-Castan A, Bailly S. Impact of heterozygous ALK1 mutations on the transcriptomic response to BMP9 and BMP10 in endothelial cells from hereditary hemorrhagic telangiectasia and pulmonary arterial hypertension donors. Angiogenesis 2024; 27:211-227. [PMID: 38294582 PMCID: PMC11021321 DOI: 10.1007/s10456-023-09902-8] [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] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/03/2023] [Indexed: 02/01/2024]
Abstract
Heterozygous activin receptor-like kinase 1 (ALK1) mutations are associated with two vascular diseases: hereditary hemorrhagic telangiectasia (HHT) and more rarely pulmonary arterial hypertension (PAH). Here, we aimed to understand the impact of ALK1 mutations on BMP9 and BMP10 transcriptomic responses in endothelial cells. Endothelial colony-forming cells (ECFCs) and microvascular endothelial cells (HMVECs) carrying loss of function ALK1 mutations were isolated from newborn HHT and adult PAH donors, respectively. RNA-sequencing was performed on each type of cells compared to controls following an 18 h stimulation with BMP9 or BMP10. In control ECFCs, BMP9 and BMP10 stimulations induced similar transcriptomic responses with around 800 differentially expressed genes (DEGs). ALK1-mutated ECFCs unexpectedly revealed highly similar transcriptomic profiles to controls, both at the baseline and upon stimulation, and normal activation of Smad1/5 that could not be explained by a compensation in cell-surface ALK1 level. Conversely, PAH HMVECs revealed strong transcriptional dysregulations compared to controls with > 1200 DEGs at the baseline. Consequently, because our study involved two variables, ALK1 genotype and BMP stimulation, we performed two-factor differential expression analysis and identified 44 BMP9-dysregulated genes in mutated HMVECs, but none in ECFCs. Yet, the impaired regulation of at least one hit, namely lunatic fringe (LFNG), was validated by RT-qPCR in three different ALK1-mutated endothelial models. In conclusion, ALK1 heterozygosity only modified the BMP9/BMP10 regulation of few genes, including LFNG involved in NOTCH signaling. Future studies will uncover whether dysregulations in such hits are enough to promote HHT/PAH pathogenesis, making them potential therapeutic targets, or if second hits are necessary.
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Affiliation(s)
- T Al Tabosh
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - H Liu
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - D Koça
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - M Al Tarrass
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - L Tu
- Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Université Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 «Pulmonary Hypertension: Pathophysiology and Novel Therapies», Hôpital Marie Lannelongue, 92350, Le Plessis-Robinson, France
| | - S Giraud
- Genetics Department, Femme-Mère-Enfants Hospital, Hospices Civils de Lyon, 69677, Bron, France
| | - L Delagrange
- Genetics Department, Femme-Mère-Enfants Hospital, Hospices Civils de Lyon, 69677, Bron, France
- National Reference Center for HHT, 69677, Bron, France
| | - M Beaudoin
- Genetics Department, Femme-Mère-Enfants Hospital, Hospices Civils de Lyon, 69677, Bron, France
- National Reference Center for HHT, 69677, Bron, France
| | - S Rivière
- Internal Medicine Department, CHU of Montpellier, St Eloi Hospital and Center of Clinical Investigation, INSERM, CIC 1411, 34295, Montpellier Cedex 7, France
| | - V Grobost
- Internal Medicine Department, CHU Estaing, 63100, Clermont-Ferrand, France
| | - M Rondeau-Lutz
- Internal Medicine Department, University Hospital of Strasbourg, 67091, Strasbourg Cedex, France
| | - O Dupuis
- Hôpital Lyon SUD, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69100, Villeurbanne, France
- Faculty of Medicine, Lyon University, 69921, Lyon, France
| | - N Ricard
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - E Tillet
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - P Machillot
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - A Salomon
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - C Picart
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - C Battail
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - S Dupuis-Girod
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
- Genetics Department, Femme-Mère-Enfants Hospital, Hospices Civils de Lyon, 69677, Bron, France
- National Reference Center for HHT, 69677, Bron, France
| | - C Guignabert
- Faculté de Médecine, Pulmonary Hypertension: Pathophysiology and Novel Therapies, Université Paris-Saclay, 94276, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 «Pulmonary Hypertension: Pathophysiology and Novel Therapies», Hôpital Marie Lannelongue, 92350, Le Plessis-Robinson, France
| | - A Desroches-Castan
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France
| | - S Bailly
- Biosanté unit U1292, Grenoble Alpes University, INSERM, CEA, 38000, Grenoble, France.
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12
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Li H, Nie H, Li D, Wang B, Huo Z, Su Y, Yan X. Transcriptome analysis provides new insights into the immune response of Ruditapes philippinarum infected with Vibrio alginolyticus. Fish & Shellfish Immunology 2024; 148:109468. [PMID: 38432537 DOI: 10.1016/j.fsi.2024.109468] [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: 11/21/2023] [Revised: 02/17/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Manila clam (Ruditapes philippinarum) is a bivalve species with commercial value, but it is easily infected by pathogenic microorganisms in aquaculture, which restricts the shellfish industry. Notably, the impact of Vibrio alginolyticus on clam culture is obvious. In this study, RNA-seq was performed to analyze clam hepatopancreas tissue in 48 h (challenge group, G48h) and 96 h (challenge group, G96h) after infection with V. alginolyticus and 0 h after injection of PBS (control group, C). The results showed that a total of 1670 differentially expressed genes were detected in the G48h vs C group, and 1427 differentially expressed genes were detected in the G96h vs C group. In addition, KEGG analysis showed that DEGs were significantly enriched in pathways such as Lysosome and Mitophagy. Moreover, 15 immune related DEGs were selected for qRT-PCR analysis to verify the accuracy of RNA-seq, and the results showed that the expression level of DEGs was consistent with that of RNA-seq. Therefore, the results obtained in this study provides a preliminary understanding of the immune defense of R. philippinarum and molecular insights for genetic breeding of V. alginolyticus resistance in Manila clam.
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Affiliation(s)
- Hongda Li
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
| | - Dongdong Li
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Bin Wang
- Dalian Jintuo Aquatic Food Co., Ltd, 116000 Dalian, China
| | - Zhongming Huo
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Yanming Su
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China.
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
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13
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Paolillo VK, Ochs ME, Lundquist EA. MAB-5/Hox regulates the Q neuroblast transcriptome, including cwn-1/Wnt, to mediate posterior migration in Caenorhabditis elegans. Genetics 2024:iyae045. [PMID: 38652773 DOI: 10.1093/genetics/iyae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024] Open
Abstract
Neurogenesis involves the precisely coordinated action of genetic programs controlling large-scale neuronal fate specification down to terminal events of neuronal differentiation. The Q neuroblasts in Caenorhabditis elegans, QL on the left and QR on the right, divide, differentiate, and migrate in a similar pattern to produce three neurons each. However, QL on the left migrates posteriorly, and QR on the right migrates anteriorly. The MAB-5/Hox transcription factor is necessary and sufficient for posterior Q lineage migration and is normally expressed only in the QL lineage. To define genes controlled by MAB-5 in the Q cells, fluorescence-activated cell sorting was utilized to isolate populations of Q cells at a time in early L1 larvae when MAB-5 first becomes active. Sorted Q cells from wild-type, mab-5 loss-of-function (lof), and mab-5 gain-of-function (gof) mutants were subject to RNA-seq and differential expression analysis. Genes enriched in Q cells included those involved in cell division, DNA replication, and DNA repair, consist with the neuroblast stem cell identity of the Q cells at this stage. Genes affected by mab-5 included those involved in neurogenesis, neural development, and interaction with the extracellular matrix. cwn-1, which encodes a Wnt signaling molecule, showed a paired response to mab-5 in the Q cells: cwn-1 expression was reduced in mab-5(lof) and increased in mab-5(gof), suggesting that MAB-5 is required for cwn-1 expression in Q cells. MAB-5 is required to prevent anterior migration of the Q lineage while it transcriptionally reprograms the Q lineage for posterior migration. Functional genetic analysis revealed that CWN-1 is required downstream of MAB-5 to inhibit anterior migration of the QL lineage, likely in parallel to EGL-20/Wnt in a noncanonical Wnt pathway. In sum, work here describes a Q cell transcriptome, and a set of genes regulated by MAB-5 in the QL lineage. One of these genes, cwn-1, acts downstream of mab-5 in QL migration, indicating that this gene set includes other genes utilized by MAB-5 to facilitate posterior neuroblast migration.
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Affiliation(s)
- Vitoria K Paolillo
- Department of Molecular Biosciences, KU Center for Genomics, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Matthew E Ochs
- Department of Molecular Biosciences, KU Center for Genomics, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Erik A Lundquist
- Department of Molecular Biosciences, KU Center for Genomics, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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14
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Aguiar TFM, Rivas MP, de Andrade Silva EM, Pires SF, Dangoni GD, Macedo TC, Defelicibus A, Barros BDDF, Novak E, Cristofani LM, Odone V, Cypriano M, de Toledo SRC, da Cunha IW, da Costa CML, Carraro DM, Tojal I, de Oliveira Mendes TA, Krepischi ACV. First Transcriptome Analysis of Hepatoblastoma in Brazil: Unraveling the Pivotal Role of Noncoding RNAs and Metabolic Pathways. Biochem Genet 2024:10.1007/s10528-024-10764-y. [PMID: 38649558 DOI: 10.1007/s10528-024-10764-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues. The analysis unveiled 1,492 differentially expressed genes (1,031 upregulated and 461 downregulated), including 920 protein-coding genes (62%). Upregulated biological processes were linked to cell differentiation, signaling, morphogenesis, and development, involving known hepatoblastoma-associated genes (DLK1, MEG3, HDAC2, TET1, HMGA2, DKK1, DKK4), alongside with novel findings (GYNG4, CDH3, and TNFRSF19). Downregulated processes predominantly centered around oxidation and metabolism, affecting amines, nicotinamides, and lipids, featuring novel discoveries like the repression of SYT7, TTC36, THRSP, CCND1, GCK and CAMK2B. Two genes, which displayed a concordant pattern of DNA methylation alteration in their promoter regions and dysregulation in the transcriptome, were further validated by RT-qPCR: the upregulated TNFRSF19, a key gene in the embryonic development, and the repressed THRSP, connected to lipid metabolism. Furthermore, based on protein-protein interaction analysis, we identified genes holding central positions in the network, such as HDAC2, CCND1, GCK, and CAMK2B, among others, that emerged as prime candidates warranting functional validation in future studies. Notably, a significant dysregulation of non-coding RNAs (ncRNAs), predominantly upregulated transcripts, was observed, with 42% of the top 50 highly expressed genes being ncRNAs. An integrative miRNA-mRNA analysis revealed crucial biological processes associated with metabolism, oxidation reactions of lipids and carbohydrates, and methylation-dependent chromatin silencing. In particular, four upregulated miRNAs (miR-186, miR-214, miR-377, and miR-494) played a pivotal role in the network, potentially targeting multiple protein-coding transcripts, including CCND1 and CAMK2B. In summary, our transcriptome analysis highlighted disrupted embryonic development as well as metabolic pathways, particularly those involving lipids, emphasizing the emerging role of ncRNAs as epigenetic regulators in hepatoblastomas. These findings provide insights into the complexity of the hepatoblastoma transcriptome and identify potential targets for future therapeutic interventions.
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Affiliation(s)
- Talita Ferreira Marques Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, USA
| | - Maria Prates Rivas
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Edson Mario de Andrade Silva
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Minas Gerais, Brazil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
| | - Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Gustavo Dib Dangoni
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Taiany Curdulino Macedo
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Dirce Maria Carraro
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil.
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15
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Kanda K, Iwata H. Tris(2-chloroethyl) phosphate (TCEP) exposure inhibits the epithelial-mesenchymal transition (EMT), mesoderm differentiation, and cardiovascular development in early chicken embryos. Sci Total Environ 2024; 922:171242. [PMID: 38417504 DOI: 10.1016/j.scitotenv.2024.171242] [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: 12/06/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024]
Abstract
Tris(2-chloroethyl) phosphate (TCEP) is an organophosphorus flame retardant used worldwide and has been detected in the tissues and eggs of wild birds. Our previous study reported that exposure to TCEP induced developmental delay and cardiovascular dysfunction with attenuated heart rate and vasculogenesis in early chicken embryos. This study aimed to investigate the molecular mechanisms underlying the cardiovascular effects of TCEP on chicken embryos using cardiac transcriptome analysis and to examine whether TCEP exposure affects epithelial-mesenchymal transition (EMT) and mesoderm differentiation during gastrulation. Transcriptome analysis revealed that TCEP exposure decreased the expression of cardiac conduction-related genes and transcription factors on day 5 of incubation. In extraembryonic blood vessels, the expression levels of genes related to fibroblast growth factor (FGF) and vascular endothelial growth factor (VEGF) were significantly reduced by TCEP exposure and vasculogenesis was suppressed. TCEP exposure also attenuated Snail family transcriptional repressor 2 (SNAI2) and T-box transcription factor T (TBXT) signaling in the chicken primitive streak, indicating that TCEP inhibits EMT and mesoderm differentiation during gastrulation at the early developmental stage. These effects on EMT and mesoderm differentiation may be related to subsequent phenotypic defects, including suppression of heart development and blood vessel formation.
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Affiliation(s)
- Kazuki Kanda
- Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan; National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Hisato Iwata
- Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
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16
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Iori S, D'Onofrio C, Laham-Karam N, Mushimiyimana I, Lucatello L, Montanucci L, Maria Lopparelli R, Bonsembiante F, Capolongo F, Pauletto M, Dacasto M, Giantin M. Generation and characterization of cytochrome P450 3A74 CRISPR/Cas9 knockout bovine foetal hepatocyte cell line (BFH12). Biochem Pharmacol 2024:116231. [PMID: 38648904 DOI: 10.1016/j.bcp.2024.116231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/04/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
In human, the cytochrome P450 3A (CYP3A) subfamily of drug-metabolizing enzymes (DMEs) is responsible for a significant number of phase I reactions, with the CYP3A4 isoform superintending the hepatic and intestinal metabolism of diverse endobiotic and xenobiotic compounds. The CYP3A4-dependent bioactivation of chemicals may result in hepatotoxicity and trigger carcinogenesis. In cattle, four CYP3A genes (CYP3A74, CYP3A76, CYP3A28 and CYP3A24) have been identified. Despite cattle being daily exposed to xenobiotics (e.g., mycotoxins, food additives, drugs and pesticides), the existing knowledge about the contribution of CYP3A in bovine hepatic metabolism is still incomplete. Nowadays, CRISPR/Cas9 mediated knockout (KO) is a valuable method to generate in vivo and in vitro models for studying the metabolism of xenobiotics. In the present study, we successfully performed CRISPR/Cas9-mediated KO of bovine CYP3A74, human CYP3A4-like, in a bovine foetal hepatocyte cell line (BFH12). After clonal expansion and selection, CYP3A74 ablation was confirmed at the DNA, mRNA, and protein level. The subsequent characterization of the CYP3A74 KO clone highlighted significant transcriptomic changes (RNA-sequencing) associated with the regulation of cell cycle and proliferation, immune and inflammatory response, as well as metabolic processes. Overall, this study successfully developed a new CYP3A74 KO in vitro model by using CRISPR/Cas9 technology, which represents a novel resource for xenobiotic metabolism studies in cattle. Furthermore, the transcriptomic analysis suggests a key role of CYP3A74 in bovine hepatocyte cell cycle regulation and metabolic homeostasis.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Caterina D'Onofrio
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Nihay Laham-Karam
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211 Kuopio, Finland
| | - Isidore Mushimiyimana
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211 Kuopio, Finland
| | - Lorena Lucatello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Ludovica Montanucci
- Department of Neurology, University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, OH 44106, USA
| | - Rosa Maria Lopparelli
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Federico Bonsembiante
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Francesca Capolongo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy.
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17
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Xu Y, Dong F, Wang R, Ajmal M, Liu X, Lin H, Chen H. Alternative splicing analysis of lignocellulose-degrading enzyme genes and enzyme variants in Aspergillus niger. Appl Microbiol Biotechnol 2024; 108:302. [PMID: 38639796 PMCID: PMC11031446 DOI: 10.1007/s00253-024-13137-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: 01/09/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
Alternative splicing (AS) greatly expands the protein diversity in eukaryotes. Although AS variants have been frequently reported existing in filamentous fungi, it remains unclear whether lignocellulose-degrading enzyme genes in industrially important fungi undergo AS events. In this work, AS events of lignocellulose-degrading enzymes genes in Aspergillus niger under two carbon sources (glucose and wheat straw) were investigated by RNA-Seq. The results showed that a total of 23 out of the 56 lignocellulose-degrading enzyme genes had AS events and intron retention was the main type of these AS events. The AS variant enzymes from the annotated endo-β-1,4-xylanase F1 gene (xynF1) and the endo-β-1,4-glucanase D gene (eglD), noted as XYNF1-AS and EGLD-AS, were characterized compared to their normal splicing products XYNF1 and EGLD, respectively. The AS variant XYNF1-AS displayed xylanase activity whereas XYNF1 did not. As for EGLD-AS and EGLD, neither of them showed annotated endo-β-1,4-glucanase activity. Instead, both showed lytic polysaccharide monooxygenase (LPMO) activity with some differences in catalytic properties. Our work demonstrated that the AS variants in A. niger were good sources for discovering novel lignocellulose-degrading enzymes. KEY POINTS: • AS events were identified in the lignocellulose-degrading enzyme genes of A. niger. • New β-1,4-xylanase and LPMO derived from AS events were characterized.
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Affiliation(s)
- Yifan Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Feiyu Dong
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruoxin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Maria Ajmal
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinyu Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Lin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
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18
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Wang H, Ai LZ, Xia YJ, Wang GQ, Xiong ZQ, Song X. Characterization of a Panel of Constitutive Promoters from Lactococcus cremoris for Fine-Tuning Gene Expression. ACS Synth Biol 2024; 13:1365-1372. [PMID: 38518262 DOI: 10.1021/acssynbio.4c00087] [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: 03/24/2024]
Abstract
Lactococcus cremoris (homotypic synonym: Lactococcus lactis) is receiving increasing attention as a prominent vehicle for the delivery of live vaccines. This can hardly be achieved without developing tools for the genetic manipulation of L. cremoris, and the paucity of studies on L. cremoris endogenous promoters has attracted our attention. Here, we report the discovery and characterization of 29 candidate promoters identified from L. cremoris subsp. cremoris NZ9000 by RNA sequencing analysis. Furthermore, 18 possible constitutive promoters were obtained by RT-qPCR screening from these 29 candidate promoters. Then, these 18 promoters were cloned and characterized by a reporter gene, gusA, encoding β-glucuronidase. Eventually, eight endogenous constitutive promoters of L. cremoris were obtained, which can be applied to genetic manipulation of lactic acid bacteria.
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Affiliation(s)
- Hui Wang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yong-Jun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Guang-Qiang Wang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
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19
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Jiang L, Wan Y, Pan J, Mao X, Sun X, Zan L, Wang H. Transcriptomic analysis reveals the inhibitory effect of beta-sitosterol on proliferation of bovine preadipocytes. Anim Biotechnol 2024:2339406. [PMID: 38634284 DOI: 10.1080/10495398.2024.2339406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Fat deposition affects beef quantity and quality via preadipocyte proliferation. Beta-sitosterol, a natural small molecular compound, has various functions, such as anti-inflammation, antibacterial, and anticancer properties. The mechanism of action of Beta-sitosterol on bovine preadipocytes remains unclear. This study, based on RNA-seq, reveals the impact of Beta -sitosterol on the proliferation of bovine preadipocytes. Compared to the control group, Beta-sitosterol demonstrated a more pronounced inhibitory effect on cell proliferation after 48 hours of treatment than after 24 hours, as evidenced by the results of EdU staining and flow cytometry. RNA-seq and Western Blot analyses further substantiated these findings. Our results suggest that the impact of Beta-sitosterol on the proliferation of bovine preadipocytes is not significant after a 24-hour treatment. It is only after extending the treatment time to 48 hours that Beta-sitosterol may induce cell cycle arrest at the G2/M phase by suppressing the expression of CCNB1, thereby inhibiting the proliferation of bovine preadipocytes.
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Affiliation(s)
- Lei Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuan Wan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinhai Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyu Mao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaolei Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- National Beef Cattle Improvement Centre, Yangling, Shaanxi, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- National Beef Cattle Improvement Centre, Yangling, Shaanxi, China
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20
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Liu X, Xu H, Peng M, Zhou C, Wei C, Hong X, Li W, Chen C, Ji L, Zhu X. Screening of temperature-responsive signalling molecules during sex differentiation in Asian yellow pond turtle (Mauremys mutica). BMC Genomics 2024; 25:383. [PMID: 38637759 PMCID: PMC11025153 DOI: 10.1186/s12864-024-10275-5] [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: 01/02/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND The Asian yellow pond turtle (Mauremys mutica) is an important commercial freshwater aquaculture species in China. This species is a highly sexually dimorphic species, with males growing at a faster rate than females and exhibits temperature-dependent sex determination (TSD), in which the incubation temperature during embryonic development determines the sexual fate. However, the mechanisms of the sex determination or sex differentiation in the Asian yellow pond turtle are remain a mystery. RESULTS Temperature-specific gonadal transcriptomics of the Asian yellow pond turtle were performed during the thermosensitive period (stage 15) using RNA-seq technology to identify candidate genes that initiate gonadal differentiation. We uncovered candidates that were the first to respond to temperature. These candidates were sexually dimorphic in expression, reflecting differences in gonadal (Cirbp, Runx1) and germline differentiation (Vasa, Nanos1, Piwil2), gametogenesis (Hmgb3, Zar1, Ovoinhibitor-like, Kif4), steroid hormone biosynthesis (Hsd17b5, Hsd17b6), heat shock (Dnajb6, Hsp90b1, Hsp90aa1) and transient receptor potential channel genes (Trpm1, Trpm4, Trpm6, Trpv1). CONCLUSIONS Our work will provide important genetic information to elucidate the mechanisms of sex control in the Asian yellow pond turtles, and will contribute important genetic resources for further studies of temperature-dependent sex determination in turtles.
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Affiliation(s)
- Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China
| | - Haoyang Xu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China
| | - Mingwei Peng
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
- School of Fishery, Zhejiang Ocean University, 316000, Zhoushan, China
| | - Chenyao Zhou
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
- School of Fishery, Zhejiang Ocean University, 316000, Zhoushan, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510380, Guangzhou, China.
- College of Life Science and Fisheries, Shanghai Ocean University, 201306, Shanghai, China.
- School of Fishery, Zhejiang Ocean University, 316000, Zhoushan, China.
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21
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Gao M, Dong C, Chen Z, Jiang R, Shaw P, Gao W, Sun Y. Different impact of short-term and long-term hindlimb disuse on bone homeostasis. Gene 2024; 918:148457. [PMID: 38641071 DOI: 10.1016/j.gene.2024.148457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/19/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Disuse osteoporosis is one of the major problems of bone health which commonly occurs in astronauts during long-term spaceflight and bedridden patients. However, the mechanisms underlying such mechanical unloading induced bone loss have not been fully understood. In this study, we employed hindlimb-unloading mice models with different length of tail suspension to investigate if the bone loss was regulated by distinct factors under different duration of disuse. Our micro-CT results showed more significant decrease of bone mass in 6W (6-week) tail-suspension mice compared to the 1W (1-week) tail-suspension ones, as indicated by greater reduction of BV/TV, Tb.N, B.Ar/T.Ar and Ct.Th. RNA-sequencing results showed significant effects of hindlimb disuse on cell locomotion and immune system process which could cause bone loss.Real-time quantitative PCR results indicated a greater number of bone formation related genes that were downregulated in short-term tail-suspension mice compared to the long-term ones. It is, thus, suggested while sustained hindlimb unloading continuously contributes to bone loss, molecular regulation of bone homeostasis tends to reach a balance during this process.
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Affiliation(s)
- Minhao Gao
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chengji Dong
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhuliu Chen
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Renhao Jiang
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Peter Shaw
- Oujiang Lab, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325000, China
| | - Weiyang Gao
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Yuanna Sun
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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22
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Yang ZL, Tian C, He J, Pan H, Ruan GP, Zhao J, Wang K, Pan XH, Zhu XQ. Whole-transcriptome profiling reveals potential biomarkers for the reversal of thymic epithelial cell senescence by umbilical cord mesenchymal stem cells. Aging (Albany NY) 2024; 16:205738. [PMID: 38637117 DOI: 10.18632/aging.205738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 03/18/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Reduced numbers and dysfunction of thymic epithelial cells (TECs) are important factors of thymic degeneration. Previous studies have found that umbilical cord mesenchymal stem cells (UCMSCs) reverse the structure and function of the senescent thymus in vivo. However, the transcriptomic regulation mechanism is unclear. METHODS TECs were cultured with H2O2 for 72 hours to induce senescence. UCMSCs were cocultured with senescent TECs for 48 hours to detect SA-β-gal, P16 and Ki67. The cocultured TECs were collected for lncRNA, mRNA and miRNA sequencing to establish a competitive endogenous regulatory network (ceRNA). And RT-qPCR, immunofluorescence staining, and western blot were used to identified key genes. RESULTS Our results showed that H2O2 induced TEC aging and that UCMSCs reversed these changes. Compared with those in aged TECs, 2260 DE mRNAs, 1033 DE lncRNAs and 67 DE miRNAs were differentially expressed, and these changes were reversed by coculturing the cells with UCMSCs. Differential mRNA enrichment analysis of ceRNA regulation revealed that the PI3K-AKT pathway was a significant signaling pathway. UCMSC coculture upregulated VEGFA, which is the upstream factor of the PI3K-AKT signaling pathway, and the expression of the key proteins PI3K and AKT. Thus, the expression of the cell cycle suppressor P27, which is downstream of the PI3K-AKT signaling pathway, was downregulated, while the expression of the cell cycle regulators CDK2 and CCNE was upregulated. CONCLUSION UCMSC coculture upregulated the expression of VEGFA, activated the PI3K-AKT signaling pathway, increased the expression of CDK2 and CCNE, decreased the expression of P27, and promoted the proliferation of TECs.
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Affiliation(s)
- Zai-Ling Yang
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
- The Second People’s Hospital of Guiyang, Medical Laboratory, Guiyang 550023, Guizhou, China
| | - Chuan Tian
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Jie He
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Hang Pan
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Guang-Ping Ruan
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Jing Zhao
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Kai Wang
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Xing-Hua Pan
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
| | - Xiang-Qing Zhu
- The Basic Medical Laboratory of the 920th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming 650032, Yunnan, China
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23
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Park HE, Kim KM, Shin JI, Choi JG, An WJ, Trinh MP, Kang KM, Yoo JW, Byun JH, Jung MH, Lee KH, Kang HL, Baik SC, Lee WK, Shin MK. Prominent transcriptomic changes in Mycobacterium intracellulare under acidic and oxidative stress. BMC Genomics 2024; 25:376. [PMID: 38632539 PMCID: PMC11022373 DOI: 10.1186/s12864-024-10292-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Mycobacterium avium complex (MAC), including Mycobacterium intracellulare is a member of slow-growing mycobacteria and contributes to a substantial proportion of nontuberculous mycobacterial lung disease in humans affecting immunocompromised and elderly populations. Adaptation of pathogens in hostile environments is crucial in establishing infection and persistence within the host. However, the sophisticated cellular and molecular mechanisms of stress response in M. intracellulare still need to be fully explored. We aimed to elucidate the transcriptional response of M. intracellulare under acidic and oxidative stress conditions. RESULTS At the transcriptome level, 80 genes were shown [FC] ≥ 2.0 and p < 0.05 under oxidative stress with 10 mM hydrogen peroxide. Specifically, 77 genes were upregulated, while 3 genes were downregulated. In functional analysis, oxidative stress conditions activate DNA replication, nucleotide excision repair, mismatch repair, homologous recombination, and tuberculosis pathways. Additionally, our results demonstrate that DNA replication and repair system genes, such as dnaB, dinG, urvB, uvrD2, and recA, are indispensable for resistance to oxidative stress. On the contrary, 878 genes were shown [FC] ≥ 2.0 and p < 0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis highlighted nitrogen and sulfur metabolism pathways as the primary responses to acidic stress. Our findings provide evidence of the critical role played by nitrogen and sulfur metabolism genes in the response to acidic stress, including narGHIJ, nirBD, narU, narK3, cysND, cysC, cysH, ferredoxin 1 and 2, and formate dehydrogenase. CONCLUSION Our results suggest the activation of several pathways potentially critical for the survival of M. intracellulare under a hostile microenvironment within the host. This study indicates the importance of stress responses in M. intracellulare infection and identifies promising therapeutic targets.
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Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Ih Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Gyu Choi
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Won-Jun An
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Minh Phuong Trinh
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyeong-Min Kang
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Myung Hwan Jung
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kon-Ho Lee
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyung-Lyun Kang
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Seung Cheol Baik
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
- Department of Convergence of Medical Science, Gyeongsang National University, Jinju, Republic of Korea.
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24
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Zeinali S, Sutton K, Zefreh MG, Mabbott N, Vervelde L. Discrimination of distinct chicken M cell subsets based on CSF1R expression. Sci Rep 2024; 14:8795. [PMID: 38627516 PMCID: PMC11021470 DOI: 10.1038/s41598-024-59368-x] [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: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
In mammals, a subset of follicle-associated epithelial (FAE) cells, known as M cells, conduct the transcytosis of antigens across the epithelium into the underlying lymphoid tissues. We previously revealed that M cells in the FAE of the chicken lung, bursa of Fabricius (bursa), and caecum based on the expression of CSF1R. Here, we applied RNA-seq analysis on highly enriched CSF1R-expressing bursal M cells to investigate their transcriptome and identify novel chicken M cell-associated genes. Our data show that, like mammalian M cells, those in the FAE of the chicken bursa also express SOX8, MARCKSL1, TNFAIP2 and PRNP. Immunohistochemical analysis also confirmed the expression of SOX8 in CSF1R-expressing cells in the lung, bursa, and caecum. However, we found that many other mammalian M cell-associated genes such as SPIB and GP2 were not expressed by chicken M cells or represented in the chicken genome. Instead, we show bursal M cells express high levels of related genes such as SPI1. Whereas our data show that bursal M cells expressed CSF1R-highly, the M cells in the small intestine lacked CSF1R and both expressed SOX8. This study offers insights into the transcriptome of chicken M cells, revealing the expression of CSF1R in M cells is tissue-specific.
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Affiliation(s)
- Safieh Zeinali
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Kate Sutton
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| | - Masoud Ghaderi Zefreh
- Division of Genetics and Genomics, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Neil Mabbott
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Lonneke Vervelde
- Division of Immunology, The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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25
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Xu C, Li J, Song LY, Guo ZJ, Song SW, Zhang LD, Zheng HL. PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants. J Exp Bot 2024; 75:2266-2279. [PMID: 38190348 DOI: 10.1093/jxb/erae007] [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: 10/29/2023] [Accepted: 01/07/2024] [Indexed: 01/10/2024]
Abstract
In plants, C-to-U RNA editing mainly occurs in plastid and mitochondrial transcripts, which contributes to a complex transcriptional regulatory network. More evidence reveals that RNA editing plays critical roles in plant growth and development. However, accurate detection of RNA editing sites using transcriptome sequencing data alone is still challenging. In the present study, we develop PlantC2U, which is a convolutional neural network, to predict plastid C-to-U RNA editing based on the genomic sequence. PlantC2U achieves >95% sensitivity and 99% specificity, which outperforms the PREPACT tool, random forests, and support vector machines. PlantC2U not only further checks RNA editing sites from transcriptome data to reduce possible false positives, but also assesses the effect of different mutations on C-to-U RNA editing based on the flanking sequences. Moreover, we found the patterns of tissue-specific RNA editing in the mangrove plant Kandelia obovata, and observed reduced C-to-U RNA editing rates in the cold stress response of K. obovata, suggesting their potential regulatory roles in plant stress adaptation. In addition, we present RNAeditDB, available online at https://jasonxu.shinyapps.io/RNAeditDB/. Together, PlantC2U and RNAeditDB will help researchers explore the RNA editing events in plants and thus will be of broad utility for the plant research community.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ling-Yu Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ze-Jun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shi-Wei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Lu-Dan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
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Pereira-Garcia C, Sanz-Sáez I, Sánchez P, Coutinho FH, Bravo AG, Sánchez O, Acinas SG. Genomic and transcriptomic characterization of methylmercury detoxification in a deep ocean Alteromonas mediterranea ISS312. Environ Pollut 2024; 347:123725. [PMID: 38467369 DOI: 10.1016/j.envpol.2024.123725] [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: 10/03/2023] [Revised: 01/12/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
Methylmercury (MeHg) is one of the most worrisome pollutants in marine systems. MeHg detoxification is mediated by merB and merA genes, responsible for the demethylation of MeHg and the reduction of inorganic mercury, respectively. Little is known about the biological capacity to detoxify this compound in marine environments, and even less the bacterial transcriptional changes during MeHg detoxification. This study provides the genomic and transcriptomic characterization of the deep ocean bacteria Alteromonas mediterranea ISS312 with capacity for MeHg degradation. Its genome sequence revealed four mer operons containing three merA gene and two merB gene copies, that could be horizontally transferred among distant related genomes by mobile genetic elements. The transcriptomic profiling in the presence of 5 μM MeHg showed that merA and merB genes are within the most expressed genes, although not all mer genes were equally transcribed. Besides, we aimed to identify functional orthologous genes that displayed expression profiles highly similar or identical to those genes within the mer operons, which could indicate they are under the same regulatory controls. We found contrasting expression profiles for each mer operon that were positively correlated with a wide array of functions mostly related to amino acid metabolism, but also to flagellar assembly or two component systems. Also, this study highlights that all merAB genes of the four operons were globally distributed across oceans layers with higher transcriptional activity in the mesopelagic deeper waters. Our study provides new insights about the transcriptional patterns related to the capacity of marine bacteria to detoxify MeHg, with important implications for the understanding of this process in marine ecosystems.
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Affiliation(s)
- Carla Pereira-Garcia
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalunya, Spain.
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain; Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Felipe H Coutinho
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalunya, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain.
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Zhao Q, Dai H, Jiang H, Zhang N, Hou F, Zheng Y, Gao Y, Liu W, Feng Z, Hu Y, Tang X, Rui H, Liu B. Activation of the IL-6/STAT3 pathway contributes to the pathogenesis of membranous nephropathy and is a target for Mahuang Fuzi and Shenzhuo Decoction (MFSD) to repair podocyte damage. Biomed Pharmacother 2024; 174:116583. [PMID: 38626520 DOI: 10.1016/j.biopha.2024.116583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUND Primary membranous nephropathy (PMN) is an autoimmune glomerular disease. IL-6 is a potential therapeutic target for PMN. Previous clinical studies have demonstrated the effectiveness of Mahuang Fuzi and Shenzhuo Decoction (MFSD) in treating membranous nephropathy. However, the mechanism of action of MFSD remains unclear. METHODS Serum IL-6 levels were measured in patients with PMN and healthy subjects. The passive Heymann nephritis (PHN) rat model was established, and high and low doses of MFSD were used for intervention to observe the repair effect of MFSD on renal pathological changes and podocyte injury. RNA-seq was used to screen the possible targets of MFSD, and the effect of MFSD targeting IL-6/STAT3 was further verified by combining the experimental results. Finally, the efficacy of tocilizumab in PHN rats was observed. RESULTS Serum IL-6 levels were significantly higher in PMN patients than in healthy subjects. These levels significantly decreased in patients in remission after MFSD treatment. MFSD treatment improved laboratory indicators in PHN rats, as well as glomerular filtration barrier damage and podocyte marker protein expression. Renal transcriptome changes showed that MFSD-targeted differential genes were enriched in JAK/STAT and cytokine-related pathways. MFSD inhibits the IL6/STAT3 pathway in podocytes. Additionally, MFSD significantly reduced serum levels of IL-6 and other cytokines in PHN rats. However, treatment of PHN with tocilizumab did not achieve the expected effect. CONCLUSION The IL-6/STAT3 signaling pathway is activated in podocytes of experimental membranous nephropathy. MFSD alleviates podocyte damage by inhibiting the IL-6/STAT3 pathway.
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Affiliation(s)
- Qihan Zhao
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Haoran Dai
- Shunyi Branch, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100310, China
| | - Hanxue Jiang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Naiqian Zhang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Fanyu Hou
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yang Zheng
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Yu Gao
- Beijing Chaoyang District emergency medical rescue center, Beijing, 100020, China
| | - Wenbin Liu
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhendong Feng
- Shunyi Branch, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100310, China
| | - Yuehong Hu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Xinyue Tang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Hongliang Rui
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Beijing Institute of Chinese Medicine, Beijing, 100010, China.
| | - Baoli Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China.
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Zhou L, Liu X, Wu T, Liu Q, Jing M, Li H, Xu N, Tang H. Identification of survival related key genes and long-term survival specific differentially expressed genes related key miRNA network of primary glioblastoma. Heliyon 2024; 10:e28439. [PMID: 38601561 PMCID: PMC11004527 DOI: 10.1016/j.heliyon.2024.e28439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Primary glioblastoma(pGBM) is the most malignant tumor of the central nervous system. Radiotherapy, chemotherapy and surgical treatment have little effect on the survival of pGBM patients. The prognosis is often poorly once the tumor recurs. It is urgent to develop new therapies for patients. In recent years, studies have been clarified that miRNA have a powerful regulating effect on the genes. However, the main group of miRNAs in regulating long-term survival specific related genes of pGBM is still unclear. Given that the survival period of most glioma patients is relatively short, studying long-term survival patients with pGBM is of great value for this disease. Our study aim to identify key miRNAs with long-term survival related genes present in pGBM and uncover their potential mechanisms. The gene expression profiles of GSE53733, GSE15824, GSE30563, GSE50161 were obtained from the Gene Expression Omnibus database. Firstly, samples were divided into 3 groups according to its survival time and each group compare to the normal control group. Then we obtained differential expression genes (DEGs) with a long-term survival specific (LTSDEGs) and a short-term survival specific DEGs (STSDEGs). Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted with LTSDEGs and STSDEGs together. Moreover, we used the UALCAN database to verify LTSDEGs and STSDEGs, and obtained long-term verified survival specific DEGs(LTVSDEGs) and short-term verified survival specific DEGs(STVSDEGs). Finally, we established the predicted key miRNAs-LTVSDEGs interaction network. The protein expressions of the top 4 LTVSDEGs were verified in the HPA database with immunohistochemical staining. In total, we found 260 genes changed in LTSDEGs and 822 genes changed in STSDEGs. GO and KEGG results shown that the major changes are focused on tumor metabolism. 9 LTVSDEGs and 18 STVSDEGs were verified in UALCAN database. As for protein expression verification in top 4 LTVSDEGs, ZNF630, BLVRB and RPA3 were verified, while TPBG was not detected. We obtained 59 key miRNA from the predicted key miRNAs-LTVSDEGs interaction network. 25 key miRNAs were verified using GSE90603. Finally, we constructed the key miRNAs-LTVSDEGs network using a Sankey diagram, including 25 miRNAs and 7 LTVSDEGs. In conclusion, our study shows that there is a close relationship between metabolic changes and survival in pGBM. Besides, we established a key miRNAs-LTVSDEGs network for pGBM, which could be the key path in prolonging the life of pGBM patients.
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Affiliation(s)
- Lingqi Zhou
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
- Guangzhou Key Laboratory of Child Neurodevelopment, Guangzhou, 510623, China
- Institute Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China
| | - Xuemei Liu
- Department of Gynecology, Shunde Hospital,Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, 528308, China
| | - Tong Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080,China
| | - Qundi Liu
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Meilian Jing
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Huahan Li
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Ning Xu
- Department of Clinical Laboratory, South China Hospital, Medical School, Shenzhen University, Shenzhen, 518111, China
| | - Hai Tang
- Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080,China
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Vendrell X, de Castro P, Escrich L, Grau N, Gonzalez-Martin R, Quiñonero A, Escribá MJ, Domínguez F. Longitudinal profiling of human androgenotes through single-cell analysis unveils paternal gene expression dynamics in early embryo development. Hum Reprod 2024:deae072. [PMID: 38622061 DOI: 10.1093/humrep/deae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
STUDY QUESTION How do transcriptomics vary in haploid human androgenote embryos at single cell level in the first four cell cycles of embryo development? SUMMARY ANSWER Gene expression peaks at the fourth cell cycle, however some androcytes exhibit unique transcriptional behaviors. WHAT IS KNOWN ALREADY The developmental potential of an embryo is determined by the competence of the oocyte and the sperm. However, studies of the contribution of the paternal genome using pure haploid androgenotes are very scarce. STUDY DESIGN, SIZE, DURATION This study was performed analyzing the single-cell transcriptomic sequencing of 38 androcytes obtained from 10 androgenote bioconstructs previously produced in vitro (de Castro et al., 2023). These results were analyzed through different bioinformatics software such as g: Profiler, GSEA, Cytoscape, and Reactome. PARTICIPANTS/MATERIALS, SETTING, METHODS Single cell sequencing was used to obtain the transcriptomic profiles of the different androcytes. The results obtained were compared between the different cycles studied using the DESeq2 program and functional enrichment pathways using g: Profiler, Cytoscape, and Reactome. MAIN RESULTS AND THE ROLE OF CHANCE A wave of paternally driven transcriptomic activation was found during the third-cell cycle, with 1128 upregulated and 225 downregulated genes and the fourth-cell cycle, with 1373 upregulated and 286 downregulated genes, compared to first-cell cycle androcytes. Differentially expressed routes related to cell differentiation, DNA-binding transcription, RNA biosynthesis and RNA polymerase II transcription regulatory complex, and cell death were found in the third and fourth with respect to the first-cell cycle. Conversely, in the fourth cell cycle, 153 downregulated and 332 upregulated genes were found compared with third cell cycle, associated with differentially expressed processes related to E-box binding and zinc finger protein 652 (ZNF652) transcription factor. Further, significant overexpression of LEUTX, PRAMEF1, DUXA, RFPL4A, TRIM43, and ZNF675 found in androgenotes, compared to biparental embryos, highlights the paternal contributions to zygote genome activation. LARGE SCALE DATA All raw sequencing data are available through the Gene Expression Omnibus (GEO) under accessions number: GSE216501. LIMITATIONS, REASONS FOR CAUTION Extrapolation of biological events from uniparental constructs to biparental embryos should be done with caution. Maternal and paternal genomes do not act independently of each other in a natural condition. The absence of one genome may affect gene transcription of the other. In this sense, the haploid condition of the bioconstructs could mask the transcriptomic patterns of the single cells. WIDER IMPLICATIONS OF THE FINDINGS The results obtained demonstrated the level of involvement of the human paternal haploid genome in the early stages of embryo development as well as its evolution at the transcriptomic level, laying the groundwork for the use of these bioconstructs as reliable models to dispel doubts about the genetic role played by the paternal genome in the early cycles of embryo development. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by Instituto de Salud Carlos III (ISCIII) through the project 'PI22/00924', co-funded by European Regional Development Fund (ERDF); 'A way to make Europe'. F.D. was supported by the Spanish Ministry of Economy and Competitiveness through the Miguel Servet program (CPII018/00002). M.J.E. was supported by Instituto de Salud Carlos III (PI19/00577 [M.J.E.]) and FI20/00086. P.dC. was supported by a predoctoral grant for training in research into health (PFIS PI19/00577) from the Instituto de Salud Carlos III. All authors declare having no conflict of interest with regard to this trial.
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Affiliation(s)
- X Vendrell
- Reproductive Genetics Department, Sistemas Genómicos-Synlab, Valencia, Spain
| | - P de Castro
- Research Department, IVIRMA Global Research Alliance, IVI Foundation-Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - L Escrich
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - N Grau
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - R Gonzalez-Martin
- Research Department, IVIRMA Global Research Alliance, IVI Foundation-Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - A Quiñonero
- Research Department, IVIRMA Global Research Alliance, IVI Foundation-Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
| | - M J Escribá
- Research Department, IVIRMA Global Research Alliance, IVI Foundation-Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
- Embryology Department, IVIRMA Valencia, Valencia, Spain
| | - F Domínguez
- Research Department, IVIRMA Global Research Alliance, IVI Foundation-Reproductive Biology and Bioengineering in Human Reproduction, IIS La Fe Health Research, Valencia, Spain
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Ma X, Wang J, Su Z, Ma H. Developmentally dependent reprogramming of the Arabidopsis floral transcriptome under sufficient and limited water availability. BMC Plant Biol 2024; 24:273. [PMID: 38605371 PMCID: PMC11007919 DOI: 10.1186/s12870-024-04916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Environmental stresses negatively impact reproductive development and yield. Drought stress, in particular, has been examined during Arabidopsis reproductive development at morphological and transcriptomic levels. However, drought-responsive transcriptomic changes at different points in reproductive development remain unclear. Additionally, an investigation of the entire transcriptome at various stages during flower development is of great interest. RESULTS Here, we treat Arabidopsis plants with well-watered and moderately and severely limiting water amounts when the first flowers reach maturity and generate RNA-seq datasets for early, middle, and late phases during flower development at 5, 6, and 7 days following treatment. Under different drought conditions, flowers in different developmental phases display differential sets of drought-responsive genes (DTGs), including those that are enriched in different GO functional categories, such as transcriptional regulation and response to stresses (early phase), lipid storage (middle phase), and pollen and seed development and metabolic processes (late phase). Some gene families have different members induced at different floral phases, suggesting that similar biochemical functions are carried out by distinct members. Developmentally-regulated genes (DVGs) with differential expression among the three floral phases belong to GO terms that are similar between water conditions, such as development and reproduction, metabolism and transport, and signaling and stress response. However, for different water conditions, such similar GO terms correspond to either distinct gene families or different members of a gene family, suggesting that drought affects the expression of distinct families or family members during reproductive development. A further comparison among transcriptomes of tissues collected on different days after treatment identifies differential gene expression, suggesting age-related genes (ARGs) might reflect the changes in the overall plant physiology in addition to drought response and development. CONCLUSION Together, our study provides new insights into global transcriptome reprogramming and candidate genes for drought response, flower development, aging and coordination among these complex biological processes.
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Affiliation(s)
- Xinwei Ma
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jun Wang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Zhao Su
- Laboratory of Plant Stress and Development, College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hong Ma
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
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Ponath F, Zhu Y, Vogel J. Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σ E-dependent small RNA with unusual mRNA activation activity. mBio 2024; 15:e0353623. [PMID: 38436569 PMCID: PMC11005410 DOI: 10.1128/mbio.03536-23] [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: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
The oral commensal Fusobacterium nucleatum can spread to extra-oral sites, where it is associated with diverse pathologies, including pre-term birth and cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of the RNA regulatory networks that allow this bacterium to adapt to its various niches. As a first step in that direction, we recently showed that F. nucleatum harbors a global stress response governed by the extracytoplasmic function sigma factor, σE, which displays a striking functional conservation with Proteobacteria and includes a noncoding arm in the form of a regulatory small RNA (sRNA), FoxI. To search for putative additional σE-dependent sRNAs, we comprehensively mapped the 5' and 3' ends of transcripts in the model strain ATCC 23726. This enabled the discovery of FoxJ, a ~156-nucleotide sRNA previously misannotated as the 5' untranslated region (UTR) of ylmH. FoxJ is tightly controlled by σE and activated by the same stress conditions as is FoxI. Both sRNAs act as mRNA repressors of the abundant porin FomA, but FoxJ also regulates genes that are distinct from the target suite of FoxI. Moreover, FoxJ differs from other σE-dependent sRNAs in that it also positively regulates genes at the post-transcriptional level. We provide preliminary evidence for a new mode of sRNA-mediated mRNA activation, which involves the targeting of intra-operonic terminators. Overall, our study provides an important resource through the comprehensive annotation of 5' and 3' UTRs in F. nucleatum and expands our understanding of the σE response in this evolutionarily distant bacterium.IMPORTANCEThe oral microbe Fusobacterium nucleatum can colonize secondary sites, including cancer tissue, and likely deploys complex regulatory systems to adapt to these new environments. These systems are largely unknown, partly due to the phylogenetic distance of F. nucleatum to other model organisms. Previously, we identified a global stress response mediated by σE that displays functional conservation with the envelope stress response in Proteobacteria, comprising a coding and noncoding regulatory arm. Through global identification of transcriptional start and stop sites, we uncovered the small RNA (sRNA) FoxJ as a novel component of the noncoding arm of the σE response in F. nucleatum. Together with its companion sRNA FoxI, FoxJ post-transcriptionally modulates the synthesis of envelope proteins, revealing a conserved function for σE-dependent sRNAs between Fusobacteriota and Proteobacteria. Moreover, FoxJ activates the gene expression for several targets, which is a mode of regulation previously unseen in the noncoding arm of the σE response.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Yan Zhu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
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Su J, Zhao L, Yang Y, Yang Y, Zhang X, Guan Z, Fang W, Chen F, Zhang F. Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum. BMC Plant Biol 2024; 24:259. [PMID: 38594635 PMCID: PMC11005212 DOI: 10.1186/s12870-024-04954-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq. RESULTS A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted. CONCLUSION The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Limin Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Yingnan Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Yang Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Xuefeng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, College of Horticulture, National Forestry and Grassland Administration, Nanjing Agricultural University, Weigang No.1, Nanjing, Jiangsu Province, 210095, P.R. China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China.
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Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. Plant Commun 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [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: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
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Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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Gallego D, Serrano M, Cordoba-Caballero J, Gámez A, Seoane P, Perkins JR, Ranea JAG, Pérez B. Transcriptomic analysis identifies dysregulated pathways and therapeutic targets in PMM2-CDG. Biochim Biophys Acta Mol Basis Dis 2024:167163. [PMID: 38599261 DOI: 10.1016/j.bbadis.2024.167163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/15/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
PMM2-CDG (MIM # 212065), the most common congenital disorder of glycosylation, is caused by the deficiency of phosphomannomutase 2 (PMM2). It is a multisystemic disease of variable severity that particularly affects the nervous system; however, its molecular pathophysiology remains poorly understood. Currently, there is no effective treatment. We performed an RNA-seq based transcriptomic study using patient-derived fibroblasts to gain insight into the mechanisms underlying the clinical symptomatology and to identify druggable targets. Systems biology methods were used to identify cellular pathways potentially affected by PMM2 deficiency, including Senescence, Bone regulation, Cell adhesion and Extracellular Matrix (ECM) and Response to cytokines. Functional validation assays using patients' fibroblasts revealed defects related to cell proliferation, cell cycle, the composition of the ECM and cell migration, and showed a potential role of the inflammatory response in the pathophysiology of the disease. Furthermore, treatment with a previously described pharmacological chaperone reverted the differential expression of some of the dysregulated genes. The results presented from transcriptomic data might serve as a platform for identifying therapeutic targets for PMM2-CDG, as well as for monitoring the effectiveness of therapeutic strategies, including pharmacological candidates and mannose-1-P, drug repurposing.
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Affiliation(s)
- Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain
| | - Mercedes Serrano
- Pediatric Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Spain
| | - Jose Cordoba-Caballero
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandra Gámez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - James R Perkins
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain.
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain.
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Li X, Chen T, Fu Y, Yang B, Lin X, Hou J, Yang X. Mechanism and functional verification of genes by virulence factors of P. gingivalis in ferroptosis. Arch Oral Biol 2024; 163:105965. [PMID: 38593562 DOI: 10.1016/j.archoralbio.2024.105965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/03/2024] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
OBJECTIVE Porphyromonas gingivalis (P. gingivalis) is a key etiological agent in periodontitis and functions as a facultative intracellular microorganism and involves many virulence factors. These virulence factors participate in multiple intracellular processes, like ferroptosis, the mechanistic underpinnings remain to be elucidated. Aim of this study was to investigate the effects of virulence factors on the host cells. DESIGN Human umbilical vein endothelial cells (HUVECs) were treated with 4% paraformaldehyde-fixed P. gingivalis, and subsequent alterations in gene expression were profiled via RNA-seq. Further, the molecules associated with ferroptosis were quantitatively analyzed using qRT-PCR and Western blot. RESULTS A total of 1125 differentially expressed genes (DEGs) were identified, encompassing 225 upregulated and 900 downregulated. Ferroptosis was conspicuously represented in the kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, with notable upregulation of Heme oxygenase 1 (HMOX1), Ferritin light chain (FTL), and Solute carrier family 3 member 2 (SLC3A2) and downregulation of Scavenger receptor class A member 5 (SCARA5) and glutaminase (GLS). Random selection of DEGs for validation through qRT-PCR corroborated the RNA-Seq data (R2 = 0.93). Kelch like ECH associated protein 1 (Keap1) protein expression decreased after 4 and 8 h, while NFE2 like bZIP transcription factor 2 (Nrf2) and HMOX1 were elevated, with significant nuclear translocation of Nrf2. CONCLUSIONS The virulence factors of P. gingivalis may potentially instigating ferroptosis through activation of the Keap1-Nrf2-HMOX1 signaling cascade, in conjunction with modulating the expression of other ferroptosis-associated elements. Further research is necessary to achieve a thorough comprehension of these complex molecular interactions.
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Affiliation(s)
- Xinzhu Li
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yinyu Fu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Bo Yang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyu Lin
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jin Hou
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Xiaojun Yang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ, Gonzalez-Padilla D, Maden SK, Kleinman JE, Hyde TM, Hicks SC, Maynard KR, Collado-Torres L. Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv 2024:2024.02.09.579665. [PMID: 38405805 PMCID: PMC10888823 DOI: 10.1101/2024.02.09.579665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Computational methods for deconvolution have been developed and benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or immunohistochemistry reference data. A major limitation in developing improved deconvolution algorithms has been the lack of integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue sample. Deconvolution algorithm performance has not yet been evaluated across different RNA extraction methods (cytosolic, nuclear, or whole cell RNA), different library preparation types (mRNA enrichment vs. ribosomal RNA depletion), or with matched single cell reference datasets. Results A rich multi-assay dataset was generated in postmortem human dorsolateral prefrontal cortex (DLPFC) from 22 tissue blocks. Assays included spatially-resolved transcriptomics, snRNA-seq, bulk RNA-seq (across six library/extraction RNA-seq combinations), and RNAScope/Immunofluorescence (RNAScope/IF) for six broad cell types. The Mean Ratio method, implemented in the DeconvoBuddies R package, was developed for selecting cell type marker genes. Six computational deconvolution algorithms were evaluated in DLPFC and predicted cell type proportions were compared to orthogonal RNAScope/IF measurements. Conclusions Bisque and hspe were the most accurate methods, were robust to differences in RNA library types and extractions. This multi-assay dataset showed that cell size differences, marker genes differentially quantified across RNA libraries, and cell composition variability in reference snRNA-seq impact the accuracy of current deconvolution methods.
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Affiliation(s)
- Louise A. Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Kelsey D. Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Sophia Cinquemani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J. Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | | | - Sean K. Maden
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
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Saizonou H, Impoinvil LM, Derilus D, Omoke D, Okeyo S, Dada N, Corredor C, Mulder N, Lenhart A, Ochomo E, Djogbénou LS. Transcriptomic analysis of Anopheles gambiae from Benin reveals overexpression of salivary and cuticular proteins associated with cross-resistance to pyrethroids and organophosphates. BMC Genomics 2024; 25:348. [PMID: 38582836 PMCID: PMC10998338 DOI: 10.1186/s12864-024-10261-x] [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: 10/03/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Insecticide resistance (IR) is one of the major threats to malaria vector control programs in endemic countries. However, the mechanisms underlying IR are poorly understood. Thus, investigating gene expression patterns related to IR can offer important insights into the molecular basis of IR in mosquitoes. In this study, RNA-Seq was used to characterize gene expression in Anopheles gambiae surviving exposure to pyrethroids (deltamethrin, alphacypermethrin) and an organophosphate (pirimiphos-methyl). RESULTS Larvae of An. gambiae s.s. collected from Bassila and Djougou in Benin were reared to adulthood and phenotyped for IR using a modified CDC intensity bottle bioassay. The results showed that mosquitoes from Djougou were more resistant to pyrethroids (5X deltamethrin: 51.7% mortality; 2X alphacypermethrin: 47.4%) than Bassila (1X deltamethrin: 70.7%; 1X alphacypermethrin: 77.7%), while the latter were more resistant to pirimiphos-methyl (1.5X: 48.3% in Bassila and 1X: 21.5% in Djougou). RNA-seq was then conducted on resistant mosquitoes, non-exposed mosquitoes from the same locations and the laboratory-susceptible An. gambiae s.s. Kisumu strain. The results showed overexpression of detoxification genes, including cytochrome P450s (CYP12F2, CYP12F3, CYP4H15, CYP4H17, CYP6Z3, CYP9K1, CYP4G16, and CYP4D17), carboxylesterase genes (COEJHE5E, COE22933) and glutathione S-transferases (GSTE2 and GSTMS3) in all three resistant mosquito groups analyzed. Genes encoding cuticular proteins (CPR130, CPR10, CPR15, CPR16, CPR127, CPAP3-C, CPAP3-B, and CPR76) were also overexpressed in all the resistant groups, indicating their potential role in cross resistance in An. gambiae. Salivary gland protein genes related to 'salivary cysteine-rich peptide' and 'salivary secreted mucin 3' were also over-expressed and shared across all resistant groups. CONCLUSION Our results suggest that in addition to metabolic enzymes, cuticular and salivary gland proteins could play an important role in cross-resistance to multiple classes of insecticides in Benin. These genes warrant further investigation to validate their functional role in An. gambiae resistance to insecticides.
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Affiliation(s)
- Helga Saizonou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi (UAC), Abomey-Calavi, Benin.
| | - Lucy Mackenzie Impoinvil
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dieunel Derilus
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Diana Omoke
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Stephen Okeyo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Nsa Dada
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi (UAC), Abomey-Calavi, Benin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Claudia Corredor
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicola Mulder
- Human, Heredity, and Health in Africa H3ABionet network, Cape Town, South Africa
| | - Audrey Lenhart
- Entomology Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Ochomo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi (UAC), Abomey-Calavi, Benin.
- Regional Institute of Public Health (IRSP), Ouidah, Benin.
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
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Gokyer D, Akinboro S, Zhou LT, Kleinhans A, Laronda MM, Duncan FE, Riley JK, Goldman KN, Babayev E. The oocyte microenvironment is altered in adolescents compared to oocyte donors. bioRxiv 2024:2024.04.04.588118. [PMID: 38617323 PMCID: PMC11014529 DOI: 10.1101/2024.04.04.588118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Study question Are the molecular signatures of cumulus cells (CCs) and follicular fluid (FF) of adolescents undergoing fertility preservation differ from that of reproductively adult oocyte donors? Summary answer The microenvironment immediately surrounding the oocyte, including the CCs and FF, is altered in adolescents undergoing fertility preservation compared to oocyte donors. What is known already Adolescents experience a period of subfecundity following menarche. Recent evidence suggests that this may be at least partially due to increased oocyte aneuploidy. Reproductive juvenescence in mammals is associated with suboptimal oocyte quality. Study design size duration This was a prospective cohort study. Adolescents (10-19 years old, N=23) and oocyte donors (22-30 years old, N=31) undergoing ovarian stimulation and oocyte retrieval at the Northwestern Fertility and Reproductive Medicine Center between November 1, 2020 and May 1, 2023 were enrolled in this study. Participants/materials setting methods Patient demographics, ovarian stimulation, and oocyte retrieval outcomes were collected for all participants. The transcriptome of CCs associated with mature oocytes was compared between adolescents (10-19 years old, n=19), and oocyte donors (22-30 years old, n=19) using bulk RNA-sequencing. FF cytokine profiles (10-19 years old, n=18 vs. 25-30 years old, n=16) were compared using cytokine arrays. Main results and the role of chance RNA-seq analysis revealed 581 differentially expressed genes (DEGs) in cumulus cells of adolescents relative to oocyte donors, with 361 genes downregulated and 220 upregulated. Genes enriched in pathways involved in cell cycle and cell division (e.g., GO:1903047, p= 3.5 × 10-43; GO:0051983, p= 4.1 × 10-30; GO:0000281, p= 7.7 × 10-15; GO:0044839, p= 5.3 × 10-13) were significantly downregulated, while genes enriched in several pathways involved in cellular and vesicle organization (e.g., GO:0010256, p= 1.2 × 10-8; GO:0051129, p= 6.8 × 10-7; GO:0016050, p= 7.4 × 10-7; GO:0051640, p= 8.1 × 10-7) were upregulated in CCs of adolescents compared to oocyte donors. The levels of 9 cytokines were significantly increased in FF of adolescents compared to oocyte donors: IL-1 alpha (2-fold), IL-1 beta (1.7-fold), I-309 (2-fold), IL-15 (1.6-fold), TARC (1.9-fold), TPO (2.1-fold), IGFBP-4 (2-fold), IL-12-p40 (1.7-fold) and ENA-78 (1.4-fold). Interestingly, 7 of these cytokines have known pro-inflammatory roles. Importantly, neither the CC transcriptomes or FF cytokine profiles were different in adolescents with or without cancer. Large scale data Original high-throughput sequencing data will be deposited in Gene Expression Omnibus (GEO) before publication, and the GEO accession number will be provided here. Limitations reasons for caution This study aims to gain insights into the associated gamete quality by studying the immediate oocyte microenvironment. The direct study of oocytes is more challenging due to sample scarcity, as they are cryopreserved for future use, but will provide a more accurate assessment of oocyte reproductive potential. Wider implications of the findings Understanding the underpinnings of altered immediate oocyte microenvironment of adolescent patients may provide insights into the reproductive potential of the associated gametes in the younger end of the age spectrum. This has implications for the fertility preservation cycles for very young patients. Study funding/competing interests This project was supported by Friends of Prentice organization SP0061324 (M.M.L and E.B.), Gesualdo Family Foundation (Research Scholar: M.M.L.), and NIH/NICHD K12 HD050121 (E.B.). The authors have declared that no conflict of interest exists.
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Affiliation(s)
- Dilan Gokyer
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
| | - Sophia Akinboro
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
- Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL, 60208
| | - Luhan T. Zhou
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
| | - Anna Kleinhans
- Department of Obstetrics and Gynecology, Northwestern Medicine Center for Fertility and Reproductive Medicine, Chicago, IL, 60611
| | - Monica M. Laronda
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, 60611
| | - Francesca E. Duncan
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
| | - Joan K. Riley
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
- Department of Obstetrics and Gynecology, Northwestern Medicine Center for Fertility and Reproductive Medicine, Chicago, IL, 60611
| | - Kara N. Goldman
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
- Department of Obstetrics and Gynecology, Northwestern Medicine Center for Fertility and Reproductive Medicine, Chicago, IL, 60611
| | - Elnur Babayev
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
- Department of Obstetrics and Gynecology, Northwestern Medicine Center for Fertility and Reproductive Medicine, Chicago, IL, 60611
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Bai H, Varsanik MA, Thaxton C, Ohashi Y, Gonzalez L, Zhang W, Aoyagi Y, Kano M, Yatsula B, Li Z, Pocivavsek L, Dardik A. Disturbed flow in the juxta-anastomotic area of an arteriovenous fistula correlates with endothelial loss, acute thrombus formation and neointimal hyperplasia. Am J Physiol Heart Circ Physiol 2024. [PMID: 38578237 DOI: 10.1152/ajpheart.00054.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Clinical failure of arteriovenous fistulae (AVF) is frequently due to juxta-anastomotic neointimal hyperplasia (JANIH). Although the mouse AVF model recapitulates human AVF maturation, previous studies focused on the outflow vein distal to the anastomosis. We hypothesized that the juxta-anastomotic area (JAA) has increased NIH compared to the outflow vein. METHOD AVF were created in C57BL/6 mice without or with chronic kidney disease (CKD). Temporal and spatial changes of the JAA were examined using histology and immunofluorescence. Computational techniques were used to model the AVF. RNA-seq and bioinformatic analyses were performed to compare the JAA with the outflow vein. The jugular vein to carotid artery AVF model was created in Wistar rats. RESULT The neointima in the JAA shows increased volume compared to the outflow vein. Computational modeling shows increased volume of disturbed flow at the JAA compared to the outflow vein. Endothelial cells are immediately lost from the wall contralateral to the fistula exit, followed by thrombus formation and JANIH. Gene Ontology (GO) enrichment analysis of the 1862 differentially expressed genes (DEG) between the JANIH and the outflow vein identified 525 overexpressed genes. The rat jugular vein to carotid artery AVF showed changes similar to the mouse AVF. CONCLUSION Disturbed flow through the JAA correlates with rapid endothelial cell loss, thrombus formation, and JANIH; late endothelialization of the JAA channel correlates with late AVF patency. Early thrombus formation in the JAA may influence later development of JANIH.
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Affiliation(s)
| | | | - Carly Thaxton
- Department of Surgery, VA Connecticut Healthcare Systems, New Haven, Connecticut, United States
| | - Yuichi Ohashi
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, United States
| | - Luis Gonzalez
- Yale School of Medicine; Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, United States
| | - Weichang Zhang
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, United States
| | - Yukihiko Aoyagi
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, United States
| | | | - Bogdan Yatsula
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, United States
| | - Zhuo Li
- Yale University, United States
| | | | - Alan Dardik
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, Connecticut, United States
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40
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Li Y, Li J, Dong Y, Wang C, Cai Z. Bovine lactoferrin inhibits inflammatory response and apoptosis in lipopolysaccharide-induced acute lung injury by targeting the PPAR-γ pathway. Mol Biol Rep 2024; 51:492. [PMID: 38578368 DOI: 10.1007/s11033-024-09436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Lactoferrin (LF) is an iron-binding multifunctional cationic glycoprotein. Previous studies have demonstrated that LF may be a potential drug for treating acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). In this study, we explored the anti-inflammatory effect and mechanism of bovine lactoferrin (bLF) in ALI using the RNA sequencing (RNA-seq) technology and transcriptome analysis. METHODS AND RESULTS Based on the differentially expressed genes (DEGs) obtained from RNA-seq of the Lung from mouse model, the bioinformatics workflow was implemented using the BGISEQ-500 platform. The protein-protein interaction (PPI) network was obtained using STRING, and the hub gene was screened using Cytoscape. To verify the results of transcriptome analysis, the effects of bLF on Lipopolysaccharide (LPS)-induced BEAS-2B cells and its anti-reactive oxygen species (ROS), anti-inflammatory, and antiapoptotic effects were studied via Cell Counting Kit-8 (CCK-8) test, active oxygen detection test, ELISA, and western blot assay. Transcriptome analysis revealed that two hub gene modules of DEGs were screened via PPI analysis using the STRING and MCODE plug-ins of Cytoscape. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these core modules are enriched in the PPAR (peroxisome proliferator-activated receptor) and AMPK (AMP-activated protein kinase) signaling pathways. Through cell experiments, our study shows that bLF can inhibit ROS, inflammatory reaction, and LPS-induced BEAS-2B cell apoptosis, which are significantly antagonized by the PPAR-γ inhibitor GW9662. CONCLUSION This study has suggested that the PPAR-γ pathway is the critical target of bLF in anti-inflammatory reactions and apoptosis of ALI, which provides a direction for further research.
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Affiliation(s)
- Yantao Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Hebei University of Chinese Medicine, Shijiazhuang, 050000, China
| | - Junhu Li
- Emergency Department, The First Affiliated Hospital of Hebei University of Chinese Medicine, Shijiazhuang, 050000, China
| | - Yan Dong
- Emergency Department, The First Affiliated Hospital of Hebei University of Chinese Medicine, Shijiazhuang, 050000, China
| | - Can Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Hebei University of Chinese Medicine, Shijiazhuang, 050000, China
| | - Zhigang Cai
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, Hebei Province, China.
- Hebei Key Laboratory of Respiratory Critical Care Medicine, No. 215 Heping West Road, Shijiazhuang, 050000, Hebei Province, China.
- Hebei Institute of Respiratory Diseases, No. 215 Heping West Road, Shijiazhuang, 050000, Hebei Province, China.
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Zou Y, Suo X, Zhang Y. Transcriptomic responses of rabbits to infections by precocious line and wild-type Eimeria media: revealing molecular signatures and pathway differences in liver and duodenum during the peak and terminal phases of oocyst production. Parasitol Res 2024; 123:175. [PMID: 38570360 DOI: 10.1007/s00436-024-08186-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Eimeria media is a principal pathogen responsible for rabbit coccidiosis, targeting the rabbit's intestinal epithelial cells. This parasitism damages the intestinal mucosal barrier, initiating a systemic immune and inflammatory response that jeopardizes the sustainable growth of rabbit farming. To understand the implications of infection on the host's immune and metabolic responses, we employed RNA-Seq to analyze RNA from the liver and duodenum tissues of post-infected rabbits infected with both the precocious line and wild-type strain of E.media. Comprehensive transcriptomic analysis revealed that the two parasites exhibit divergent transcriptomic imprints on host tissues. While the precocious line predominantly modulates immune-centric pathways with significant differential gene enrichment, wild-type strain favors pathways that affect metabolism. In addition, our study pinpointed a set of genes that undergo significant modifications in response to these effects. These revelations grant a fresh avenue to probe deeper into the symbiotic intricacies of the E.media and its rabbit host.
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Affiliation(s)
- Yijin Zou
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xun Suo
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Yuanyuan Zhang
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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Wu F, Huang F, Jiang N, Su J, Yao S, Liang B, Li W, Yan T, Zhou S, Zhou Q. Identification of ferroptosis related genes and pathways in prostate cancer cells under erastin exposure. BMC Urol 2024; 24:78. [PMID: 38575966 PMCID: PMC10996193 DOI: 10.1186/s12894-024-01472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/31/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Few studies are focusing on the mechanism of erastin acts on prostate cancer (PCa) cells, and essential ferroptosis-related genes (FRGs) that can be PCa therapeutic targets are rarely known. METHODS In this study, in vitro assays were performed and RNA-sequencing was used to measure the expression of differentially expressed genes (DEGs) in erastin-induced PCa cells. A series of bioinformatic analyses were applied to analyze the pathways and DEGs. RESULTS Erastin inhibited the expression of SLC7A11 and cell survivability in LNCaP and PC3 cells. After treatment with erastin, the concentrations of malondialdehyde (MDA) and Fe2+ significantly increased, whereas the glutathione (GSH) and the oxidized glutathione (GSSG) significantly decreased in both cells. A total of 295 overlapping DEGs were identified under erastin exposure and significantly enriched in several pathways, including DNA replication and cell cycle. The percentage of LNCaP and PC3 cells in G1 phase was markedly increased in response to erastin treatment. For four hub FRGs, TMEFF2 was higher in PCa tissue and the expression levels of NRXN3, CLU, and UNC5B were lower in PCa tissue. The expression levels of SLC7A11 and cell survivability were inhibited after the knockdown of TMEFF2 in androgen-dependent cell lines (LNCaP and VCaP) but not in androgen-independent cell lines (PC3 and C4-2). The concentration of Fe2+ only significantly increased in TMEFF2 downregulated LNCaP and VCaP cells. CONCLUSION TMEFF2 might be likely to develop into a potential ferroptosis target in PCa and this study extends our understanding of the molecular mechanism involved in erastin-affected PCa cells.
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Affiliation(s)
- Fan Wu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China
| | - Fei Huang
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China
| | - Nili Jiang
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Jinfeng Su
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China
| | - Siyi Yao
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China
| | - Boying Liang
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China
| | - Wen Li
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Tengyue Yan
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Sufang Zhou
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China.
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China.
| | - Qingniao Zhou
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China.
- Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Guangxi Medical University, Nanning, China.
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Yadav S, Yadava YK, Meena S, Kalwan G, Bharadwaj C, Paul V, Kansal R, Gaikwad K, Jain PK. Novel insights into drought-induced regulation of ribosomal genes through DNA methylation in chickpea. Int J Biol Macromol 2024; 266:131380. [PMID: 38580022 DOI: 10.1016/j.ijbiomac.2024.131380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Modifications within the epigenome of an organism in response to external environmental conditions allow it to withstand the hostile stress factors. Drought in chickpea is a severely limiting abiotic stress factor which is known to cause huge yield loss. To analyse the methylome of chickpea in response to drought stress conditions and how it affects gene expression, we performed whole-genome bisulfite sequencing (WGBS) and RNA-seq of two chickpea genotypes which contrast for drought tolerance. It was observed that the mCHH was most variable under drought stress and the drought tolerant (DT) genotype exhibited substantial genome-wide hypomethylation as compared to the drought sensitive (DS) genotype. Specifically, there was substantial difference in gene expression and methylation for the ribosomal genes for the tolerant and sensitive genotypes. The differential expression of these genes was in complete agreement with earlier reported transcriptomes in chickpea. Many of these genes were hypomethylated (q < 0.01) and downregulated under drought stress (p < 0.01) in the sensitive genotype. The gene RPS6 (ribosomal protein small subunit) was found to be downregulated and hypomethylated in the drought sensitive genotype which could possibly lead to reduced ribosomal biosynthesis. This study provides novel insights into regulation of drought-responsive genes in chickpea.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vijay Paul
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rekha Kansal
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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Li S, Zhao S, Sinson JC, Bajic A, Rosenfeld JA, Neeley MB, Pena M, Worley KC, Burrage LC, Weisz-Hubshman M, Ketkar S, Craigen WJ, Clark GD, Lalani S, Bacino CA, Machol K, Chao HT, Potocki L, Emrick L, Sheppard J, Nguyen MTT, Khoramnia A, Hernandez PP, Nagamani SC, Liu Z, Eng CM, Lee B, Liu P. The clinical utility and diagnostic implementation of human subject cell transdifferentiation followed by RNA sequencing. Am J Hum Genet 2024:S0002-9297(24)00080-6. [PMID: 38593811 DOI: 10.1016/j.ajhg.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
RNA sequencing (RNA-seq) has recently been used in translational research settings to facilitate diagnoses of Mendelian disorders. A significant obstacle for clinical laboratories in adopting RNA-seq is the low or absent expression of a significant number of disease-associated genes/transcripts in clinically accessible samples. As this is especially problematic in neurological diseases, we developed a clinical diagnostic approach that enhanced the detection and evaluation of tissue-specific genes/transcripts through fibroblast-to-neuron cell transdifferentiation. The approach is designed specifically to suit clinical implementation, emphasizing simplicity, cost effectiveness, turnaround time, and reproducibility. For clinical validation, we generated induced neurons (iNeurons) from 71 individuals with primary neurological phenotypes recruited to the Undiagnosed Diseases Network. The overall diagnostic yield was 25.4%. Over a quarter of the diagnostic findings benefited from transdifferentiation and could not be achieved by fibroblast RNA-seq alone. This iNeuron transcriptomic approach can be effectively integrated into diagnostic whole-transcriptome evaluation of individuals with genetic disorders.
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Affiliation(s)
- Shenglan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sen Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jefferson C Sinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Neeley
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Mezthly Pena
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Gary D Clark
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Cain Pediatric Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Lisa Emrick
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Jennifer Sheppard
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - My T T Nguyen
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Anahita Khoramnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sandesh Cs Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA.
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Palliyath GK, Jangam AK, Katneni VK, Kaikkolante N, Panjan Nathamuni S, Jayaraman R, Jagabattula S, Moturi M, Shekhar MS. Meta-analysis to Unravel Core Transcriptomic Responses in Penaeus vannamei Exposed to Biotic and Abiotic Stresses. Biochem Genet 2024:10.1007/s10528-024-10772-y. [PMID: 38570440 DOI: 10.1007/s10528-024-10772-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics. Scope of this study is to identify the core transcriptomic responses in the shrimp species Penaeus vannamei exposed to various abiotic and biotic stress conditions and to decipher their functional importance. To achieve our objective, we gathered and analyzed multiple RNA-seq datasets related to twelve abiotic and nine biotic stress conditions. Through the in silico meta-analysis, we predicted 961 differentially expressed genes (meta-DEGs) for abiotic stress conditions and 517 meta-DEGs for biotic stress conditions, respectively. These meta-DEGs represent genes that are commonly expressed across different stress factors and are indicative of the organism's general response to stress. The annotation of nineteen core up-regulated meta-DEGs revealed their diverse functions in detoxification, cell adhesion, metal ion binding, and oxidative phosphorylation. These genes play a crucial role in stress response and immune defense. For abiotic stress, significant pathways associated with the stress response include tryptophan metabolism, starch and sucrose metabolism, fatty acid degradation, carbohydrate digestion and absorption, phenylalanine metabolism, drug metabolism-other enzymes, arachidonic acid metabolism, and fatty acid elongation. Similarly, for biotic stress, metabolism of xenobiotics by cytochrome P450, pentose and glucuronate interconversions, steroid hormone biosynthesis, and drug metabolism-cytochrome P450 were found to be significant pathway associations. In addition, the study also predicted 17 stress regulatory motifs present in the identified meta-DEGs. These motifs have significance in identifying the stress responses of the organism. The metabolic pathways and regulatory motifs associated with abiotic and biotic stress factors identified through this study could be a valuable resource for developing stress management approaches in shrimp aquaculture.
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Affiliation(s)
| | | | | | | | | | - Roja Jayaraman
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, India
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Yuan C, Duan Y, Li X, Zhang Y, Cao L, Feng T, Ge J, Wang Q, Zheng H. Transcriptional and ultrastructural changes of macrophages after african swine fever virus infection. Vet Microbiol 2024; 293:110074. [PMID: 38603982 DOI: 10.1016/j.vetmic.2024.110074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
African swine fever (ASF) is a highly impactful infectious disease in the swine industry, leading to substantial economic losses globally. The causative agent, African swine fever virus (ASFV), possesses intricate pathogenesis, warranting further exploration. In this study, we investigated the impact of ASFV infection on host gene transcription and organelle changes through macrophage transcriptome sequencing and ultrastructural transmission electron microscopy observation. According to the results of the transcriptome sequencing, ASFV infection led to significant alterations in the gene expression pattern of porcine bone marrow derived macrophages (BMDMs), with 2404 genes showing upregulation and 1579 genes downregulation. Cytokines, and chemokines were significant changes in the expression of BMDMs; there was significant activation of pattern recognition receptors such as Toll-like receptors and Nod-like receptors. According to the observation of the ultrastructure, mitochondrial damage and mitochondrial autophagy were widely present in ASFV-infected cells. The reduced number of macrophage pseudopodia suggested that virus-induced structural changes may compromise pathogen recognition, phagocytosis, and signal communication in macrophages. Additionally, the decreased size and inhibited acidification of secondary lysosomes in macrophages implied suppressed phagocytosis. Overall, ASFV infection resulted in significant changes in the expression of cytokines and chemokines, accompanied by the activation of NLR and TLR signaling pathways. We reported for the first time that ASFV infection led to a reduction in pseudopodia numbers and a decrease in the size and acidification of secondary lysosomes.
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Affiliation(s)
- Cong Yuan
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China; Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Yueyue Duan
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China; Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Xiangtong Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China; Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Yu Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China; Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Liyan Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China; Chengdu National Agricultural Science and Technology Center, Chengdu, China
| | - Tao Feng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Junwei Ge
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
| | - Qi Wang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China; Chengdu National Agricultural Science and Technology Center, Chengdu, China.
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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Sato Y, Minamikawa MF, Pratama BB, Koyama S, Kojima M, Takebayashi Y, Sakakibara H, Igawa T. Autonomous differentiation of transgenic cells requiring no external hormone application: the endogenous gene expression and phytohormone behaviors. Front Plant Sci 2024; 15:1308417. [PMID: 38633452 PMCID: PMC11021773 DOI: 10.3389/fpls.2024.1308417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
The ectopic overexpression of developmental regulator (DR) genes has been reported to improve the transformation in recalcitrant plant species because of the promotion of cellular differentiation during cell culture processes. In other words, the external plant growth regulator (PGR) application during the tissue and cell culture process is still required in cases utilizing DR genes for plant regeneration. Here, the effect of Arabidopsis BABY BOOM (BBM) and WUSCHEL (WUS) on the differentiation of tobacco transgenic cells was examined. We found that the SRDX fusion to WUS, when co-expressed with the BBM-VP16 fusion gene, significantly influenced the induction of autonomous differentiation under PGR-free culture conditions, with similar effects in some other plant species. Furthermore, to understand the endogenous background underlying cell differentiation toward regeneration, phytohormone and RNA-seq analyses were performed using tobacco leaf explants in which transgenic cells were autonomously differentiating. The levels of active auxins, cytokinins, abscisic acid, and inactive gibberellins increased as cell differentiation proceeded toward organogenesis. Gene Ontology terms related to phytohormones and organogenesis were identified as differentially expressed genes, in addition to those related to polysaccharide and nitrate metabolism. The qRT-PCR four selected genes as DEGs supported the RNA-seq data. This differentiation induction system and the reported phytohormone and transcript profiles provide a foundation for the development of PGR-free tissue cultures of various plant species, facilitating future biotechnological breeding.
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Affiliation(s)
- Yuka Sato
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Mai F. Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, Chiba, Japan
| | - Berbudi Bintang Pratama
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Shohei Koyama
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomoko Igawa
- Plant Cell Technology Laboratory, Graduate School of Horticulture, Chiba University, Matsudo, Japan
- Plant Molecular Science Center, Chiba University, Chiba, Japan
- Research Center for Space Agriculture and Horticulture, Chiba University, Matsudo, Japan
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Saunders PA, Ferre-Ortega C, Hill PL, Simakov O, Ezaz T, Burridge CP, Wapstra E. Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes. Genome Biol Evol 2024; 16:evae060. [PMID: 38526014 PMCID: PMC11003529 DOI: 10.1093/gbe/evae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/26/2024] Open
Abstract
To understand the biology of a species, it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many nonmodel species, sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays can be challenging. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has environmentally induced sex reversal. With transcriptomes from three males and three females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related lizard genome and readily design multiple single locus polymerase chain reaction primers to sex C. ocellatus and related species. Our approach also facilitates valuable comparisons of sex determining systems on a broad taxonomic scale.
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Affiliation(s)
- Paul A Saunders
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Carles Ferre-Ortega
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Peta L Hill
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Vienna 1010, Austria
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
| | - Erik Wapstra
- Discipline of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7000, Australia
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Liu L, Jin M, Han X, Dou D. Identifying biomarkers of ginseng medicines with different natures on heart failure. J Ethnopharmacol 2024; 329:118134. [PMID: 38574777 DOI: 10.1016/j.jep.2024.118134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The nature of Chinese medicine is a unique index to measure its efficacy. Generally, treating the hot syndrome with cold nature medicine and vice versa. Ginseng medicines, a renowned Chinese medicine known for its qi tonifying action, encompasses various herbal materials such as ginseng, red ginseng, and black ginseng (GS, RG, and BG, respectively), ginseng leaves (GL), and American ginseng (AG), which exhibited different natures, thought contained similar ginsenosides. This traditional effect of GS and RG "reinvigorate the pulse for relieving qi depletion". It is closely linked to anti-heart failure (HF), HF is a clinical manifestation of deficiency of "heart-qi". However, the elucidation of the mechanism underlying the anti-HF effects of ginseng medicines with different natures remains a significant challenge. AIM OF THE STUDY To elucidate pharmacological mechanisms underlying the effect of ginseng medicines on HF, and to identify biomarkers associated with their various natures. Furthermore, it provides the basis for the different applications of ginseng medicines with various natures. MATERIALS AND METHODS This study established a rat model of HF induced by isoproterenol (ISO) combined with a specific diet. Four representative hot/cold herbs were selected as compared references for the medicine natures. The divergent effects of these herbs on the HF model were investigated by analyzing RNA-seq data to identify genes expressed differentially. Additionally, pathways associated with medicine natures were obtained using KEGG. Furthermore, UPLC-QqQ-MS/MS, as well as ELISA, were used to measure indexes associated with the nervous system, energy metabolisms, and endocrinology systems, such as BNP, CK, IL-1, T3, T4, cAMP, cGMP, AD, adrenal hormones (DOC, CORT, and COR), progestogens (pregnenolone, P, 17-OH-PR, and 17-OH-P), androgens (DHEA, A4, and T), and estrogens hormones (E2). RESULTS All ginseng medicines demonstrated varying levels of efficacy in alleviating HF and GS exhibited a significant protective effect on HF. The ginseng medicines with qi tonifying primarily achieve their effect by enhancing the levels of adrenal hormones (DOC, CORT, and COR), T4, elevation of cAMP/cGMP, and activation of AchE. Warm nature qi tonifying ginseng medicines increased the levels of 17-OH-PR and P while decreasing 17-OH-P and the ratio of E2/T. On the other hand, cold nature qi tonifying ginseng medicines decreased the levels of A4 and T while increasing the ratio of E2/T. CONCLUSION Overall, the effects of warm nature ginseng medicines are stronger on HF compared to cold nature ginseng medicines. Our research firstly reported that the E2/T ratio, progestogens (17-OH-PR, 17-OH-P, and P), and androgens (A4 and T) have been identified as significant biomarkers for discerning the mechanism differences of ginseng medicines with differences natures in treatment of HF.
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Affiliation(s)
- Linlin Liu
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Mozhu Jin
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Xueying Han
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Deqiang Dou
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China.
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Adema K, Schon MA, Nodine MD, Kohlen W. Lost in space: what single-cell RNA sequencing cannot tell you. Trends Plant Sci 2024:S1360-1385(24)00066-9. [PMID: 38570278 DOI: 10.1016/j.tplants.2024.03.010] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the spatiotemporal context of cells. However, positional information is inherently lost during scRNA-seq, limiting its potential to characterize complex biological systems. In this review we highlight how current single-cell analysis pipelines cannot completely recover spatial information, which confounds biological interpretation. Various strategies exist to identify the location of RNA, from classical RNA in situ hybridization to spatial transcriptomics. Herein we discuss the possibility of utilizing this spatial information to supervise single-cell analyses. An integrative approach will maximize the potential of each technology, and lead to insights which go beyond the capability of each individual technology.
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Affiliation(s)
- Kelvin Adema
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael A Schon
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael D Nodine
- Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Cell and Developmental Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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