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Li T, Xing HM, Qian HD, Gao Q, Xu SL, Ma H, Chi ZL. Small extracellular vesicles derived from human induced pluripotent stem cell-differentiated neural progenitor cells mitigate retinal ganglion cell degeneration in a mouse model of optic nerve injury. Neural Regen Res 2025; 20:587-597. [PMID: 38819069 PMCID: PMC11317950 DOI: 10.4103/nrr.nrr-d-23-01414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00034/figure1/v/2024-05-28T214302Z/r/image-tiff Several studies have found that transplantation of neural progenitor cells (NPCs) promotes the survival of injured neurons. However, a poor integration rate and high risk of tumorigenicity after cell transplantation limits their clinical application. Small extracellular vesicles (sEVs) contain bioactive molecules for neuronal protection and regeneration. Previous studies have shown that stem/progenitor cell-derived sEVs can promote neuronal survival and recovery of neurological function in neurodegenerative eye diseases and other eye diseases. In this study, we intravitreally transplanted sEVs derived from human induced pluripotent stem cells (hiPSCs) and hiPSCs-differentiated NPCs (hiPSC-NPC) in a mouse model of optic nerve crush. Our results show that these intravitreally injected sEVs were ingested by retinal cells, especially those localized in the ganglion cell layer. Treatment with hiPSC-NPC-derived sEVs mitigated optic nerve crush-induced retinal ganglion cell degeneration, and regulated the retinal microenvironment by inhibiting excessive activation of microglia. Component analysis further revealed that hiPSC-NPC derived sEVs transported neuroprotective and anti-inflammatory miRNA cargos to target cells, which had protective effects on RGCs after optic nerve injury. These findings suggest that sEVs derived from hiPSC-NPC are a promising cell-free therapeutic strategy for optic neuropathy.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hui-Min Xing
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hai-Dong Qian
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qiao Gao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Sheng-Lan Xu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hua Ma
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zai-Long Chi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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Li X, Liu H, He F, Li M, Zi Y, Long R, Zhao G, Zhu L, Hong L, Wang S, Kang J, Yang Q, Lin C. Multi-omics integrative analysis provided new insights into alkaline stress in alfalfa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109048. [PMID: 39159534 DOI: 10.1016/j.plaphy.2024.109048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 07/29/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024]
Abstract
Saline-alkali stress is one of the main abiotic stresses that limits plant growth. Salt stress has been widely studied, but alkaline salt degradation caused by NaHCO3 has rarely been investigated. In the present study, the alfalfa cultivar 'Zhongmu No. 1' was treated with 50 mM NaHCO3 (0, 4, 8, 12 and 24 h) to study the resulting enzyme activity and changes in mRNA, miRNA and metabolites in the roots. The results showed that the enzyme activity changed significantly after alkali stress treatment. The genomic analysis revealed 14,970 differentially expressed mRNAs (DEMs), 53 differentially expressed miRNAs (DEMis), and 463 differentially accumulated metabolites (DAMs). Combined analysis of DEMs and DEMis revealed that 21 DEMis negatively regulated 42 DEMs. In addition, when combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEMs and DAMs, we found that phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism and plant hormone signal transduction played important roles in the alkali stress response. The results of this study further elucidated the regulatory mechanism underlying the plant response to alkali stress and provided valuable information for the breeding of new saline-alkaline tolerance plant varieties.
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Affiliation(s)
- Xianyang Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Hao Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunfei Zi
- Institute of Forage Crop Science, Ordos Academy of Agricultural and Animal Husbandry Sciences, Ordos, 017000, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guoqing Zhao
- Institute of Forage Crop Science, Ordos Academy of Agricultural and Animal Husbandry Sciences, Ordos, 017000, China
| | - Lihua Zhu
- Institute of Forage Crop Science, Ordos Academy of Agricultural and Animal Husbandry Sciences, Ordos, 017000, China
| | - Ling Hong
- Institute of Forage Crop Science, Ordos Academy of Agricultural and Animal Husbandry Sciences, Ordos, 017000, China
| | - Shiqing Wang
- Institute of Forage Crop Science, Ordos Academy of Agricultural and Animal Husbandry Sciences, Ordos, 017000, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chen Lin
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Piombo E, Vetukuri RR, Konakalla NC, Kalyandurg PB, Sundararajan P, Jensen DF, Karlsson M, Dubey M. RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions. BMC Biol 2024; 22:219. [PMID: 39343898 PMCID: PMC11441109 DOI: 10.1186/s12915-024-02014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Small RNA (sRNAs)- mediated RNA silencing is emerging as a key player in host-microbe interactions. However, its role in fungus-plant interactions relevant to biocontrol of plant diseases is yet to be explored. This study aimed to investigate Dicer (DCL)-mediated endogenous and cross-kingdom gene expression regulation in the biocontrol fungus Clonostachys rosea and wheat roots during interactions. RESULTS C. rosea Δdcl2 strain exhibited significantly higher root colonization than the WT, whereas no significant differences were observed for Δdcl1 strains. Dual RNA-seq revealed the upregulation of CAZymes, membrane transporters, and effector coding genes in C. rosea, whereas wheat roots responded with the upregulation of stress-related genes and the downregulation of growth-related genes. The expression of many of these genes was downregulated in wheat during the interaction with DCL deletion strains, underscoring the influence of fungal DCL genes on wheat defense response. sRNA sequencing identified 18 wheat miRNAs responsive to C. rosea, and three were predicted to target the C. rosea polyketide synthase gene pks29. Two of these miRNAs (mir_17532_x1 and mir_12061_x13) were observed to enter C. rosea from wheat roots with fluorescence analyses and to downregulate the expression of pks29, showing plausible cross-kingdom RNA silencing of the C. rosea gene by wheat miRNAs. CONCLUSIONS We provide insights into the mechanisms underlying the interaction between biocontrol fungi and plant roots. Moreover, the study sheds light on the role of sRNA-mediated gene expression regulation in C. rosea-wheat interactions and provides preliminary evidence of cross-kingdom RNA silencing between plants and biocontrol fungi.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Naga Charan Konakalla
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Pruthvi B Kalyandurg
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Poorva Sundararajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Wang M, Liu Z, Cheng A, Wang M, Wu Y, Yang Q, Tian B, Ou X, Sun D, Zhang S, Zhu D, Jia R, Chen S, Liu M, Zhao XX, Huang J. Host miRNA and mRNA profiles during in DEF and duck after DHAV-1 infection. Sci Rep 2024; 14:22575. [PMID: 39343789 PMCID: PMC11439951 DOI: 10.1038/s41598-024-72992-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
DHAV-1 is a highly infectious pathogen that can cause acute hepatitis in ducklings. MicroRNA (miRNA) plays an essential regulatory role in virus response. We characterized and compared miRNA and mRNA expression profiles in duck embryonic fibroblasts (DEF) and the liver of ducklings infected with DHAV-1. DHAV-1 infected DEF was divided into infection group (D group) and blank group (M group), and DHAV-1 infected duckling group was divided into infection group (H group) and blank group (N group). D vs. M have 130 differentially expressed (DE) miRNA (DEM) and 2204 differentially expressed (DE) mRNA (DEG), H vs. N have 72 DEM and 1976 DEG. By the intersection of D vs. M and H vs. N comparisons, 15 upregulated DEM, 5 downregulated DEM, 340 upregulated DEG and 50 downregulated DEG were found with both in vivo and in vitro DHAV-1 infection. In particular, we identified the same DE miRNA target genes and functional annotations of DE mRNA. We enriched with multiple gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which may have important roles in viral virulence, host immunity, and metabolism. We selected miR-155, which is co-upregulated, and found that miR-155 targets SOCS1 to inhibit DHVA-1 replication.
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Affiliation(s)
- Meng Wang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Zezheng Liu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China.
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China.
| | - Mingshu Wang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Ying Wu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Bin Tian
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Xuming Ou
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Di Sun
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Shun Chen
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Xin Xin Zhao
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
| | - Juan Huang
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, chengdu, China
- International Joint Research Center, Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
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Gu L, Lai Y, Zhang G, Yang Y, Zhang B, Wang J, Zhang Z, Li M. Genome-Wide Identification of the Rehmannia glutinosa miRNA Family and Exploration of Their Expression Characteristics Caused by the Replant Disease Formation-Related Principal Factor. Genes (Basel) 2024; 15:1239. [PMID: 39336830 PMCID: PMC11431045 DOI: 10.3390/genes15091239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 09/15/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Background/Objectives: Rehmannia glutinosa, a highly valuable medicinal plant in China, is encountering severe replant disease. Replant disease represents a complex stress driven by multiple principal factors (RDFs), including allelochemicals, microbes, and their interactions. miRNAs are recognized as key regulators of plant response to stresses; however, their specific roles within RDFs are not entirely clear. Methods: This study builds six RDF treatments, comprising R. glutinosa continuously planted (SP), normally planted (NP), and NP treated with ferulic acid (FA), Fusarium oxysporum (FO), and a combination of FA with FO (FAFO). sRNA-seq technology was used to identify crucial miRNAs in response to diverse RDFs. Results: In total, 30 sRNA datasets were generated from the SP, NP, FA, FO, and FAFO samples. A total of 160 known and 41 novel miRNAs (RgmiRNAs) were identified in the R. glutinosa genome based on the sRNA database. Abundance analysis revealed that RgmiRNAs in SP exhibited a distinct expression profile in comparison with others. Of these, 124, 86, 86, and 90 RgmiRNAs were differentially expressed in SP, FA, FO, and FAFO compared with NP. Target analysis indicated that RgmiRNAs downregulated in both SP and RDFs impede the organism growth of R. glutinosa. RgmiRNAs upregulated in SP can disrupt root formation and nutrient metabolism, in which, two RgmiR398 were uniquely expressed in SP. It was confirmed to target RgCSD genes. The expression patterns of RgmiR398 and RgCSD indicated that replant disease induces the oxidative damage of R. glutinosa through RgmiR398. Conclusions:RgmiRNA profiling under RDFs provides a theoretical basis for the further clarification of RgmiRNA function in replant disease.
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Affiliation(s)
- Li Gu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanlin Lai
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guojun Zhang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanhui Yang
- College of Bioengineering, Henan University of Technology, Zhengzhou 450001, China
| | - Bao Zhang
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Jianming Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongyi Zhang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingjie Li
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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6
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Xia S, Chen Y, Lai J, Zhang Z, Yang C, Han D. Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis. THE PLANT GENOME 2024:e20511. [PMID: 39291540 DOI: 10.1002/tpg2.20511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 09/19/2024]
Abstract
MicroRNAs (miRNAs) play an essential role as non-coding-RNA-type epigenetic regulators in response to high-temperature stress in plants. There are crucial roles for global transcriptional regulation under SUMO (small ubiquitin-related MOdifier) stress response (SSR). However, the molecular mechanisms underlying its downstream regulation remain unclear. In this study, SUMO-specific chromatin immunoprecipitation sequencing analysis detected specific binding in the promoter region of miRNAs under high-temperature stress. A correlation analysis between this binding and miRNA profiling revealed that the location of SUMO on the chromosome was correlated with the expression pattern of miRNAs, particularly miR398a and miR824a. In contrast, knockout mutants of the SSR-dependent SUMO E3 ligase SAP AND MIZ 1 in Arabidopsis exhibited opposing trends in target gene expression for the SUMO-related miRNAs compared to the wild type. Multi-omics correlation analyses identified 34 SUMO-candidate proteins that might be involved in the regulation of miRNA response to high-temperature stress. Therefore, we propose a potential model whereby high-temperature exposure induces nuclear entry of SUMO molecules, modifying specific transcription factors that bind to miRNA gene promoters and potentially regulate miRNA expression.
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Affiliation(s)
- Simin Xia
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Yue Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Zhonghui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, China
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7
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Vattathil SM, Gerasimov ES, Canon SM, Lori A, Tan SSM, Kim PJ, Liu Y, Lai EC, Bennett DA, Wingo TS, Wingo AP. Genetic regulation of microRNAs in the older adult brain and their contribution to neuropsychiatric conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.610174. [PMID: 39314369 PMCID: PMC11419020 DOI: 10.1101/2024.09.10.610174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
MicroRNAs are essential post-transcriptional regulators of gene expression and involved in many biological processes; however, our understanding of their genetic regulation and role in brain illnesses is limited. Here, we mapped brain microRNA expression quantitative trait loci (miR-QTLs) using genome-wide small RNA sequencing profiles from dorsolateral prefrontal cortex (dlPFC) samples of 604 older adult donors of European ancestry. miR-QTLs were identified for 224 miRNAs (48% of 470 tested miRNAs) at false discovery rate < 1%. We found that miR-QTLs were enriched in brain promoters and enhancers, and that intragenic miRNAs often did not share QTLs with their host gene. Additionally, we integrated the brain miR-QTLs with results from 16 GWAS of psychiatric and neurodegenerative diseases using multiple independent integration approaches and identified four miRNAs that contribute to the pathogenesis of bipolar disorder, major depression, post-traumatic stress disorder, schizophrenia, and Parkinson's disease. This study provides novel insights into the contribution of miRNAs to the complex biological networks that link genetic variation to disease.
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Affiliation(s)
- Selina M Vattathil
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | | | - Se Min Canon
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriana Lori
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Sze Min Tan
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul J Kim
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yue Liu
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Thomas S Wingo
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
- Alzheimer's Disease Research Center, University of California, Davis, Sacramento, CA, USA
| | - Aliza P Wingo
- Department of Psychiatry, University of California, Davis, Sacramento, CA, USA
- Veterans Affairs Northern California Health Care System, Sacramento, CA, USA
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8
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Ou J, Wang X, Luan X, Yu S, Chen H, Dong H, Zhang B, Xu Z, Liu Y, Zhao W. Comprehensive analysis of the mRNA and miRNA transcriptome implicated in the immune response of Procambarus clarkii to Spiroplasma eriocheiris. Microb Pathog 2024; 196:106928. [PMID: 39270754 DOI: 10.1016/j.micpath.2024.106928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 07/09/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024]
Abstract
In recent years, the red swamp crayfish (Procambarus clarkii, P. clarkii) farming industry has suffered huge economic losses due to the pathogenic bacterium Spiroplasma eriocheiris (S. eriocheiris). To elucidate the immune response mechanism and identify hub immune genes as well as their associated microRNAs that regulate the host response of P. clarkii against S. eriocheiris infection, we conducted a comprehensive analysis on P. clarkii hemocyte mRNA and microRNA (miRNA) transcriptomes at different infection stages using third- and second-generation sequencing technologies. In full-length transcriptome functional annotation, 8155 unigenes were annotated, and 1168 potential new transcripts were predicted. In the mRNA transcriptome, a total of 3168 differentially expressed genes were identified at different infection stages, including 1492 upregulated and 1676 downregulated genes (duplicate genes excluded). Transcriptome analysis revealed 880 differentially expressed genes involved in multiple pathways and processes such as endocytosis, autophagy, lysosome, mTOR signaling, phagosome, and the Fanconi anemia pathway. Mfuzz analysis was employed to integrate and cluster the differential expression trends of genes across the three infection stages. In the miRNA transcriptome, 234 miRNAs and 966 predicted target genes were identified, with 86 differentially expressed miRNAs identified across the three time periods. A significant difference (P < 0.05) was observed for miRNAs including pcl-miR-146-3p, pcl-miR-74-3p, pcl-miR-225-5p, and pcl-miR-68-5p. These miRNAs are involved in multiple immune and autophagy-related pathways and have regulatory effects on immune genes including Vps26, lqf, and ERK-A. Based on the differentially expressed immune-related genes, we constructed a protein-protein interaction (PPI) network, which revealed the interactions among hub genes including Rac1, Akt1, Rho1, and Egfr. We also constructed a miRNA-gene interaction network in immune and autophagy-related processes, highlighting the potential regulatory effects of miRNAs including pcl-miR-183-5p, pcl-miR-146-3p, pcl-miR-176-5p, and pcl-miR-225-5p on proteins including LST8, SNAP29, Rab-7A, and ERK-A. To conclude, this study has identified hub immune genes and corresponding regulatory miRNAs in P. clarkii hemocytes in response to S. eriocheiris infection and explored the roles of these genes in selected pathways and processes. These findings are expected to provide further insights into the molecular mechanisms that confer resistance to S. eriocheiris infection in P. clarkii.
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Affiliation(s)
- Jiangtao Ou
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China.
| | - Xiang Wang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Xiaoqi Luan
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China; Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Shuai Yu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Hao Chen
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Huizi Dong
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Benhou Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Zheqi Xu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Yang Liu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Weihong Zhao
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
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9
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Küçük C, Esmeray Sönmez E, Hatipoğlu T, Yuan H, Hu X, Ceylan A, Siviş ZÖ, Demirağ B, Ataseven E, İnce D, Altun Z, Aktaş S, Özsan N, Erdağ TK, Ayhan YS, Demir Gündoğan B, Çetingül N, Özer E, Kutluk T, Olgun N. Potential diagnostic and prognostic biomarkers of pediatric Burkitt lymphoma identified through miRNA expression profiling. Pediatr Res 2024:10.1038/s41390-024-03478-9. [PMID: 39261659 DOI: 10.1038/s41390-024-03478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/16/2024] [Accepted: 08/01/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Pediatric Burkitt lymphoma (pBL) is the most common non-Hodgkin lymphoma in children. These patients require prompt diagnosis and initiation of therapy due to rapid tumor growth. The roles of tumor tissue and circulating microRNAs (miRNAs) in the diagnosis or prognostication have not been fully elucidated in pBLs. METHODS Differentially expressed (DE) miRNAs were identified with microRNA sequencing (miRNA-Seq) in tumor tissues and plasma of diagnostic pBLs. The diagnostic potential of total miRNA concentrations and overexpressed miRNAs were evaluated through receiver operating characteristic (ROC) analyses. Log-rank test was employed to evaluate survival differences associated with DE miRNAs. Selected miRNA expressions were cross-validated with quantitative reverse transcription PCR (qRT-PCR). RESULTS Total circulating cell-free miRNAs were higher in pBL cases compared to controls. Cancer-associated pathways were enriched among miRNAs differentially expressed in pBL tumor tissues. Several upregulated miRNAs in pBL tumors demonstrated high diagnostic potential. Similarly, ROC analysis of overexpressed plasma miRNAs revealed circulating cell-free or exosomal miRNAs that can distinguish pBLs from control cases. Indeed, integrative analysis of overexpressed circulating exosomal miRNAs showed an enhanced diagnostic potential for certain triple combinations. Kaplan-Meier analyses of DE miRNAs in tumor tissues identified miRNAs predicting overall survival. CONCLUSIONS Differentially expressed miRNAs in tumor tissue and plasma of pBL have the potential to improve diagnosis and prognosis. IMPACT Differentially expressed miRNAs in treatment-naive pediatric Burkitt lymphoma cases have diagnostic or prognostic biomarker potential. This is the first study that applied miRNA-Seq on treatment-naive pediatric Burkitt lymphoma cases for identification of differentially expressed miRNAs both in tumor tissue and plasma samples with diagnostic potential. Through systematic analysis of differentially expressed miRNAs, tumor tissue miRNAs associated with the overall survival of pBLs have been discovered. The clinically significant, differentially expressed miRNAs identified in pediatric Burkitt lymphoma cases can potentially improve the current tissue-based or non-invasive clinical practice in terms of diagnosis or prognostication.
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Affiliation(s)
- Can Küçük
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, İzmir, Türkiye.
- İzmir Biomedicine and Genome Center, İzmir, Türkiye.
| | - Esra Esmeray Sönmez
- İzmir Biomedicine and Genome Center, İzmir, Türkiye
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Tevfik Hatipoğlu
- İzmir Biomedicine and Genome Center, İzmir, Türkiye
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Hongling Yuan
- Department of Basic Oncology, Oncology Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Xiaozhou Hu
- Department of Medical Biochemistry, Faculty of Medicine, Dokuz Eylül University, İzmir, Türkiye
| | - Arda Ceylan
- İzmir Biomedicine and Genome Center, İzmir, Türkiye
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Zuhal Önder Siviş
- İzmir Tepecik Education and Research Hospital, Health Sciences University, İzmir, Türkiye
| | - Bengü Demirağ
- Dr. Behçet Uz Pediatric Diseases and Surgery Training and Research Hospital, Health Sciences University, İzmir, Türkiye
| | - Eda Ataseven
- Department of Child Health and Diseases, Faculty of Medicine, Ege University, İzmir, Türkiye
| | - Dilek İnce
- Department of Clinical Oncology, Oncology Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Zekiye Altun
- Department of Basic Oncology, Oncology Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Safiye Aktaş
- Department of Basic Oncology, Oncology Institute, Dokuz Eylül University, İzmir, Türkiye
| | - Nazan Özsan
- Department of Medical Pathology, Ege University, İzmir, Türkiye
| | - Taner Kemal Erdağ
- Department of Otorhinolaryngology, Dokuz Eylül University School of Medicine, İzmir, Türkiye
| | - Yavuz Selim Ayhan
- Department of Child Health and Diseases, Faculty of Medicine, Mersin University, Mersin, Türkiye
| | - Begümhan Demir Gündoğan
- Department of Child Hematology and Oncology, Faculty of Medicine, Mersin University, Mersin, Türkiye
| | - Nazan Çetingül
- Dr. Behçet Uz Pediatric Diseases and Surgery Training and Research Hospital, Health Sciences University, İzmir, Türkiye
| | - Erdener Özer
- Department of Medical Pathology, Faculty of Medicine, Dokuz Eylül University, İzmir, Türkiye
| | - Tezer Kutluk
- Department of Pediatric Oncology, Faculty of Medicine and Cancer Institute, Hacettepe University, Ankara, Türkiye
| | - Nur Olgun
- Department of Pediatric Oncology, Oncology Institute, Dokuz Eylül University, İzmir, Türkiye
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10
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Dhori X, Gioiosa S, Gonfloni S. An integrated analysis of multiple datasets reveals novel gene signatures in human granulosa cells. Sci Data 2024; 11:972. [PMID: 39242561 PMCID: PMC11379948 DOI: 10.1038/s41597-024-03715-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 08/01/2024] [Indexed: 09/09/2024] Open
Abstract
Granulosa cells (GCs) play crucial roles in oocyte maturation. Through gap junctions and extracellular vesicles, they mediate the exchange of molecules such as microRNAs and messenger RNAs. Different ovarian cell types exhibit unique gene expression profiles, reflecting their specialized functions and stages. By combining RNA-seq data from various cell types forming the follicle, we aimed at capturing a wide range of expression patterns, offering insights into the functional diversity and complexity of the transcriptome regulation across GCs. Herein, we performed an integrated bioinformatics analysis of RNA sequencing datasets present in public databases, with a unique and standardized workflow., By combining the data from different studies, we successfully increased the robustness and reliability of our findings and discovered novel genes, miRNAs, and signaling pathways associated with GCs function and oocyte maturation. Moreover, our results provide a valuable resource for further wet-lab research on GCs biology and their impact on oocyte development and competence.
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Affiliation(s)
- Xhulio Dhori
- CINECA, Super Computing Applications and Innovation Department, Via dei Tizii 6B, 000185, Roma, Italy
- Department of Biology, University of Roma, via della Ricerca Scientifica 00133, Roma, Italy
| | - Silvia Gioiosa
- CINECA, Super Computing Applications and Innovation Department, Via dei Tizii 6B, 000185, Roma, Italy.
| | - Stefania Gonfloni
- Department of Biology, University of Roma, via della Ricerca Scientifica 00133, Roma, Italy.
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11
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Li Q, Chao T, Wang Y, Xuan R, Guo Y, He P, Zhang L, Wang J. Transcriptome analysis reveals miRNA expression profiles in hypothalamus tissues during the sexual development of Jining grey goats. BMC Genomics 2024; 25:832. [PMID: 39232653 PMCID: PMC11373458 DOI: 10.1186/s12864-024-10735-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/22/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Exploring the physiological and molecular mechanisms underlying goat sexual maturation can enhance breeding practices and optimize reproductive efficiency and is therefore substantially important for practical breeding purposes. As an essential neuroendocrine organ in animals, the hypothalamus is involved in sexual development and other reproductive processes in female animals. Although microRNAs (miRNAs) have been identified as significant regulators of goat reproduction, there is a lack of research on the molecular regulatory mechanisms of hypothalamic miRNAs that are involved in the sexual development of goats. Therefore, we examined the dynamic changes in serum hormone profiles and hypothalamic miRNA expression profiles at four developmental stages (1 day (neonatal, D1, n = 5), 2 months (prepubertal, M2, n = 5), 4 months (sexual maturity, M4, n = 5), and 6 months (breeding period, M6, n = 5)) during sexual development in Jining grey goats. RESULTS Transcriptome analysis revealed 95 differentially expressed miRNAs (DEMs) in the hypothalamus of goats across the four developmental stages. The target genes of these miRNAs were significantly enriched in the GnRH signalling pathway, the PI3K-Akt signalling pathway, and the Ras signalling pathway (P < 0.05). Additionally, 16 DEMs are common among the M2 vs. D1, M4 vs. D1, and M6 vs. D1 comparisons, indicating that the transition from D1 to M2 represents a potentially critical period for sexual development in Jining grey goats. The bioinformatics analysis results indicate that miR-193a/miR-193b-3p-Annexin A7 (ANXA7), miR-324-5p-Adhesion G protein-coupled receptor A1 (ADGRA1), miR-324-3p-Erbb2 receptor tyrosine kinase 2 (ERBB2), and miR-324-3p-Rap guanine nucleotide exchange factor 3 (RAPGEF3) are potentially involved in biological processes such as hormone secretion, energy metabolism, and signal transduction. In addition, we further confirmed that miR-324-3p targets the regulatory gene RAPGEF3. CONCLUSION These results further enrich the expression profile of hypothalamic miRNAs in goats and provide important insights for studying the regulatory effects of hypothalamic miRNAs on the sexual development of goats after birth.
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Affiliation(s)
- Qing Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Yanyan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Yanfei Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Peipei He
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Lu Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China.
- Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Tai'an City, 271014, Shandong Province, China.
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12
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Zhang L, Li Y, Fu C, Yang L, Li G, Wu Y, Tong H, Tian G, Wang K, Wang J, Ying X, Li Z. Exploration and validation of ceRNA regulatory networks in colorectal cancer based on associations whole transcriptome sequencing. Sci Rep 2024; 14:20446. [PMID: 39227669 PMCID: PMC11372121 DOI: 10.1038/s41598-024-71465-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
Colorectal cancer (CRC) is a wide-spread gastrointestinal cancer that is associated with augmented morbidity and mortality, and we do not yet have a deep understanding of its epidemiology and carcinogenicity. The transcriptome can reveal the complexity and heterogeneity of tumors and uncover new biomarkers or treatment options. In this study, we identified messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), round RNAs (circRNAs), and microRNAs (miRNAs) using whole-transcriptome sequencing and generated competing endogenous RNA (ceRNA) modulatory axes. We conducted whole transcriptome sequencing on 10 CRC and para-cancer (CRCP) samples and discovered 2465 differentially expressed (DE) mRNAs (DEmRNAs), 77 DE miRNAs (DEmiRNAs). 2852 DE lncRNAs (DElncRNAs) and 1477 DE circRNAs (DEcircRNAs). In addition, utilizing co-DE analysis, we generated the ceRNA axis. Subsequently, we employed the ceRNA axis to identify essential genes and corresponding associations with lncRNAs, circRNAs, and miRNAs in CRC. ceRNA regulatory network including mRNA-miRNA-lncRNA and mRNA-miRNA-circRNA. These modulatory axes potentially modulate the positive regulation of smooth muscle contraction, melanosome, plasma membrane, integral plasma membrane component and so on. Finally, the results of RNA sequencing (RNA-SEQ) were combined with the TCGA and GEO databases, and the DEGs strongly correlated with the TCGA-COAD overall survival (OS) as estimated by univariate cox and logarithmic rank analyses were cross-analyzed, and the co-upregulated DEGs were screened. Among the many DEs, KPNA2 was chosen for additional analysis. Using invitro experimentations, western blot, CCK8, EdU and other experiments were performed to verify the results. We found siRNA-based KPNA2 depletion reduces bladder cancer cells' viability, migratory, and proliferative activities, which showed that the DEmRNA profiles were comparable to the sequencing information, confirming that the sequencing data were very reliable. These evidences highlight the ceRNA regulatory mechanisms in CRC and will aid future research into the molecular mechanisms behind colorectal cancer prevention and treatment.
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Affiliation(s)
- Lulu Zhang
- Medical research center, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Yulei Li
- Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Chao Fu
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - LiXia Yang
- Medical research center, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Gang Li
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Yiyang Wu
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Huanjun Tong
- Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Guojiang Tian
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Kaifang Wang
- Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau Special Adiministrative Region, China
| | - Jun Wang
- Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China
| | - Xiaojiang Ying
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
| | - Zhenjun Li
- Department of Colorectal and Anal Surgery, Shaoxing People's Hospital, No. 568, Zhongxing North Road, Shaoxing, 312000, Zhejiang, China.
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13
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Elshafie NO, Gribskov M, Lichti NI, Sayedahmed EE, Childress MO, Pires Dos Santos A. MicroRNAs implicated in canine diffuse large B-cell lymphoma prognosis. FEBS Open Bio 2024. [PMID: 39218619 DOI: 10.1002/2211-5463.13887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 07/16/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most prevalent subtype of non-Hodgkin lymphoma (NHL) in domestic dogs, with many similarities to its human counterpart. The progression of the disease is rapid, and treatment must be initiated early to achieve cancer remission and extend life. This study examined the relationship between progression-free survival (PFS) and microRNA (miRNA) expression in dogs with DLBCL. miRNAs are small non-coding RNA molecules that typically regulate gene expression post-transcriptionally. They are involved in several pathophysiological processes, including the growth and progression of cancer. Based on the analysis of small RNA sequencing (sRNA-seq) data, we validated a group of miRNAs in lymph nodes from 44 DLBCL-affected dogs with known outcomes. We used quantitative PCR to quantify their expression and report a specific subset of miRNAs is associated with decreased PFS in dogs with DLBCL. The miR-192-5p and miR-16-5p expression were significantly downregulated in dogs with increased PFS. These results indicate that miRNA profiling may potentially identify dogs with DLBCL that will experience poor outcomes following treatment. Identifying specific miRNAs that correlate with the progression of canine DLBCL could aid the development of individualized treatment regimens for dogs.
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Affiliation(s)
- Nelly O Elshafie
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Ekramy E Sayedahmed
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Michael O Childress
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Andrea Pires Dos Santos
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
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14
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Hegde S, Wagh K, Narayana SM, Abikar A, Nambiar S, Ananthamurthy S, Narayana NH, Reddihalli PV, Chandraiah S, Ranganathan P. microRNA profile of endometrial cancer from Indian patients-identification of potential biomarkers for prognosis. Biochem Biophys Rep 2024; 39:101812. [PMID: 39282095 PMCID: PMC11395764 DOI: 10.1016/j.bbrep.2024.101812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024] Open
Abstract
Endometrial cancer is one of the major cancers in women throughout the world. If diagnosed early, these cancers are treatable and the prognosis is usually good. However, one major problem in treating endometrial cancer is accurate diagnosis and staging. Till date, the choice method for diagnosis and staging is histopathology. Although there are few molecular markers identified, they are not always sufficient in making accurate diagnosis and deciding on therapeutic strategy. As a result, very often patients are under treated or over treated. In this study, our group has profiled microRNAs from Indian patients using NGS-based approach. We have identified 212 differentially expressed microRNAs in endometrial cancer. Among these, there are 17 novel miRNAs. Since this data represents only Indian cohort and also lacks survival data, validation across other populations is necessary before being considered as biomarkers. As one approach towards this, these microRNAs have also been compared to data from TCGA, which represent other populations and also correlated to relevance in overall survival. Using in-silico approaches, mRNA targets of the miRNAs have been predicted. After comparing with TCGA, we have identified 16 miRNA-mRNA pairs which could be potential prognostic biomarkers for endometrial cancer. This is the first miRNA profiling report from Indian cohort and one of the very few studies which have identified potential biomarkers of prognosis in endometrial cancer.
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Affiliation(s)
| | | | | | - Apoorva Abikar
- Centre for Human Genetics, Bengaluru, India
- Manipal Academy for Higher Education, Manipal, India
| | | | | | | | | | - Savitha Chandraiah
- Vani Vilas Hospital, Bangalore Medical College and Research Institute, Bengaluru, India
| | - Prathibha Ranganathan
- Centre for Human Genetics, Bengaluru, India
- Manipal Academy for Higher Education, Manipal, India
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15
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Park S, Raghunathan VK, Ramarapu R, Moshiri A, Yiu G, Casanova MI, Cosert K, McCorkell M, Leonard BC, Thomasy SM. Biomechanic, proteomic and miRNA transcriptional changes in the trabecular meshwork of primates injected with intravitreal triamcinolone. Vision Res 2024; 222:108456. [PMID: 38991466 DOI: 10.1016/j.visres.2024.108456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
Although biomechanical changes of the trabecular meshwork (TM) are important to the pathogenesis of glucocorticoids-induced ocular hypertension (GC-OHT), there is a knowledge gap in the underlying molecular mechanisms of the development of it. In this study, we performed intravitreal triamcinolone injection (IVTA) in one eye of 3 rhesus macaques. Following IVTA, we assessed TM stiffness using atomic force microscopy and investigated changes in proteomic and miRNA expression profiles. One of 3 macaques developed GC-OHT with a difference in intraocular pressure of 4.2 mmHg and a stiffer TM with a mean increase in elastic moduli of 0.60 kPa versus the non-injected control eye. In the IVTA-treated eyes, proteins associated with extracellular matrix remodeling, cytoskeletal rearrangement, and mitochondrial oxidoreductation were significantly upregulated. The significantly upregulated miR-29b and downregulated miR-335-5p post-IVTA supported the role of oxidative stress and mitophagy in the GC-mediated biomechanical changes in TM, respectively. The significant upregulation of miR-15/16 cluster post-IVTA may indicate a resultant TM cell apoptosis contributing to the increase in outflow resistance. Despite the small sample size, these results expand our knowledge of GC-mediated responses in the TM and furthermore, may help explain steroid responsiveness in clinical settings.
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Affiliation(s)
- Sangwan Park
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | | | - Raneesh Ramarapu
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, University of California-Davis, Davis, CA, 95817, USA
| | - Glenn Yiu
- Department of Ophthalmology & Vision Science, School of Medicine, University of California-Davis, Davis, CA, 95817, USA
| | - M Isabel Casanova
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Krista Cosert
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Michelle McCorkell
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA; Department of Ophthalmology & Vision Science, School of Medicine, University of California-Davis, Davis, CA, 95817, USA
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA; Department of Ophthalmology & Vision Science, School of Medicine, University of California-Davis, Davis, CA, 95817, USA; California National Primate Research Center, University of California-Davis, Davis, CA, 95616, USA.
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16
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Pažur K, Francuzik W, El-Mahmoud H, Kraft M, Worm M. Proteomic, miRNA and bacterial biomarker patterns in atopic dermatitis patients and their course upon anti-IL-4Rα therapy. J Eur Acad Dermatol Venereol 2024; 38:1749-1759. [PMID: 38379385 DOI: 10.1111/jdv.19911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Identification of biomarkers is required for a systems medicine approach and personalized treatment in atopic dermatitis (AD). These biomarkers may not only aid in diagnosing but also might be suitable to predict the effectiveness of targeted treatment. OBJECTIVE We aimed to identify proteomic, microbial and miRNA biomarkers in AD patients and investigated their course in relation to the clinical response upon anti-IL-4Rα therapy. METHODS Proteomic and miRNA screening was performed in AD patients in comparison to healthy controls. Differentially regulated serum proteins, miRNA and selected skin microbiota were measured consecutively in 50 AD patients before and upon systemic dupilumab treatment. A random forest classifier was used to predict the outcome of dupilumab therapy based on the initial biomarker patterns. RESULTS We identified 27 proteomic candidates, miRNA and three microbial strains to be dysregulated in AD. CCL17, CCL13, CCL22, E-selectin and BDNF were differently regulated and significantly associated with treatment response. In contrast, neither the microbial composition nor the miRNA pattern was associated with treatment response upon dupilumab treatment. CONCLUSION AD patients display defined dysregulations regarding their systemic proteomic serum profile, miRNA patterns and their skin microbiome. The proteomic profile and selected skin bacteria changed profoundly upon anti-IL-4Rα therapy which was associated with an overall clinical response. This was not seen in miRNA-related biomarkers. Our findings support the hypothesis that biomarker profiles reflect treatment responses and may in the future be used to develop a personalized medicine approach for the treatment of AD patients.
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Affiliation(s)
- K Pažur
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W Francuzik
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - H El-Mahmoud
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - M Kraft
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - M Worm
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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17
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Lanctôt S, Blouin R, Thibault C, Lacasse P. Effect of milk stasis on mammary gland involution and the microRNA profile. J Dairy Sci 2024; 107:7435-7445. [PMID: 38788842 DOI: 10.3168/jds.2023-24603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/02/2024] [Indexed: 05/26/2024]
Abstract
The presence of an autocrine factor in milk that can trigger mammary gland involution was proposed more than 50 yr ago. To provide evidence for the existence of one or more autocrine factors, 10 multiparous cows in late lactation were quarter-milked for 7 d. Following this baseline period, the right front quarter of each cow was left unmilked, and the other quarters were milked for 7 d. Before the last milking of that period, milk (mammary secretions) was collected aseptically from both front quarters. After that milking, 250 mL of the collected samples were infused in the cows' respective rear quarters. No quarters were milked for the following 7 d (milk stasis period), and quarter milking was then resumed in all quarters for the last 7 d of the experiment (remilking period). Quarter milk samples were collected during the baseline period, before the milk stasis period, and during the remilking period. These samples were used for measuring milk components and the concentration of involution markers (SCC, BSA, and lactoferrin). Samples of mammary secretions were collected manually from the quarters during the milk stasis period for involution marker determination. We extracted RNA from samples collected from front quarters before the last milking before the milk stasis period for microRNA (miRNA) determination. As anticipated, the longer milk stasis period implemented for the right front quarter resulted in a more advanced involution than in the left front quarter, based on the concentration of involution markers in the mammary secretions, lower milk production recovery, and changes in milk composition during the remilking period. All 3 involution marker concentrations in the mammary secretions increased in both rear quarters, but were greater in the right quarter secretions than in the left quarter secretions. Resuming milking reinitiated milk production in all quarters, but milk production recovery in the right rear quarters was less robust than that in the left rear quarters (54.3 ± 1.4% vs. 61.6 ± 1.4%, respectively). Milk from the quarters infused with mammary secretions (right rear) had a lower lactose content, but a higher milk protein content and higher SCC than the quarters infused with milk. We detected a total of 359 miRNAs, 76 of which were differentially expressed in milk and mammary secretions. Expression of bta-miR-221 and bta-miR-223 was upregulated in mammary secretions 34- and 40-fold, respectively. The results of the present experiment support the contention that milk stasis leads to the accumulation of one or more factors that trigger involution. The results also indicate that milk stasis leads to changes in the miRNA profile of the milk, but whether such changes are a cause or a consequence of the involution process remains to be established.
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Affiliation(s)
- S Lanctôt
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - R Blouin
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - C Thibault
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - P Lacasse
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada.
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18
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Yu R, Yang X, Xiao D, Bao H, Wang Y. MiRNAs profiles among three poplar varieties provide insights into different molecular responses in resistance to newly emerging bacterial pathogen. PHYSIOLOGIA PLANTARUM 2024; 176:e14498. [PMID: 39223906 DOI: 10.1111/ppl.14498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Canker caused by Lonsdalea populi has seriously reduced the economic and ecological benefits of poplar. MicroRNAs play vital roles in the response of plants to biotic stress. However, there is little research about the regulatory mechanism of miRNAs among different tree varieties upon pathogen infection. To dissect miRNAs involved in L. populi resistance, three poplar varieties, 2025 (susceptible), 107 (moderately resistant) and Populus. tomentosa cv 'henan' (resistant) were selected to elucidate the expression profiles of miRNAs using small RNA-seq. A total of 227 miRNAs were identified from all varieties. Intriguingly, miR160, miR169, miR171 and miR482b-5p were only identified in the resistant variety P. tomentosa upon pathogen infection, and these miRNAs might be important candidates for future investigation to improve the tolerance of poplar to L. populi. Among all identified miRNAs, 174 were differentially expressed in all varieties. Functional annotation analysis indicated that an array of miRNAs, including miR482, miR472, miR169, miR481, and miR172, should be involved in disease resistance and phytohormone signal transduction. Furthermore, correlation analysis of small RNA-seq and RNA-seq identified a handful of L. populi-responsive miRNAs and target genes, which exhibited that miR159 and miR172 played key roles in resistant variety P. tomentosa by targeting MYB and ERF, while miR6462c-5p and miR828 were related to the susceptibility of 2025 by targeting MYB. The comprehensive integration analysis in this research provides new insights into the regulatory pathways involved in the defence response of poplar to L. populi and offers crucial candidate miRNAs-target genes modules for poplar resistance improvement.
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Affiliation(s)
- Ruen Yu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Dandan Xiao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hai Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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19
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Tsai WA, Brosnan CA, Mitter N, Dietzgen RG. Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures. Pathogens 2024; 13:745. [PMID: 39338939 PMCID: PMC11434723 DOI: 10.3390/pathogens13090745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
The orthotospovirus capsicum chlorosis virus (CaCV) is an important pathogen affecting capsicum plants. Elevated temperatures may affect disease progression and pose a potential challenge to capsicum production. To date, CaCV-resistant capsicum breeding lines have been established; however, the impact of an elevated temperature of 35 °C on this genetic resistance remains unexplored. Thus, this study aimed to investigate how high temperature (HT) influences the response of CaCV-resistant capsicum to the virus. Phenotypic analysis revealed a compromised resistance in capsicum plants grown at HT, with systemic necrotic spots appearing in 8 out of 14 CaCV-infected plants. Molecular analysis through next-generation sequencing identified 105 known and 83 novel microRNAs (miRNAs) in CaCV-resistant capsicum plants. Gene ontology revealed that phenylpropanoid and lignin metabolic processes, regulated by Can-miR408a and Can- miR397, are likely involved in elevated-temperature-mediated resistance-breaking responses. Additionally, real-time PCR validated an upregulation of Can-miR408a and Can-miR397 by CaCV infection at HT; however, only the Laccase 4 transcript, targeted by Can-miR397, showed a tendency of negative correlation with this miRNA. Overall, this study provides the first molecular insights into how elevated temperature affects CaCV resistance in capsicum plants and reveals the potential role of miRNA in temperature-sensitive tospovirus resistance.
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Affiliation(s)
- Wei-An Tsai
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | | | - Ralf G. Dietzgen
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
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20
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Wang Y, Zhang H, Zhang Z, Hua B, Liu J, Miao M. Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.). BMC PLANT BIOLOGY 2024; 24:812. [PMID: 39198785 PMCID: PMC11360537 DOI: 10.1186/s12870-024-05416-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/12/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND The yield of major crops is generally limited by sink capacity and source strength. Cucumber is a typical raffinose family oligosaccharides (RFOs)-transporting crop. Non-coding RNAs and alternative polyadenylation (APA) play important roles in the regulation of growth process in plants. However, their roles on the sink‒source regulation have not been demonstrated in RFOs-translocating species. RESULTS Here, whole-transcriptome sequencing was applied to compare the leaves of cucumber under different sink strength, that is, no fruit-carrying leaves (NFNLs) and fruit-carrying leaves (FNLs) at 12th node from the bottom. The results show that 1101 differentially expressed (DE) mRNAs, 79 DE long non-coding RNAs (lncRNAs) and 23 DE miRNAs were identified, which were enriched in photosynthesis, energy production and conversion, plant hormone signal transduction, starch and carbohydrate metabolism and protein synthesis pathways. Potential co-expression networks like, DE lncRNAs-DE mRNAs/ DE miRNAs-DE mRNAs, and competing endogenous RNA (ceRNA) regulation models (DE lncRNAs-DE miRNAs-DE mRNAs) associated with sink‒source allocation, were constructed. Furthermore, 37 and 48 DE genes, which enriched in MAPK signaling and plant hormone signal transduction pathway, exist differentially APA, and SPS (CsaV3_2G033300), GBSS1 (CsaV3_5G001560), ERS1 (CsaV3_7G029600), PNO1 (CsaV3_3G003950) and Myb (CsaV3_3G022290) may be regulated by both ncRNAs and APA between FNLs and NFNLs, speculating that ncRNAs and APA are involved in the regulation of gene expression of cucumber sink‒source carbon partitioning. CONCLUSIONS These results reveal a comprehensive network among mRNAs, ncRNAs, and APA in cucumber sink-source relationships. Our findings also provide valuable information for further research on the molecular mechanism of ncRNA and APA to enhance cucumber yield.
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Affiliation(s)
- Yudan Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Huimin Zhang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226541, China
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Bing Hua
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jiexia Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
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21
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Keogh K, McGee M, Kenny DA. Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency. Sci Rep 2024; 14:20046. [PMID: 39209905 PMCID: PMC11362461 DOI: 10.1038/s41598-024-70669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Identifying and breeding cattle that are more feed efficient is of great benefit to beef production. Additionally, it is crucial that genes contributing to feed efficiency are robust across varying management settings including dietary source as well as being relevant across contrasting breeds of cattle. The aim of this study was to determine miRNAs that are contributing to the expression of residual feed intake (RFI) across two breeds and dietary sources. miRNA profiling was undertaken in Longissimus dorsi tissue of Charolais and Holstein-Friesian steers divergent for RFI phenotype following two contrasting consecutive diets (high-forage and high-concentrate). Ten miRNA were identified as differentially expressed (adj. P < 0.1) across the breed and diet contrasts examined. Of particular interest was the differential expression of miR-2419-5p and miR-2415-3p, both of which were up-regulated in the Low-RFI Charolais steers across each dietary phase. Pathway analysis of target mRNA genes of differentially expressed miRNA revealed enrichment (P < 0.05) for pathways including metabolic related pathways, insulin receptor signalling, adipogenesis as well as pathways related to skeletal muscle growth. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential molecular regulatory mechanisms relating to feed efficiency in beef cattle.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
| | - M McGee
- Livestock Systems Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - D A Kenny
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
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22
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Zhang Q, Lu B. The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs. Int J Mol Sci 2024; 25:9225. [PMID: 39273174 PMCID: PMC11395517 DOI: 10.3390/ijms25179225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/18/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Newts are excellent vertebrate models for investigating tissue regeneration due to their remarkable regenerative capabilities. To investigate the mRNA and microRNAs (miRNAs) profiles within the blastema niche of regenerating newt limbs, we amputated the limbs of Chinese fire belly newts (Cynops orientalis) and conducted comprehensive analyses of the transcriptome and microRNA profiles at five distinct time points post-amputation (0 hours, 1 day, 5 days 10 days and 20 days). We identified 24 significantly differentially expressed (DE) genes and 20 significantly DE miRNAs. Utilizing weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) enrichment analysis, we identified four genes likely to playing crucial roles in the early stages of limb regeneration: Cemip, Rhou, Gpd2 and Pcna. Moreover, mRNA-miRNA integration analysis uncovered seven human miRNAs (miR-19b-1, miR-19b-2, miR-21-5p, miR-127-5p, miR-150-5p, miR-194-5p, and miR-210-5p) may regulate the expression of these four key genes. The temporal expression patterns of these key genes and miRNAs further validated the robustness of the identified mRNA-miRNA landscape. Our study successfully identified candidate key genes and elucidated a portion of the genetic regulatory mechanisms involved in newt limb regeneration. These findings offer valuable insights for further exploration of the intricate processes of tissue regeneration.
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Affiliation(s)
- Qi Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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23
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Xu F, Zheng H, Dong X, Zhou A, Emu Q. miRNA expression signatures induced by pasteurella multocida infection in goats lung. Sci Rep 2024; 14:19626. [PMID: 39179681 PMCID: PMC11343864 DOI: 10.1038/s41598-024-69654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 08/07/2024] [Indexed: 08/26/2024] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and are involved in bacterial pathogenesis and host-pathogen interactions. In this study, we investigated the function of miRNAs in the regulation of host responses to Pasteurella multocida infection. Using next-generation sequencing, we analyzed miRNA expression pattern and identified differentially expressed miRNAs in Pasteurella multocida-infected goat lungs. In addition, we investigated the function of differentially expressed miRNAs andtheir targeted signaling pathways in bacterial infection processes. The results showed that Pasteurella multocida infection led to 69 significantly differentially expressed miRNAs, including 28 known annotated miRNAs with miR-497-3p showing the most significant difference. Gene target prediction and functional enrichment analyses showed that the target genes were mainly involved in cell proliferation, regulation of the cellular metabolic process, positive regulation of cellular process, cellular senescence, PI3K-Akt signaling pathway, FoxO signaling pathway and infection-related pathways. In conclusion, these data provide a new perspective on the roles of miRNAs in Pasteurella multocida infection.
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Affiliation(s)
- Feng Xu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Animal Science Academy of Sichuan Province, Chengdu, China
| | - Hao Zheng
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan, China
| | - Xia Dong
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan, China
| | - Ao Zhou
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan, China.
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Animal Science Academy of Sichuan Province, Chengdu, China.
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Kumar D, Venkadesan S, Prabha R, Begam S, Dutta B, Mishra DC, Chaturvedi KK, Jha GK, Solanke AU, Sevanthi AM. RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice. Database (Oxford) 2024; 2024:baae076. [PMID: 39167719 PMCID: PMC11338179 DOI: 10.1093/database/baae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/27/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
MicroRNAs are key players involved in stress responses in plants and reports are available on the role of miRNAs in drought stress response in rice. This work reports the development of a database, RiceMetaSys: Drought-miR, based on the meta-analysis of publicly available sRNA datasets. From 28 drought stress-specific sRNA datasets, we identified 216 drought-responsive miRNAs (DRMs). The major features of the database include genotype-, tissue- and miRNA ID-specific search options and comparison of genotypes to identify common miRNAs. Co-localization of the DRMs with the known quantitative trait loci (QTLs), i.e., meta-QTL regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising DRMs. To identify the high confidence target genes of DRMs under drought stress, degradome datasets and web resource on drought-responsive genes (RiceMetaSys: DRG) were used. Out of the 216 unique DRMs, only 193 had targets with high stringent parameters. Out of the 1081 target genes identified by Degradome datasets, 730 showed differential expression under drought stress in at least one accession. To retrieve complete information on the target genes, the database has been linked with RiceMetaSys: DRG. Further, we updated the RiceMetaSys: DRGv1 developed earlier with the addition of DRGs identified from RNA-seq datasets from five rice genotypes. We also identified 759 putative novel miRNAs and their target genes employing stringent criteria. Novel miRNA search has all the search options of known miRNAs and additionally, it gives information on their in silico validation features. Simple sequence repeat markers for both the miRNAs and their target genes have also been designed and made available in the database. Network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. Co-localization of the hub genes with the meta-QTL regions governing drought tolerance narrowed down this to 16 most promising DRGs. Database URL: http://14.139.229.201/RiceMetaSys_miRNA Updated database of RiceMetaSys URL: http://14.139.229.201/RiceMetaSysA/Drought/.
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Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | | | - Ratna Prabha
- AKMU, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Shbana Begam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Girish Kumar Jha
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Amolkumar U Solanke
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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Rooda I, Hassan J, Hao J, Wagner M, Moussaud-Lamodière E, Jääger K, Otala M, Knuus K, Lindskog C, Papaikonomou K, Gidlöf S, Langenskiöld C, Vogt H, Frisk P, Malmros J, Tuuri T, Salumets A, Jahnukainen K, Velthut-Meikas A, Damdimopoulou P. In-depth analysis of transcriptomes in ovarian cortical follicles from children and adults reveals interfollicular heterogeneity. Nat Commun 2024; 15:6989. [PMID: 39168975 PMCID: PMC11339373 DOI: 10.1038/s41467-024-51185-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
The ovarian cortical reserve of follicles is vital for fertility. Some medical treatments are toxic to follicles, leading to premature ovarian insufficiency. Ovarian tissue cryopreservation is an established method to preserve fertility in adults and even applied in prepuberty despite unproven efficacy. Here, we analyze transcriptomes of 120 cortical follicles from children and adults for detailed comparison. We discover heterogeneity with two main types of follicles in both age groups: one with expected oocyte-granulosa profiles and another with predicted role in signaling. Transcriptional changes during growth to the secondary stage are similar overall in children and adults, but variations related to extracellular matrix, theca cells, and miRNA profiles are found. Notably, cyclophosphamide dose correlates with interferon signaling in child follicles. Additionally, morphology alone is insufficient for follicle categorization suggesting a need for additional markers. Marker genes for early follicle activation are determined. These findings will help refine follicular classification and fertility preservation techniques across critical ages.
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Affiliation(s)
- Ilmatar Rooda
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden.
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden.
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
| | - Jasmin Hassan
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jie Hao
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Reproductive Medicine, Xiangya Hospital, Central South University, Changsha, PR China
| | - Magdalena Wagner
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabeth Moussaud-Lamodière
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Kersti Jääger
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Marjut Otala
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Katri Knuus
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kiriaki Papaikonomou
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Gidlöf
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Langenskiöld
- Department of Pediatric Oncology, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hartmut Vogt
- Crown Princess Victoria Children's Hospital, and Division of Children's and Women's Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Per Frisk
- Department of Women's and Children's Health, Uppsala University Children's Hospital, Uppsala, Sweden
| | - Johan Malmros
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Andres Salumets
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kirsi Jahnukainen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Women's and Children's Health, NORDFERTIL Research Lab Stockholm, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Pauliina Damdimopoulou
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, Stockholm, Sweden.
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden.
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26
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Shen C, Li X, Qin J, Duan L. Characterization of miRNA profiling in konjac-derived exosome-like nanoparticles and elucidation of their multifaceted roles in human health. FRONTIERS IN PLANT SCIENCE 2024; 15:1444683. [PMID: 39175488 PMCID: PMC11338808 DOI: 10.3389/fpls.2024.1444683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Plant-derived exosome-like nanoparticles (ELNs) have demonstrated cross-kingdom capabilities in regulating intercellular communication, facilitating drug delivery, and providing therapeutic interventions in humans. However, the functional attributes of konjac-derived ELNs (K-ELNs) remain largely unexplored. This study investigates the isolation, characterization, and functional analysis of K-ELNs, along with the profiling and differential expression analysis of associated miRNAs in both K-ELNs and Konjac tissues. K-ELNs were successfully isolated and characterized from two konjac species using ultracentrifugation, followed by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Small RNA sequencing identified a total of 3,259 miRNAs across all samples. Differential expression analysis revealed significant differences in miRNA profiles between K-ELNs and tissue samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of target genes provided insights into their roles in modulating pathways associated with diseases such as cancer and neurodegenerative disorders. Additionally, six miRNAs were selected for validation of sequencing results via RT-qPCR. The 5'RLM-RACE method was employed to validate the cleavage sites between differentially expressed miRNAs (DEMs) and their predicted target genes, further substantiating the regulatory roles of miRNAs in konjac. The findings of this study enhance our understanding of the molecular mechanisms underlying the biological functions and applications of K-ELNs, laying the groundwork for future research into their potential therapeutic roles in human health.
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Affiliation(s)
- Chuan Shen
- Shaannan Eco-economy Research Center, Ankang University, Ankang, China
| | - Xia Li
- Department of Electronic and Information Engineering, Ankang University, Ankang, China
| | - Jianfeng Qin
- Ankang Municipality Agricultural Science Research Institute, Ankang, China
| | - Longfei Duan
- Ankang Municipality Agricultural Science Research Institute, Ankang, China
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27
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Whitehead B, Sørensen Rossen L, Zippor M, Boysen AT, Indira Chandran V, Skallerup P, Thamsborg SM, Nejsum P. Micro RNA profiles of host extracellular vesicles are modulated by Ascaris suum infection but parasite extracellular vesicle miRNAs are systemically undetectable using in-depth miRNA sequencing. Int J Parasitol 2024:S0020-7519(24)00151-6. [PMID: 39116918 DOI: 10.1016/j.ijpara.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/05/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
The intestinal helminth Ascaris lumbricoides infects over 800 million people. Infections are often chronic and immunity is not sterilizing due to host-immune modulation, therefore reinfection is common after antihelmintic treatment. We have previously demonstrated a role for Ascaris spp. extracellular vesicles (EVs) in host immune modulation but whether EVs are recognized by the adaptive immune system and are present systemically in the host remains unknown. Therefore, we employed a well-established trickle infection model in pigs to mimic natural Ascaris infection in humans. EVs were isolated from adult Ascaris suum followed by immunoblotting of EV and EV-depleted secretory fractions using plasma from infected and uninfected pigs. Next, EVs were isolated from pig plasma at day 56 post first infection and subjected to deep small RNAseq analysis. RNAs were aligned to A. suum and Sus scrofa miRNA complements to detect A. suum EVs and elucidate the host EV micro RNA (miRNA) response to infection, respectively. Infection generates robust antibody responses against A. suum EVs that is distinct from EV-depleted fractions. However, A. suum miRNAs were not detectable in EVs from the peripheral blood. Notably, host plasma-derived EV miRNA profiles showed significant changes between infected and uninfected pigs, indicating that Ascaris infection drives systemic changes in host EV composition.
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Affiliation(s)
- Bradley Whitehead
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
| | - Litten Sørensen Rossen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Mads Zippor
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Anders T Boysen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Vineesh Indira Chandran
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | | | - Stig M Thamsborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
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28
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Niu Y, Guo D, Wei Y, Li J, Bai Y, Liu Z, Jia X, Chen Z, Li L, Shi B, Zhang X, Zhao Z, Hu J, Wang J, Liu X, Li S. Comparative Transcriptome Analysis of mRNA and miRNA during the Development of Longissimus Dorsi Muscle of Gannan Yak and Tianzhu White Yak. Animals (Basel) 2024; 14:2278. [PMID: 39123804 PMCID: PMC11311108 DOI: 10.3390/ani14152278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
The Gannan yak, a superior livestock breed found on the Tibetan Plateau, exhibits significantly enhanced body size, weight, and growth performance in comparison to the Tianzhu white yak. MiRNAs play a pivotal role in regulating muscle growth by negatively modulating target genes. In this study, we found the average diameter, area, and length of myofibers in Gannan yaks were significantly higher than those of Tianzhu white yaks. Further, we focused on analyzing the longissimus dorsi muscle from both Gannan yaks and Tianzhu white yaks through transcriptome sequencing to identify differentially expressed (DE)miRNAs that influence skeletal muscle development. A total of 254 DE miRNAs were identified, of which 126 miRNAs were up-regulated and 128 miRNAs were down-regulated. GO and KEGG enrichment analysis showed that the target genes of these DE miRNAs were significantly enriched in signaling pathways associated with muscle growth and development. By constructing a DE miRNA- DE mRNA interaction network, we screened 18 key miRNAs, and notably, four of the candidates (novel-m0143-3p, novel-m0024-3p, novel-m0128-5p, and novel-m0026-3p) targeted six genes associated with muscle growth and development (DDIT4, ADAMTS1, CRY2, AKIRIN2, SIX1, and FOXO1). These findings may provide theoretical references for further studies on the role of miRNAs in muscle growth and development in Gannan yaks.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.N.); (D.G.); (Y.W.); (J.L.); (Y.B.); (Z.L.); (X.J.); (Z.C.); (L.L.); (B.S.); (X.Z.); (J.H.); (J.W.); (X.L.); (S.L.)
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29
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Phan P, Fogarty CE, Eamens AL, Duke MG, McManus DP, Wang T, Cummins SF. ARGONAUTE2 Localizes to Sites of Sporocysts in the Schistosome-Infected Snail, Biomphalaria glabrata. Genes (Basel) 2024; 15:1023. [PMID: 39202383 PMCID: PMC11353429 DOI: 10.3390/genes15081023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
MicroRNAs (miRNAs) are a class of small regulatory RNA that are generated via core protein machinery. The miRNAs direct gene-silencing mechanisms to mediate an essential role in gene expression regulation. In mollusks, miRNAs have been demonstrated to be required to regulate gene expression in various biological processes, including normal development, immune responses, reproduction, and stress adaptation. In this study, we aimed to establishment the requirement of the miRNA pathway as part of the molecular response of exposure of Biomphalaria glabrata (snail host) to Schistosoma mansoni (trematode parasite). Initially, the core pieces of miRNA pathway protein machinery, i.e., Drosha, DGCR8, Exportin-5, Ran, and Dicer, together with the central RNA-induced silencing complex (RISC) effector protein Argonaute2 (Ago2) were elucidated from the B. glabrata genome. Following exposure of B. glabrata to S. mansoni miracidia, we identified significant expression up-regulation of all identified pieces of miRNA pathway protein machinery, except for Exportin-5, at 16 h post exposure. For Ago2, we went on to show that the Bgl-Ago2 protein was localized to regions surrounding the sporocysts in the digestive gland of infected snails 20 days post parasite exposure. In addition to documenting elevated miRNA pathway protein machinery expression at the early post-exposure time point, a total of 13 known B. glabrata miRNAs were significantly differentially expressed. Of these thirteen B. glabrata miRNAs responsive to S. mansoni miracidia exposure, five were significantly reduced in their abundance, and correspondingly, these five miRNAs were determined to putatively target six genes with significantly elevated expression and that have been previously associated with immune responses in other animal species, including humans. In conclusion, this study demonstrates the central importance of a functional miRNA pathway in snails, which potentially forms a critical component of the immune response of snails to parasite exposure. Further, the data reported in this study provide additional evidence of the complexity of the molecular response of B. glabrata to S. mansoni infection: a molecular response that could be targeted in the future to overcome parasite infection and, in turn, human schistosomiasis.
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Affiliation(s)
- Phong Phan
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Conor E. Fogarty
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia;
| | - Mary G. Duke
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Scott F. Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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30
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Chen Y, De Schutter K. Biosafety aspects of RNAi-based pests control. PEST MANAGEMENT SCIENCE 2024; 80:3697-3706. [PMID: 38520331 DOI: 10.1002/ps.8098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 03/25/2024]
Abstract
While the overuse of classical chemical pesticides has had a detrimental impact on the environment and human health, the discovery of RNA interference (RNAi) offered the opportunity to develop new and sustainable approaches for pest management. RNAi is a naturally occurring regulation and defense mechanism that can be exploited to effectively protect crops by silencing key genes affecting the growth, development, behavior or fecundity of pests. However, as with all technologies, there is a range of potential risks and challenges associated with the application of RNAi, such as dsRNA stability, the potential for off-target effects, the safety of non-target organisms, and other application challenges. A better understanding of the molecular mechanisms involved in RNAi and in-depth discussion and analysis of these associated safety risks, is required to limit or mitigate potential adverse effects. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yimeng Chen
- Molecular Entomology Lab, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kristof De Schutter
- Molecular Entomology Lab, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Gao C, Nie H. Exploring the Heat-Responsive miRNAs and their Target Gene Regulation in Ruditapes philippinarum Under Acute Heat Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:810-826. [PMID: 39046591 DOI: 10.1007/s10126-024-10348-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/13/2024] [Indexed: 07/25/2024]
Abstract
This study aimed to investigate the inherent molecular regulatory mechanisms of Ruditapes philippinarum in response to extremely high-temperature environments and to enhance the sustainable development of the R. philippinarum aquaculture industry. In this study, we established a differential expression profile of miRNA under acute heat stress and identified a total of 46 known miRNAs and 80 novel miRNAs, three of which were detected to be significantly differentially expressed. We analyzed the functions of target genes regulated by differentially expressed miRNAs (DEMs) of R. philippinarum. The findings of the KEGG enrichment analysis revealed that 29 enriched pathways in the group were subjected to acute heat stress. Notably, fatty acid metabolism, FoxO signaling pathway, TGF-β signaling pathway, and ubiquitin-mediated proteolysis were found to play significant roles in response to acute heat stress. We established a regulatory map of DEMs and their target genes in response to heat stress and constructed the miRNA-mRNA regulation network. This study provides valuable insights into the response of R. philippinarum to high temperature, helping to understand its underlying molecular regulatory mechanisms under high-temperature stress.
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Affiliation(s)
- Changsheng Gao
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China.
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China.
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32
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Röszer T. MicroRNA Profile of Mouse Adipocyte-Derived Extracellular Vesicles. Cells 2024; 13:1298. [PMID: 39120327 PMCID: PMC11311276 DOI: 10.3390/cells13151298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
The post-transcriptional control of gene expression is a complex and evolving field in adipocyte biology, with the premise that the delivery of microRNA (miRNA) species to the obese adipose tissue may facilitate weight loss. Cells shed extracellular vesicles (EVs) that may deliver miRNAs as intercellular messengers. However, we know little about the miRNA profile of EVs secreted by adipocytes during postnatal development. Here, we defined the miRNA cargo of EVs secreted by mouse adipocytes in two distinct phases of development: on postnatal day 6, when adipocytes are lipolytic and thermogenic, and on postnatal day 56, when adipocytes have active lipogenesis. EVs were collected from cell culture supernatants, and their miRNA profile was defined by small RNA sequencing. The most abundant miRNA of mouse adipocyte-derived EVs was mmu-miR-148a-3p. Adipocyte EVs on postnatal day 6 were hallmarked with mmu-miR-98-5p, and some miRNAs were specific to this developmental stage, such as mmu-miR-466i-5p and 12 novel miRNAs. Adipocytes on postnatal day 56 secreted mmu-miR-365-3p, and 16 miRNAs were specific to this developmental stage. The miRNA cargo of adipocyte EVs targeted gene networks of cell proliferation, insulin signaling, interferon response, thermogenesis, and lipogenesis. We provided here a database of miRNAs secreted by developing mouse adipocytes, which may be a tool for further studies on the regulation of gene networks that control mouse adipocyte development.
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Affiliation(s)
- Tamás Röszer
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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Lin H, Chen X, Wang L, Zhu T, Feng X, Liu X, Chen H, Pan S. Unraveling the role of microRNAs: potential biomarkers for gestational diabetes mellitus revealed through RNA sequencing analysis. Arch Gynecol Obstet 2024; 310:1255-1264. [PMID: 38814453 PMCID: PMC11258170 DOI: 10.1007/s00404-024-07518-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) poses significant health risks for both mothers and children, contributing to long-term complications such as type 2 diabetes and cardiovascular disease. This study explores the potential of microRNAs (miRNAs) as biomarkers for GDM by analyzing peripheral blood samples from GDM patients. METHOD Ten samples, including peripheral blood from 5 GDM patients and 5 controls, were collected to perform the RNA sequencing analysis. Differentially expressed miRNAs were further validated by quantitative real-time polymerase chain reaction. RESULTS A total of 2287 miRNAs were identified, 229 of which showed differential expression. Validation by qRT-PCR confirmed significant up-regulation of miR-5193, miR-5003-3p, miR-3127-5p, novel-miR-96, miR-6734-5p, and miR-122-5p, while miR-10395-3p was down-regulated. Bioinformatics analyses revealed the involvement of these miRNAs in pathways associated with herpes simplex virus 1 infection. CONCLUSION This study provides insights into the differential expression of miRNAs in GDM patients and their potential roles in disease pathogenesis. It suggests that the differentially expressed miRNAs could serve as potential biomarkers for GDM, shedding light on the complex molecular mechanisms involved.
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Affiliation(s)
- Huizhen Lin
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Xiao Chen
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Lisui Wang
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Tang Zhu
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, School of Basic Medicine Science, Putian, 351100, Fujian, China
| | - Xiaohui Feng
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Xiaomei Liu
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Haiying Chen
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, School of Basic Medicine Science, Putian, 351100, Fujian, China
| | - Si Pan
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, School of Basic Medicine Science, Putian, 351100, Fujian, China.
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Lin S, Lai D, Tian Y, Lai F, Long M, Ji C, Hao G. MicroRNA hsa-let-7e-5p in hUC-MSC-EVs alleviates oral mucositis by targeting TAB2. Scand J Immunol 2024:e13399. [PMID: 39073054 DOI: 10.1111/sji.13399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/30/2024]
Abstract
Oral mucositis (OM) is a severe side effect of anti-cancer therapy, with limited available treatments. Mesenchymal stem cells (MSCs) and their secreted extracellular vesicles (EVs) have demonstrated effective protection against OM. However, the underlying mechanism remains elusive. In the current study, we purified EVs secreted by human umbilical cord MSCs (hUC-MSC-EVs) and investigated their role in lipopolysaccharide (LPS)-induced human oral keratinocytes (HOKs). We observed that treatment with hUC-MSC-EVs significantly reduced the inflammatory response of HOKs to LPS induction. Through small RNA-seq using miRNAs extracted from hUC-MSC-EVs, we identified hsa-let-7e-5p as one of the most highly expressed miRNAs. Bioinformatic analysis data indicated that hsa-let-7e-5p may inhibit the NF-κB signalling pathway by targeting TAB2. Overexpression of the hsa-let-7e-5p inhibitor significantly attenuated the anti-inflammatory effect of hUC-MSC-EVs in LPS-induced HOKs, which could be reversed by the knockdown of TAB2. In addition, we administered hUC-MSC-EVs in a hamster model for OM and observed that these EVs alleviated OM phenotypes. Taken together, our observations suggest that hsa-let-7e-5p in hUC-MSC-EVs could protect the oral mucosa from OM by repressing TAB2 expression.
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Affiliation(s)
- Shuting Lin
- Department of Transfusion, Central Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Dong Lai
- Department of Transfusion, Central Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Yan Tian
- Department of Transfusion, Central Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Fei Lai
- Department of Transfusion, Central Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Min Long
- Department of Transfusion, Central Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Changfu Ji
- Department of Transfusion, Central Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Gengxin Hao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
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Dekkers MC, Lambooij JM, Pu X, Fagundes RR, Enciso-Martinez A, Kats K, Giepmans BNG, Guigas B, Zaldumbide A. Extracellular vesicles derived from stressed beta cells mediate monocyte activation and contribute to islet inflammation. Front Immunol 2024; 15:1393248. [PMID: 39114661 PMCID: PMC11303142 DOI: 10.3389/fimmu.2024.1393248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Objective Beta cell destruction in type 1 diabetes (T1D) results from the combined effect of inflammation and recurrent autoimmunity. In recent years, the role played by beta cells in the development of T1D has evolved from passive victims of the immune system to active contributors in their own destruction. We and others have demonstrated that perturbations in the islet microenvironment promote endoplasmic reticulum (ER) stress in beta cells, leading to enhanced immunogenicity. Among the underlying mechanisms, secretion of extracellular vesicles (EVs) by beta cells has been suggested to mediate the crosstalk with the immune cell compartment. Methods To study the role of cellular stress in the early events of T1D development, we generated a novel cellular model for constitutive ER stress by modulating the expression of HSPA5, which encodes BiP/GRP78, in EndoC-βH1 cells. To investigate the role of EVs in the interaction between beta cells and the immune system, we characterized the EV miRNA cargo and evaluated their effect on innate immune cells. Results Analysis of the transcriptome showed that HSPA5 knockdown resulted in the upregulation of signaling pathways involved in the unfolded protein response (UPR) and changes the miRNA content of EVs, including reduced levels of miRNAs involved in IL-1β signaling. Treatment of primary human monocytes with EVs from stressed beta cells resulted in increased surface expression of CD11b, HLA-DR, CD40 and CD86 and upregulation of IL-1β and IL-6. Conclusion These findings indicate that the content of EVs derived from stressed beta cells can be a mediator of islet inflammation.
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Affiliation(s)
- Mette C. Dekkers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Joost M. Lambooij
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Xudong Pu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Raphael R. Fagundes
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Agustin Enciso-Martinez
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Oncode institute, Leiden University Medical Center, Leiden, Netherlands
- Amsterdam Vesicle Center, Biomedical Engineering and Physics and Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Kim Kats
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ben N. G. Giepmans
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bruno Guigas
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
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Liu Y, Sun D, Xu C, Liu X, Tang M, Ying S. In-depth transcriptome profiling of Cherry Valley duck lungs exposed to chronic heat stress. Front Vet Sci 2024; 11:1417244. [PMID: 39104549 PMCID: PMC11298465 DOI: 10.3389/fvets.2024.1417244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Amidst rising global temperatures, chronic heat stress (CHS) is increasingly problematic for the poultry industry. While mammalian CHS responses are well-studied, avian-specific research is lacking. This study uses in-depth transcriptome sequencing to evaluate the pulmonary response of Cherry Valley ducks to CHS at ambient temperatures of 20°C and a heat-stressed 29°C. We detailed the CHS-induced gene expression changes, encompassing mRNAs, lncRNAs, and miRNAs. Through protein-protein interaction network analysis, we identified central genes involved in the heat stress response-TLR7, IGF1, MAP3K1, CIITA, LCP2, PRKCB, and PLCB2. Subsequent functional enrichment analysis of the differentially expressed genes and RNA targets revealed significant engagement in immune responses and regulatory processes. KEGG pathway analysis underscored crucial immune pathways, specifically those related to intestinal IgA production and Toll-like receptor signaling, as well as Salmonella infection and calcium signaling pathways. Importantly, we determined six miRNAs-miR-146, miR-217, miR-29a-3p, miR-10926, miR-146b-5p, and miR-17-1-3p-as potential key regulators within the ceRNA network. These findings enhance our comprehension of the physiological adaptation of ducks to CHS and may provide a foundation for developing strategies to improve duck production under thermal stress.
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Affiliation(s)
- Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dongyue Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Congcong Xu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiaoyong Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shijia Ying
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Thapliyal A, Tomar AK, Naglot S, Dhiman S, Datta SK, Sharma JB, Singh N, Yadav S. Exploring Differentially Expressed Sperm miRNAs in Idiopathic Recurrent Pregnancy Loss and Their Association with Early Embryonic Development. Noncoding RNA 2024; 10:41. [PMID: 39051375 PMCID: PMC11270218 DOI: 10.3390/ncrna10040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
The high incidence of idiopathic recurrent pregnancy loss (iRPL) may stem from the limited research on male contributory factors. Many studies suggest that sperm DNA fragmentation and oxidative stress contribute to iRPL, but their roles are still debated. MicroRNAs (miRNAs) are short non-coding RNAs that regulate various biological processes by modulating gene expression. While differential expression of specific miRNAs has been observed in women suffering from recurrent miscarriages, paternal miRNAs remain unexplored. We hypothesize that analyzing sperm miRNAs can provide crucial insights into the pathophysiology of iRPL. Therefore, this study aims to identify dysregulated miRNAs in the spermatozoa of male partners of iRPL patients. Total mRNA was extracted from sperm samples of iRPL and control groups, followed by miRNA library preparation and high-output miRNA sequencing. Subsequently, raw sequence reads were processed for differential expression analysis, target prediction, and bioinformatics analysis. Twelve differentially expressed miRNAs were identified in the iRPL group, with eight miRNAs upregulated (hsa-miR-4454, hsa-miR-142-3p, hsa-miR-145-5p, hsa-miR-1290, hsa-miR-1246, hsa-miR-7977, hsa-miR-449c-5p, and hsa-miR-92b-3p) and four downregulated (hsa-miR-29c-3p, hsa-miR-30b-5p, hsa-miR-519a-2-5p, and hsa-miR-520b-5p). Functional enrichment analysis revealed that gene targets of the upregulated miRNAs are involved in various biological processes closely associated with sperm quality and embryonic development.
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Affiliation(s)
- Ayushi Thapliyal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sarla Naglot
- Division of Reproductive, Child Health and Nutrition, Indian Council of Medical Research (ICMR), New Delhi 110029, India
| | - Soniya Dhiman
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sudip Kumar Datta
- Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jai Bhagwan Sharma
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Neeta Singh
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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Talevi V, Melas K, Pehlivan G, Imtiaz MA, Krüger DM, Centeno TP, Aziz NA, Fischer A, Breteler MMB. Peripheral whole blood microRNA expression in relation to vascular function: a population-based study. J Transl Med 2024; 22:670. [PMID: 39030538 PMCID: PMC11264787 DOI: 10.1186/s12967-024-05407-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/15/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND As key regulators of gene expression, microRNAs affect many cardiovascular mechanisms and have been associated with several cardiovascular diseases. In this study, we aimed to investigate the relation of whole blood microRNAs with several quantitative measurements of vascular function, and explore their biological role through an integrative microRNA-gene expression analysis. METHODS Peripheral whole blood microRNA expression was assessed through RNA-Seq in 2606 participants (45.8% men, mean age: 53.93, age range: 30 to 95 years) from the Rhineland Study, an ongoing population-based cohort study in Bonn, Germany. Weighted gene co-expression network analysis was used to cluster microRNAs with highly correlated expression levels into 14 modules. Through linear regression models, we investigated the association between each module's expression and quantitative markers of vascular health, including pulse wave velocity, total arterial compliance index, cardiac index, stroke index, systemic vascular resistance index, reactive skin hyperemia and white matter hyperintensity burden. For each module associated with at least one trait, one or more hub-microRNAs driving the association were defined. Hub-microRNAs were further characterized through mapping to putative target genes followed by gene ontology pathway analysis. RESULTS Four modules, represented by hub-microRNAs miR-320 family, miR-378 family, miR-3605-3p, miR-6747-3p, miR-6786-3p, and miR-330-5p, were associated with total arterial compliance index. Importantly, the miR-320 family module was also associated with white matter hyperintensity burden, an effect partially mediated through arterial compliance. Furthermore, hub-microRNA miR-192-5p was related to cardiac index. Functional analysis corroborated the relevance of the identified microRNAs for vascular function by revealing, among others, enrichment for pathways involved in blood vessel morphogenesis and development, angiogenesis, telomere organization and maintenance, and insulin secretion. CONCLUSIONS We identified several microRNAs robustly associated with cardiovascular function, especially arterial compliance and cardiac output. Moreover, our results highlight miR-320 as a regulator of cerebrovascular damage, partly through modulation of vascular function. As many of these microRNAs were involved in biological processes related to vasculature development and aging, our results contribute to the understanding of vascular physiology and provide putative targets for cardiovascular disease prevention.
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Affiliation(s)
- Valentina Talevi
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127, Bonn, Germany
| | - Konstantinos Melas
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127, Bonn, Germany
| | - Gökhan Pehlivan
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127, Bonn, Germany
| | - Mohammed A Imtiaz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127, Bonn, Germany
| | - Dennis Manfred Krüger
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Tonatiuh Pena Centeno
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - N Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127, Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Department for Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, Building 99, 53127, Bonn, Germany.
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany.
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Xiong JL, Wang YX, Luo JY, Wang SM, Sun JJ, Xi QY, Chen T, Zhang YL. Pituitary-derived small extracellular vesicles promote liver repair by its cargo miR-143-3p. Sci Rep 2024; 14:16635. [PMID: 39025906 PMCID: PMC11258314 DOI: 10.1038/s41598-024-67434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
The small Extracellular vesicles (sEV) has been recognized to be significant for intercellular communication due to their ability to transfer important cellular cargoes like miRNAs through circulation. The pituitary gland has not been clearly known about the role of its secreted sEV under normal physiological conditions. And Liver disease is a global public health burden. The present study is the first to investigate the effect of pituitary sEV on the liver. Sequencing and qRT-PCR revealed miR-143-3p is one of the richest in the pituitary sEV. MiR-143 Knockout (KO) mice resulted in a remarkable decrease in insulin-like growth factor 1 (IGF-1) levels and a significant increase in insulin-like growth factor binding protein 5 (IGFBP5) levels along with a reduction in liver primary cell growth. More importantly, compared with miR-143-KO-sEV, WT-sEV possesses a more robust capacity to improve miR-143 KO mice liver repair through the Wnt/β-catenin pathway after an acute injury caused by carbon tetrachloride (CCl4). Our results indicate that pituitary-derived sEV promotes hepatocyte proliferation and liver repair by its cargo miR-143-3p and provides new insight into the regulation mechanism of the pituitary-liver axis, and open a new window for endocrine regulation by using sEV.
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Affiliation(s)
- Jia-Li Xiong
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- College of Medicine, Jiaxing University, Jiaxing, 314000, Zhejiang, China
| | - Yu-Xuan Wang
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jun-Yi Luo
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Shu-Meng Wang
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jia-Jie Sun
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qian-Yun Xi
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ting Chen
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
| | - Yong-Liang Zhang
- College of Animal Science, Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Kumar D, Budachetri K, Rikihisa Y, Karim S. Analysis of Amblyomma americanum microRNAs in response to Ehrlichia chaffeensis infection and their potential role in vectorial capacity. Front Cell Infect Microbiol 2024; 14:1427562. [PMID: 39086604 PMCID: PMC11288922 DOI: 10.3389/fcimb.2024.1427562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Background MicroRNAs (miRNAs) represent a subset of small noncoding RNAs and carry tremendous potential for regulating gene expression at the post-transcriptional level. They play pivotal roles in distinct cellular mechanisms including inhibition of bacterial, parasitic, and viral infections via immune response pathways. Intriguingly, pathogens have developed strategies to manipulate the host's miRNA profile, fostering environments conducive to successful infection. Therefore, changes in an arthropod host's miRNA profile in response to pathogen invasion could be critical in understanding host-pathogen dynamics. Additionally, this area of study could provide insights into discovering new targets for disease control and prevention. The main objective of the present study is to investigate the functional role of differentially expressed miRNAs upon Ehrlichia chaffeensis, a tick-borne pathogen, infection in tick vector, Amblyomma americanum. Methods Small RNA libraries from uninfected and E. chaffeensis-infected Am. americanum midgut and salivary gland tissues were prepared using the Illumina Truseq kit. Small RNA sequencing data was analyzed using miRDeep2 and sRNAtoolbox to identify novel and known miRNAs. The differentially expressed miRNAs were validated using a quantitative PCR assay. Furthermore, a miRNA inhibitor approach was used to determine the functional role of selected miRNA candidates. Results The sequencing of small RNA libraries generated >147 million raw reads in all four libraries and identified a total of >250 miRNAs across the four libraries. We identified 23 and 14 differentially expressed miRNAs in salivary glands, and midgut tissues infected with E. chaffeensis, respectively. Three differentially expressed miRNAs (miR-87, miR-750, and miR-275) were further characterized to determine their roles in pathogen infection. Inhibition of target miRNAs significantly decreased the E. chaffeensis load in tick tissues, which warrants more in-depth mechanistic studies. Conclusions The current study identified known and novel miRNAs and suggests that interfering with these miRNAs may impact the vectorial capacity of ticks to harbor Ehrlichia. This study identified several new miRNAs for future analysis of their functions in tick biology and tick-pathogen interaction studies.
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Affiliation(s)
- Deepak Kumar
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Khemraj Budachetri
- Laboratory of Molecular, Cellular, and Environmental Rickettsiology, Department of Veterinary Biosciences, College of Veterinary Medicine, Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Yasuko Rikihisa
- Laboratory of Molecular, Cellular, and Environmental Rickettsiology, Department of Veterinary Biosciences, College of Veterinary Medicine, Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Shahid Karim
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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Eirin A, Siddiqi S, Hughes AG, Jiang Y, Zhu XY, Kazeminia S, Lu B, Xing L, Lu B, Tang H, Xue A, Lerman A, Textor SC, Lerman LO. Renovascular Disease and Mitochondrial Dysfunction in Human Mesenchymal Stem Cells. J Am Soc Nephrol 2024:00001751-990000000-00370. [PMID: 39012704 DOI: 10.1681/asn.0000000000000440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Key Points
Renovascular disease impairs the capacity of human adipose tissue–derived mesenchymal stem/stromal cells to repair ischemic murine kidneys.miR-378h modulated the capacity of renovascular disease adipose tissue–derived mesenchymal stem/stromal cells to repair ischemic kidneys in vivo.
Background
Renovascular disease leads to renal ischemia, hypertension, and eventual kidney failure. Autologous transplantation of adipose tissue–derived mesenchymal stem/stromal cells (MSCs) improves perfusion and oxygenation in stenotic human kidneys, but associated atherosclerosis and hypertension might blunt their effectiveness. We hypothesized that renovascular disease alters the human MSC transcriptome and impairs their reparative potency.
Methods
MSCs were harvested from subcutaneous abdominal fat of patients with renovascular disease and healthy volunteers (n=3 each), characterized and subsequently injected (5×105/200 μl) into mice 2 weeks after renal artery stenosis or sham surgery (n=6/group). Two weeks later, mice underwent imaging and tissue studies. MSCs from healthy volunteers and in those with renovascular disease were also characterized by mRNA/microRNA (miRNA) sequencing. Based on these, MSC proliferation and mitochondrial damage were assessed in vitro before and after miRNA modulation and in vivo in additional renal artery stenosis mice administered with MSCs from renovascular disease pretreated with miR-378h mimic (n=5) or inhibitor (n=4).
Results
MSCs engrafted in stenotic mouse kidneys. Healthy volunteer MSCs (but not renovascular disease MSCs) decreased BP, improved serum creatinine levels and stenotic-kidney cortical perfusion and oxygenation, and attenuated peritubular capillary loss, tubular injury, and fibrosis. Genes upregulated in renovascular disease MSCs versus healthy volunteer MSCs were mostly implicated in transcription and cell proliferation, whereas those downregulated encoded mainly mitochondrial proteins. Upregulated miRNAs, including miR-378h, primarily target nuclear-encoded mitochondrial genes, whereas downregulated miRNAs mainly target genes implicated in transcription and cell proliferation. MSC proliferation was similar, but their mitochondrial structure and reparative function both in vivo and in vitro improved after miR-378h inhibition.
Conclusions
Renovascular disease impaired the reparative capacity of human MSCs, possibly by dysregulating miR-378h that targets mitochondrial genes.
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
| | - Sarosh Siddiqi
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Autumn G Hughes
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Yamei Jiang
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Sara Kazeminia
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Bo Lu
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Li Xing
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Brandon Lu
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hui Tang
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ailing Xue
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amir Lerman
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
| | - Stephen C Textor
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
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Ding W, Gong W, Liu H, Hu H, Shi L, Ren X, Cao Y, Zhang A, Shi X, Li Z, Bou T, Dugarjaviin M, Bai D. Changes of mRNA, miRNA and lncRNA expression contributing to skeletal muscle differences between fetus and adult Mongolian horses. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101294. [PMID: 39180870 DOI: 10.1016/j.cbd.2024.101294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/27/2024]
Abstract
The growth and development of myofibers, as the fundamental units comprising muscle tissue, and their composition type are indeed among the most crucial factors influencing skeletal muscle types. Muscle fiber adaptation is closely associated with alterations in physiological conditions. Muscle fiber types undergo dynamic changes in fetus and adult horses. Our aim is to investigate the mechanisms influencing the differences in muscle fiber types between fetal and adult stages of Mongolian horses. The study investigated the distribution of muscle fiber types within longissimus dorsi muscle of fetus and adult Mongolian horses. A total of 652 differentially expressed genes (DEGs), 476 Differentially expressed lncRNAs (DELs), and 174 Differentially expressed miRNAs (DEMIRs) were identified using deep RNA-seq analysis. The results of functional analysis reveal the transformations in muscle fiber type from the fetal to adult stage in Mongolian horses. The up-regulated DEGs were implicated in the development and differentiation of muscle fibers, while down-regulated DEGs were associated with muscle fiber contraction, transformation, and metabolism. Additionally, connections between non-coding RNA and mRNA landscapes were identified based on their functional alterations, some non-coding RNA target genes may be associated with immunity. These data have broadened our understanding of the specific roles and interrelationships among regulatory molecules involved in Mongolian horse development, this provides new perspectives for selecting and breeding superior individuals and for disease prevention.
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Affiliation(s)
- Wenqi Ding
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wendian Gong
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Huiying Liu
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hanwen Hu
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lin Shi
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiujuan Ren
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuying Cao
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Aaron Zhang
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiaoyuan Shi
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zheng Li
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Tugeqin Bou
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Manglai Dugarjaviin
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Dongyi Bai
- Key Laboratory of Equus Germplasm Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
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Lenart M, Siemińska I, Szatanek R, Mordel A, Szczepanik A, Rubinkiewicz M, Siedlar M, Baj-Krzyworzeka M. Identification of miRNAs Present in Cell- and Plasma-Derived Extracellular Vesicles-Possible Biomarkers of Colorectal Cancer. Cancers (Basel) 2024; 16:2464. [PMID: 39001526 PMCID: PMC11240749 DOI: 10.3390/cancers16132464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Globally, an increasing prevalence of colorectal cancer (CRC) prompts a need for the development of new methods for early tumor detection. MicroRNAs (also referred to as miRNAs) are short non-coding RNA molecules that play a pivotal role in the regulation of gene expression. MiRNAs are effectively transferred to extracellular vesicle (EVs) membrane sacs commonly released by cells. Our study aimed to examine the expression of miRNAs in four CRC cell lines and EVs derived from them (tumor EVs) in comparison to the normal colon epithelium cell line and its EVs. EVs were isolated by ultracentrifugation from the culture supernatant of SW480, SW620, SW1116, HCT116 and normal CCD841CoN cell lines and characterized according to the MISEV2023 guidelines. MiRNAs were analyzed by small RNA sequencing and validated by quantitative PCR. The performed analysis revealed 22 common miRNAs highly expressed in CRC cell lines and effectively transferred to tumor EVs, including miR-9-5p, miR-182-5p, miR-196b-5p, miR-200b-5p, miR-200c-3p, miR-425-5p and miR-429, which are associated with development, proliferation, invasion and migration of colorectal cancer cells, as well as in vesicle maturation and transport-associated pathways. In parallel, normal cells expressed miRNAs, such as miR-369 and miR-143, which play a role in proinflammatory response and tumor suppression. The analysis of selected miRNAs in plasma-derived EVs and tumor samples from CRC patients showed the similarity of miRNA expression profile between the patients' samples and CRC cell lines. Moreover, miR-182-5p, miR-196-5p, miR-425-5p and miR-429 were detected in several EV samples isolated from patients' plasma. Our results suggest that miR-182-5p, miR-196b-5p and miR-429 are differentially expressed between EVs from CRC patients and healthy donors, which might have clinical implications.
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Affiliation(s)
- Marzena Lenart
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
| | - Izabela Siemińska
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
- Institute of Veterinary Sciences, University Center of Veterinary Medicine JU-AU, University of Agriculture in Krakow, 30-059 Krakow, Poland
| | - Rafał Szatanek
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
| | - Anna Mordel
- Department of Clinical Immunology, University Children's Hospital of Cracow, 30-663 Krakow, Poland
| | - Antoni Szczepanik
- Third Department of Surgery, Faculty of Medicine, Jagiellonian University Medical College, 31-202 Krakow, Poland
| | - Mateusz Rubinkiewicz
- Second Department of Surgery, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
| | - Monika Baj-Krzyworzeka
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
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Ramos YFM, Rice SJ, Ali SA, Pastrello C, Jurisica I, Rai MF, Collins KH, Lang A, Maerz T, Geurts J, Ruiz-Romero C, June RK, Thomas Appleton C, Rockel JS, Kapoor M. Evolution and advancements in genomics and epigenomics in OA research: How far we have come. Osteoarthritis Cartilage 2024; 32:858-868. [PMID: 38428513 DOI: 10.1016/j.joca.2024.02.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most prevalent musculoskeletal disease affecting articulating joint tissues, resulting in local and systemic changes that contribute to increased pain and reduced function. Diverse technological advancements have culminated in the advent of high throughput "omic" technologies, enabling identification of comprehensive changes in molecular mediators associated with the disease. Amongst these technologies, genomics and epigenomics - including methylomics and miRNomics, have emerged as important tools to aid our biological understanding of disease. DESIGN In this narrative review, we selected articles discussing advancements and applications of these technologies to OA biology and pathology. We discuss how genomics, deoxyribonucleic acid (DNA) methylomics, and miRNomics have uncovered disease-related molecular markers in the local and systemic tissues or fluids of OA patients. RESULTS Genomics investigations into the genetic links of OA, including using genome-wide association studies, have evolved to identify 100+ genetic susceptibility markers of OA. Epigenomic investigations of gene methylation status have identified the importance of methylation to OA-related catabolic gene expression. Furthermore, miRNomic studies have identified key microRNA signatures in various tissues and fluids related to OA disease. CONCLUSIONS Sharing of standardized, well-annotated omic datasets in curated repositories will be key to enhancing statistical power to detect smaller and targetable changes in the biological signatures underlying OA pathogenesis. Additionally, continued technological developments and analysis methods, including using computational molecular and regulatory networks, are likely to facilitate improved detection of disease-relevant targets, in-turn, supporting precision medicine approaches and new treatment strategies for OA.
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Affiliation(s)
- Yolande F M Ramos
- Dept. Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Sarah J Rice
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shabana Amanda Ali
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad Farooq Rai
- Department of Biological Sciences, Center for Biotechnology, College of Medicine & Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Kelsey H Collins
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Annemarie Lang
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jeroen Geurts
- Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR), Unidad de Proteómica, INIBIC -Hospital Universitario A Coruña, SERGAS, A Coruña, Spain
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, USA
| | - C Thomas Appleton
- Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jason S Rockel
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.
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Cao M, Xiong L, Wang X, Guo S, Hu L, Kang Y, Wu X, Bao P, Chu M, Liang C, Pei J, Guo X. Comprehensive analysis of differentially expressed mRNAs, circRNAs, and miRNAs and their ceRNA network in the testis of cattle-yak, yak, and cattle. Genomics 2024; 116:110872. [PMID: 38849017 DOI: 10.1016/j.ygeno.2024.110872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Cattle-yak is a hybrid offspring resulting from the crossbreeding of yak and cattle, and it exhibits substantial heterosis in production performance. However, male sterility in cattle-yak remains a concern. Reports suggest that noncoding RNAs are involved in the regulation of spermatogenesis. Therefore, in this study, we comprehensively compared testicular transcription profiles among cattle, yak, and cattle-yak. Numerous differentially expressed genes (DEGs), differentially expressed circRNAs (DECs), and differentially expressed miRNAs (DEMs) were identified in the intersection of two comparison groups, namely cattle versus cattle-yak and yak versus cattle-yak, with the number of DEGs, DECs, and DEMs being 4968, 360, and 59, respectively. The DEGs in cattle-yaks, cattle, and yaks were mainly associated with spermatogenesis, male gamete generation, and sexual reproduction. Concurrently, GO and KEGG analyses indicated that DEC host genes and DEM source genes were involved in the regulation of spermatogenesis. The construction of a potential competing endogenous RNA network revealed that some differentially expressed noncoding RNAs may be involved in regulating the expression of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, and miR-15b, as well as previously unreported miR-6123 and miR-1306, along with various miRNA-circRNA interaction pairs. This study serves as a valuable reference for further investigations into the mechanisms underlying male sterility in cattle-yaks.
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Affiliation(s)
- Mengli Cao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Liyan Hu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyu Wu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
| | - Xian Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
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Zhang J, Zhao C, Yao M, Qi J, Tan Y, Shi K, Wang J, Zhou S, Li Z. Transcriptome sequencing reveals non-coding RNAs respond to porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in Kele piglets. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:663-681. [PMID: 39165737 PMCID: PMC11331363 DOI: 10.5187/jast.2023.e46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 08/22/2024]
Abstract
Co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and Haemophilus parasuis (HPS) has severely restricted the healthy development of pig breeding. Exploring disease resistance of non-coding RNAs in pigs co-infected with PRRSV and HPS is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in Kele piglets and to innovate the use of local pig germplasm resources in China. RNA-seq of lungs from Kele piglets with single-infection of PRRSV or HPS and co-infection of both pathogens was performed. Two hundred and twenty-five differentially expressed long non-coding RNAs (DElncRNAs) and 30 DEmicroRNAs (DEmiRNAs) were identified and characterized in the PRRSV and HPS co-infection (PRRSV-HPS) group. Compared with the single-infection groups, 146 unique DElncRNAs, 17 unique DEmiRNAs, and 206 target differentially expressed genes (DEGs) were identified in the PRRSV-HPS group. The expression patterns of 20 DEmiRNAs and DElncRNAs confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) were consistent with those determined by high-throughput sequencing. In the PRRSV-HPS group, the target DEGs were enriched in eight immune Gene Ontology terms relating to two unique DEmiRNAs and 16 DElncRNAs, and the unique target DEGs participated the host immune response to pathogens infection by affecting 15 immune-related Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Notably, competitive endogenous RNA (ceRNA) networks of different groups were constructed, and the ssc-miR-671-5p miRNA was validated as a potential regulatory factor to regulate DTX4 and AEBP1 genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. These results provided insight into further study on the molecular mechanisms of resistance to PRRSV and HPS co-infection in Kele piglets.
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Affiliation(s)
- Jing Zhang
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Chunping Zhao
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Min Yao
- Inspection and Testing Department, Guizhou
Testing Center for Livestock and Poultry Germplasm, Guiyang
550002, China
| | - Jing Qi
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Ya Tan
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Kaizhi Shi
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Jing Wang
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Sixuan Zhou
- Institute of Animal Husbandry and
Veterinary Science, Guizhou Academy of Agricultural Sciences,
Guiyang 550002, China
| | - Zhixin Li
- College of Animal Science, Guizhou
University, Guiyang 550002, China
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Liu L, Gao L, Zhou K, Li Q, Xu H, Feng X, Wang L, Song L. The expression patterns of exosomal miRNAs in the Pacific oyster after high-temperature stress or Vibrio stimulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 156:105174. [PMID: 38548001 DOI: 10.1016/j.dci.2024.105174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
The exosomal miRNA plays a crucial role in the intercellular communication response to environmental stress and pathogenic stimulation. In the present study, the expression of exosomal miRNAs in the Pacific oyster Crassostrea gigas after high-temperature stress or Vibrio splendidus stimulation was investigated through high-throughput sequencing. The exosomes were identified to be teardrop-like vesicles with the average size of 81.7 nm by transmission electron microscopy. There were 66 known miRNAs and 33 novel miRNAs identified, of which 10 miRNAs were differentially expressed after both high-temperature stress and Vibrio stimulation compared to the control group. A total of 1868 genes were predicted as the putative targets of miRNAs, of which threonine aspartase 1-like was targeted by the highest number of related miRNAs. The robustness and reliability of miRNA expression from the sRNA sequencing data were verified by employing eight miRNAs for qPCR. GO and KEGG clustering analyses revealed that apoptosis was significantly enriched by the target genes of differentially expressed exosomal miRNAs after high-temperature stress, and autophagy and cytokine activity were significantly enriched after Vibrio stimulation. Energy metabolism was found to be significantly shared in the target gene enrichments after both high-temperature stress and Vibrio stimulation. These findings would improve our understanding of the regulatory mechanisms of exosomal miRNAs in C. gigas after high-temperature stress or Vibrio stimulation.
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Affiliation(s)
- Lu Liu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lei Gao
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Keli Zhou
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Qingsong Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Hairu Xu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Xingyi Feng
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
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Chen Q, Zhang Y, Rong J, Chen C, Wang S, Wang J, Li Z, Hou Z, Liu D, Tao J, Xu J. MicroRNA expression profile of chicken liver at different times after Histomonas meleagridis infection. Vet Parasitol 2024; 329:110200. [PMID: 38744230 DOI: 10.1016/j.vetpar.2024.110200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Histomonas meleagridis, an anaerobic intercellular parasite, is known to infect gallinaceous birds, particularly turkeys and chickens. The resurgence of histomonosis in recent times has resulted in significant financial setbacks due to the prohibition of drugs used for disease treatment. Currently, research on about H. meleagridis primarily concentrate on the examination of its virulence, gene expression analysis, and the innate immunity response of the host organism. However, there is a lack of research on differentially expressed miRNAs (DEMs) related to liver infection induced by H. meleagridis. In this study, the weight gain and pathological changes at various post-infection time points were evaluated through animal experiments to determine the peak and early stages of infection. Next, High-throughput sequencing was used to examine the expression profile of liver miRNA at 10 and 15 days post-infection (DPI) in chickens infected with the Chinese JSYZ-F strain of H. meleagridis. A comparison with uninfected controls revealed the presence of 120 and 118 DEMs in the liver of infected chickens at 10 DPI and 15 DPI, respectively, with 74 DEMs being shared between the two time points. Differentially expressed microRNAs (DEMs) were categorized into three groups based on the time post-infection. The first group (L1) includes 45 miRNAs that were differentially expressed only at 10 DPI and were predicted to target 1646 genes. The second group (L2) includes 43 miRNAs that were differentially expressed only at 15 DPI and were predicted to target 2257 genes. The third group (L3) includes 75 miRNAs that were differentially expressed at both 10 DPI and 15 DPI and were predicted to target 1623 genes. At L1, L2, and L3, there were 89, 87, and 41 significantly enriched Gene Ontology (GO) terms, respectively (p<0.05). The analysis of differentially expressed miRNA target genes using KEGG pathways revealed significant enrichment at L1, L2, and L3, with 3, 4, and 5 pathways identified, respectively (p<0.05). This article suggests that the expression of liver miRNA undergoes dynamic alterations due to H. meleagridis and the host. It showed that the expression pattern of L1 class DEMs was more conducive to regulating the development of the inflammatory response, while the L2 class DEMs were more conducive to augmenting the inflammatory response. The observed patterns of miRNA expression associated with inflammation were in line with the liver's inflammatory process following infection. The results of this study provide a basis for conducting a comprehensive analysis of the pathogenic mechanism of H. meleagridis from the perspective of host miRNAs.
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Affiliation(s)
- Qiaoguang Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yuming Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Animal Husbandry and Veterinary Station of Daxindian, Penglai District, Yantai 265600, China
| | - Jie Rong
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Chen Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Shuang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jiege Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zaifan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhaofeng Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Dandan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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Hu L, Zheng X, Zhou M, Wang J, Tong L, Dong M, Xu T, Li Z. Optimized AF4 combined with density cushion ultracentrifugation enables profiling of high-purity human blood extracellular vesicles. J Extracell Vesicles 2024; 13:e12470. [PMID: 39001700 PMCID: PMC11245685 DOI: 10.1002/jev2.12470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/11/2024] [Indexed: 07/15/2024] Open
Abstract
Extracellular vesicles (EVs) have emerged as a promising tool for clinical liquid biopsy. However, the identification of EVs derived from blood samples is hindered by the presence of abundant plasma proteins, which impairs the downstream biochemical analysis of EV-associated proteins and nucleic acids. Here, we employed optimized asymmetric flow field-flow fractionation (AF4) combined with density cushion ultracentrifugation (UC) to obtain high-purity and intact EVs with very low lipoprotein contamination from human plasma and serum. Further proteomic analysis revealed more than 1000 EV-associated proteins, a large proportion of which has not been previously reported. Specifically, we found that cell-line-derived EV markers are incompatible with the identification of plasma-EVs and proposed that the proteins MYCT1, TSPAN14, MPIG6B and MYADM, as well as the traditional EV markers CD63 and CD147, are plasma-EV markers. Benefiting from the high-purity of EVs, we conducted comprehensive miRNA profiling of plasma EVs and nanosized particles (NPs), as well as compared plasma- and serum-derived EVs, which provides a valuable resource for the EV research community. Overall, our findings provide a comprehensive assessment of human blood EVs as a basis for clinical biopsy applications.
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Affiliation(s)
- Liqiao Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Guangzhou National LaboratoryGuangzhouChina
| | - Xinyue Zheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Maoge Zhou
- Guangzhou National LaboratoryGuangzhouChina
| | - Jifeng Wang
- Laboratory of Proteomics, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Lingjun Tong
- Jinan Central Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Ming Dong
- Guangzhou National LaboratoryGuangzhouChina
| | - Tao Xu
- Guangzhou National LaboratoryGuangzhouChina
- Jinan Central Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of SciencesBeijingChina
- School of Biomedical EngineeringGuangzhou Medical UniversityGuangzhouChina
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Gravina T, Favero F, Rosano S, Parab S, Diaz Alcalde A, Bussolino F, Doronzo G, Corà D. Integrative Bioinformatics Analysis Reveals a Transcription Factor EB-Driven MicroRNA Regulatory Network in Endothelial Cells. Int J Mol Sci 2024; 25:7123. [PMID: 39000232 PMCID: PMC11241138 DOI: 10.3390/ijms25137123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Various human diseases are triggered by molecular alterations influencing the fine-tuned expression and activity of transcription factors, usually due to imbalances in targets including protein-coding genes and non-coding RNAs, such as microRNAs (miRNAs). The transcription factor EB (TFEB) modulates human cellular networks, overseeing lysosomal biogenesis and function, plasma-membrane trafficking, autophagic flux, and cell cycle progression. In endothelial cells (ECs), TFEB is essential for the maintenance of endothelial integrity and function, ensuring vascular health. However, the comprehensive regulatory network orchestrated by TFEB remains poorly understood. Here, we provide novel mechanistic insights into how TFEB regulates the transcriptional landscape in primary human umbilical vein ECs (HUVECs), using an integrated approach combining high-throughput experimental data with dedicated bioinformatics analysis. By analyzing HUVECs ectopically expressing TFEB using ChIP-seq and examining both polyadenylated mRNA and small RNA sequencing data from TFEB-silenced HUVECs, we have developed a bioinformatics pipeline mapping the different gene regulatory interactions driven by TFEB. We show that TFEB directly regulates multiple miRNAs, which in turn post-transcriptionally modulate a broad network of target genes, significantly expanding the repertoire of gene programs influenced by this transcription factor. These insights may have significant implications for vascular biology and the development of novel therapeutics for vascular disease.
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Affiliation(s)
- Teresa Gravina
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Francesco Favero
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Stefania Rosano
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Sushant Parab
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Alejandra Diaz Alcalde
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
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