201
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Du YW, Liu L, Feng NJ, Zheng DF, Liu ML, Zhou H, Deng P, Wang YX, Zhao HM. Combined transcriptomic and metabolomic analysis of alginate oligosaccharides alleviating salt stress in rice seedlings. BMC PLANT BIOLOGY 2023; 23:455. [PMID: 37770835 PMCID: PMC10540332 DOI: 10.1186/s12870-023-04470-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Salt stress is one of the key factors limiting rice production. Alginate oligosaccharides (AOS) enhance plant stress resistance. However, the molecular mechanism underlying salt tolerance in rice induced by AOS remains unclear. FL478, which is a salt-tolerant indica recombinant inbred line and IR29, a salt-sensitive rice cultivar, were used to comprehensively analyze the effects of AOS sprayed on leaves in terms of transcriptomic and metabolite profiles of rice seedlings under salt stress. RESULTS In this experiment, exogenous application of AOS increased SOD, CAT and APX activities, as well as GSH and ASA levels to reduce the damage to leaf membrane, increased rice stem diameter, the number of root tips, aboveground and subterranean biomass, and improved rice salt tolerance. Comparative transcriptomic analyses showed that the regulation of AOS combined with salt treatment induced the differential expression of 305 and 1030 genes in FL478 and IR29. The expressed genes enriched in KEGG pathway analysis were associated with antioxidant levels, photosynthesis, cell wall synthesis, and signal transduction. The genes associated with light-trapping proteins and RLCK receptor cytoplasmic kinases, including CBA, LHCB, and Lhcp genes, were fregulated in response to salt stress. Treatment with AOS combined with salt induced the differential expression of 22 and 50 metabolites in FL478 and IR29. These metabolites were mainly related to the metabolism of amino and nucleotide sugars, tryptophan, histidine, and β -alanine. The abundance of metabolites associated with antioxidant activity, such as 6-hydroxymelatonin, wedelolactone and L-histidine increased significantly. Combined transcriptomic and metabolomic analyses revealed that dehydroascorbic acid in the glutathione and ascorbic acid cycles plays a vital role in salt tolerance mediated by AOS. CONCLUSION AOS activate signal transduction, regulate photosynthesis, cell wall formation, and multiple antioxidant pathways in response to salt stress. This study provides a molecular basis for the alleviation of salt stress-induced damage by AOS in rice.
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Affiliation(s)
- You-Wei Du
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
| | - Ling Liu
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
| | - Nai-Jie Feng
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China.
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.
| | - Dian-Feng Zheng
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China.
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.
| | - Mei-Ling Liu
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
| | - Hang Zhou
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
| | - Peng Deng
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
| | - Ya-Xing Wang
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
| | - Hui-Min Zhao
- College of Coastal Agriculture Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- South China Center of National Saline-tolerant Rice Technology Innovation Center, Zhanjiang, 524088, China
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202
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Huang H, Wang C, Pei S, Wang Y. A chromosome-level reference genome of an aromatic medicinal plant Adenosma buchneroides. Sci Data 2023; 10:660. [PMID: 37770464 PMCID: PMC10539347 DOI: 10.1038/s41597-023-02571-8] [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: 06/09/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023] Open
Abstract
Adenosma buchneroides Bonati, belonging to the genus Adenosum (Plantaginaceae), is an aromatic medicinal plant and utilized in traditional Chinese medicine. It has been widely used as plant-based repellents to prevent vector-borne diseases. However, the lack of a reference genome limits the study of conservation management and molecular biology of A. buchneroides. Here, we generated a chromosome-level de novo genome assembly of A. buchneroides which is a high-quality chromosome-scale assembly of aromatic medicinal plant in Plantaginaceae. The genome has a total length of 442.84 Mb with scaffold N50 of 27.98 Mb and 95.55% of the genome assigned to 14 chromosomes. BUSCO assessment yielded a completeness score of 97.2%. Furthermore, we predicted 24,367 protein-coding genes, and 95.79% of them was functionally annotated. The chromosome-scale genome of A. buchneroides will be a significant resource for understanding the genetic basis and evolution of active components biosynthesis, which will facilitate further study and exploit of A. buchneroides.
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Affiliation(s)
- Hui Huang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Chen Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shengji Pei
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yuhua Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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203
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Yao H, Zhou Y, Li T, Li Y, Li F, Zhang G, Fu X, Kang Y, Wu Q. Bioinformatic identification and experiment validation revealed that ACTG1 is a promising prognostic signature and therapeutic target for sepsis. J Leukoc Biol 2023; 114:325-334. [PMID: 37368839 DOI: 10.1093/jleuko/qiad072] [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: 12/16/2022] [Revised: 05/24/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
In the intensive care unit, sepsis is a prevalent clinical syndrome (i.e. the final pathway to death from most infections). Peripheral blood gene expression profiling is becoming more and more accepted as a potential diagnostic or prognostic tool. This work aimed to recognize genes related to sepsis, providing potential translational therapeutic targets. RNA sequencing was performed on peripheral blood mononuclear cells from 20 healthy control subjects and 51 sepsis patients. Weighted gene coexpression network analysis was employed to pick out sepsis-related and immunocyte-related gene modules. Genes in the yellow module are primarily involved in excessive inflammation and immune suppression. STRING and Cytoscape were combined to identify ACTG1 and IQGAP1 as hub genes with highest connective degree, and prognostic predication value of ACTG1 was confirmed. Both univariate and multivariate logistic regression analyses were carried out. ACTG1 messenger RNA expression was increased in animal and in cell-related sepsis models. Small interfering RNA revealed decreasing ACTG1 can reduce the in vitro sepsis model apoptosis. We have authenticated ACTG1 as a reliable signature of a poor outcome of sepsis and promising therapeutic targets for sepsis.
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Affiliation(s)
- Hua Yao
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yue Zhou
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Tingting Li
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yao Li
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Fan Li
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Geng Zhang
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Xin Fu
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yan Kang
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Qin Wu
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
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204
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Huang P, Li C, Lin F, Liu Y, Zong Y, Li B, Zheng Y. Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species ( Dalbergia cultrata Pierre Graham ex Benth) provide insights into its evolutionary and cold stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1212967. [PMID: 37810393 PMCID: PMC10552272 DOI: 10.3389/fpls.2023.1212967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/28/2023] [Indexed: 10/10/2023]
Abstract
Dalbergia cultrata Pierre Graham ex Benth (D. cultrata) is a precious rosewood tree species that grows in the tropical and subtropical regions of Asia. In this study, we used PacBio long-reading sequencing technology and Hi-C assistance to sequence and assemble the reference genome of D. cultrata. We generated 171.47 Gb PacBio long reads and 72.43 Gb Hi-C data and yielded an assembly of 10 pseudochromosomes with a total size of 690.99 Mb and Scaffold N50 of 65.76 Mb. The analysis of specific genes revealed that the triterpenoids represented by lupeol may play an important role in D. cultrata's potential medicinal value. Using the new reference genome, we analyzed the resequencing of 19 Dalbergia accessions and found that D. cultrata and D. cochinchinensis have the latest genetic relationship. Transcriptome sequencing of D. cultrata leaves grown under cold stress revealed that MYB transcription factor and E3 ubiquitin ligase may be playing an important role in the cold response of D. cultrata. Genome resources and identified genetic variation, especially those genes related to the biosynthesis of phytochemicals and cold stress response, will be helpful for the introduction, domestication, utilization, and further breeding of Dalbergia species.
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Affiliation(s)
- Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, China
| | - Yichen Zong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Laboratory of Forest Silviculture and Tree Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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205
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Lim HGM, Fann YC, Lee YCG. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2. Brief Bioinform 2023; 24:bbad280. [PMID: 37738400 PMCID: PMC10516370 DOI: 10.1093/bib/bbad280] [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: 12/30/2022] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 09/24/2023] Open
Abstract
Implementing a specific cloud resource to analyze extensive genomic data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a challenge when resources are limited. To overcome this, we repurposed a cloud platform initially designed for use in research on cancer genomics (https://cgc.sbgenomics.com) to enable its use in research on SARS-CoV-2 to build Cloud Workflow for Viral and Variant Identification (COWID). COWID is a workflow based on the Common Workflow Language that realizes the full potential of sequencing technology for use in reliable SARS-CoV-2 identification and leverages cloud computing to achieve efficient parallelization. COWID outperformed other contemporary methods for identification by offering scalable identification and reliable variant findings with no false-positive results. COWID typically processed each sample of raw sequencing data within 5 min at a cost of only US$0.01. The COWID source code is publicly available (https://github.com/hendrick0403/COWID) and can be accessed on any computer with Internet access. COWID is designed to be user-friendly; it can be implemented without prior programming knowledge. Therefore, COWID is a time-efficient tool that can be used during a pandemic.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
- Department of Medical Research, Tzu Chi Hospital Indonesia, Pantai Indah Kapuk, Greater Jakarta, Indonesia 14470
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
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206
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Wang L, Zhang Z, Han P, Liang Y, Zhang H, Fu Z, Zhao S, E Y, Zhang H, Wu X, Zhang B, Chang Y, Tang K, Zheng W, Chen L, Wang R, Gao W, Hasi A, Li X, Bai C. Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines. Sci Rep 2023; 13:15422. [PMID: 37723186 PMCID: PMC10507079 DOI: 10.1038/s41598-023-42182-2] [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: 04/27/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Due to the relatively brief domestication history of sugar beet (Beta vulgaris ssp. vulgaris), our understanding of the genomic diversity and functional genes in its cultivars is limited, resulting in slow breeding progress. To address this issue, a total of 306 germplasm materials of major cultivars and breeding lines from China, the USA, and Europe were selected for genome resequencing. We investigated population structure and genetic diversity and performed selective scanning of genomic regions, identifying six novel genes associated with important agronomic traits: the candidate genes DFAX2 and P5CS for skin roughness; the candidate genes FRO5, GL24, and PPR91 for root yield and sugar yield, and the pleiotropic candidate gene POLX for flourishing growth vigour, plant height, crown size, flesh coarseness, and sugar yield. In addition, we constructed a protein-protein interaction network map and a phenotype-gene network map, which provide valuable information for identifying and characterizing functional genes affecting agronomic traits in sugar beet. Overall, our study sheds light on the future improvement of sugar beet agronomic traits at the molecular level.
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Affiliation(s)
- Liang Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ziqiang Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Pingan Han
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yahui Liang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Huizhong Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Zengjuan Fu
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Shangmin Zhao
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yuanyuan E
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hui Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Xinrong Wu
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Bizhou Zhang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yue Chang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Kuangang Tang
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenzhe Zheng
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Li Chen
- College of Modern Agriculture and Ecological Environment, Heilongjiang University, Heilongjiang, China
| | - Ronghua Wang
- Beet Breeding and Seed Processing Laboratory, Institute for Sugar Beet Research, Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Weishi Gao
- Research Industrial of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumuqi, China
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Xiaodong Li
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
| | - Chen Bai
- Key Laboratory of Sugar Beet Genetics and Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.
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207
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Wang Y, Drum DL, Sun R, Zhang Y, Chen F, Sun F, Dal E, Yu L, Jia J, Arya S, Jia L, Fan S, Isakoff SJ, Kehlmann AM, Dotti G, Liu F, Zheng H, Ferrone CR, Taghian AG, DeLeo AB, Ventin M, Cattaneo G, Li Y, Jounaidi Y, Huang P, Maccalli C, Zhang H, Wang C, Yang J, Boland GM, Sadreyev RI, Wong L, Ferrone S, Wang X. Stressed target cancer cells drive nongenetic reprogramming of CAR T cells and solid tumor microenvironment. Nat Commun 2023; 14:5727. [PMID: 37714830 PMCID: PMC10504259 DOI: 10.1038/s41467-023-41282-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
The poor efficacy of chimeric antigen receptor T-cell therapy (CAR T) for solid tumors is due to insufficient CAR T cell tumor infiltration, in vivo expansion, persistence, and effector function, as well as exhaustion, intrinsic target antigen heterogeneity or antigen loss of target cancer cells, and immunosuppressive tumor microenvironment (TME). Here we describe a broadly applicable nongenetic approach that simultaneously addresses the multiple challenges of CAR T as a therapy for solid tumors. The approach reprograms CAR T cells by exposing them to stressed target cancer cells which have been exposed to the cell stress inducer disulfiram (DSF) and copper (Cu)(DSF/Cu) plus ionizing irradiation (IR). The reprogrammed CAR T cells acquire early memory-like characteristics, potent cytotoxicity, enhanced in vivo expansion, persistence, and decreased exhaustion. Tumors stressed by DSF/Cu and IR also reprogram and reverse the immunosuppressive TME in humanized mice. The reprogrammed CAR T cells, derived from peripheral blood mononuclear cells of healthy donors or metastatic female breast cancer patients, induce robust, sustained memory and curative anti-solid tumor responses in multiple xenograft mouse models, establishing proof of concept for empowering CAR T by stressing tumor as a promising therapy for solid tumors.
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Affiliation(s)
- Yufeng Wang
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - David L Drum
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruochuan Sun
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Gastrointestinal Surgery and General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yida Zhang
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Chen
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Fengfei Sun
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emre Dal
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ling Yu
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jingyu Jia
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shahrzad Arya
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lin Jia
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Song Fan
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven J Isakoff
- Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Allison M Kehlmann
- Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gianpietro Dotti
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Fubao Liu
- Department of Hepatobiliary & Pancreatic Surgery and Liver Transplantation, Anhui Medical University, Hefei, Anhui, China
| | - Hui Zheng
- Biostatistics Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alphonse G Taghian
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Albert B DeLeo
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marco Ventin
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Giulia Cattaneo
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yongxiang Li
- Department of Gastrointestinal Surgery and General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Youssef Jounaidi
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Peigen Huang
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Hanyu Zhang
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cheng Wang
- Vincent Center for Reproductive Biology, Vincent Department of Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jibing Yang
- Center for Comparative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - LaiPing Wong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Soldano Ferrone
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Orthopaedics, Massachusetts General Hospital, Boston, MA, USA
| | - Xinhui Wang
- Division of Gastrointestinal and Oncologic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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208
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He K, Nie Z. System analysis based on the lysosome-related genes identifies HPS4 as a novel therapy target for liver hepatocellular carcinoma. Front Oncol 2023; 13:1221498. [PMID: 37781184 PMCID: PMC10535104 DOI: 10.3389/fonc.2023.1221498] [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: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Liver cancer is a leading cause of cancer-related deaths worldwide. Lysosomal dysfunction is implicated in cancer progression; however, prognostic prediction models based on lysosome-related genes (LRGs) are lacking in liver cancer. This study aimed to establish an LRG-based model to improve prognosis prediction and explore potential therapeutic targets in liver cancer. Methods Expression profiles of 61 LRGs were analyzed in The Cancer Genome Atlas liver cancer cohorts. There were 14 LRGs identified, and their association with clinical outcomes was evaluated. Unsupervised clustering, Cox regression, and functional assays were performed. Results Patients were classified into high-risk and low-risk subgroups based on the 14 LRGs. The high-risk group had significantly worse overall survival. Aberrant immune infiltration and checkpoint expression were observed in the high-risk group. Furthermore, HPS4 was identified as an independent prognostic indicator. Knockdown of HPS4 suppressed liver cancer cell proliferation and induced apoptosis. Conclusion This study developed an LRG-based prognostic model to improve risk stratification in liver cancer. The potential value of HPS4 as a therapeutic target and biomarker was demonstrated. Regulation of HPS4 may offer novel strategies for precision treatment in liver cancer patients.
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Affiliation(s)
- Ke‐Jie He
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Quzhou, Zhejiang, China
| | - Zhiqiang Nie
- Global Health Research Center, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
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209
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Yu C, Zhang M, Xiong Y, Wang Q, Wang Y, Wu S, Hussain S, Wang Y, Zhang Z, Rao N, Zhang S, Zhang X. Comparison of miRNA transcriptome of exosomes in three categories of somatic cells with derived iPSCs. Sci Data 2023; 10:616. [PMID: 37696871 PMCID: PMC10495316 DOI: 10.1038/s41597-023-02493-5] [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: 03/02/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023] Open
Abstract
Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) through epigenetic manipulation. While the essential role of miRNA in reprogramming and maintaining pluripotency is well studied, little is known about the functions of miRNA from exosomes in this context. To fill this research gap,we comprehensively obtained the 17 sets of cellular mRNA transcriptomic data with 3.93 × 1010 bp raw reads and 18 sets of exosomal miRNA transcriptomic data with 2.83 × 107 bp raw reads from three categories of human somatic cells: peripheral blood mononuclear cells (PBMCs), skin fibroblasts(SFs) and urine cells (UCs), along with their derived iPSCs. Additionally, differentially expressed molecules of each category were identified and used to perform gene set enrichment analysis. Our study provides sets of comparative transcriptomic data of cellular mRNA and exosomal miRNA from three categories of human tissue with three individual biological controls in studies of iPSCs generation, which will contribute to a better understanding of donor cell variation in functional epigenetic regulation and differentiation bias in iPSCs.
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Affiliation(s)
- Chunlai Yu
- University of Electronic Science and Technology of China, Chengdu, Sichuang, China
| | - Mei Zhang
- Binzhou Medical University, Yantai, Shandong, China
| | - Yucui Xiong
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qizheng Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuanhua Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Shaoling Wu
- Department of Rehabilitation Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Sajjad Hussain
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Zhizhong Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Nini Rao
- University of Electronic Science and Technology of China, Chengdu, Sichuang, China.
| | - Sheng Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
| | - Xiao Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China.
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210
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Liu W, Zhu P, Li M, Li Z, Yu Y, Liu G, Du J, Wang X, Yang J, Tian R, Seim I, Kaya A, Li M, Li M, Gladyshev VN, Zhou X. Large-scale across species transcriptomic analysis identifies genetic selection signatures associated with longevity in mammals. EMBO J 2023; 42:e112740. [PMID: 37427458 PMCID: PMC10476176 DOI: 10.15252/embj.2022112740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Lifespan varies significantly among mammals, with more than 100-fold difference between the shortest and longest living species. This natural difference may uncover the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and longevity, we conducted a comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species. We found that few genes exhibit common expression patterns with longevity in the three organs analyzed. However, pathways related to translation fidelity, such as nonsense-mediated decay and eukaryotic translation elongation, correlated with longevity across mammals. Analyses of selection pressure found that selection intensity related to the direction of longevity-correlated genes is inconsistent across organs. Furthermore, expression of methionine restriction-related genes correlated with longevity and was under strong selection in long-lived mammals, suggesting that a common strategy is utilized by natural selection and artificial intervention to control lifespan. Our results indicate that lifespan regulation via gene expression is driven through polygenic and indirect natural selection.
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Affiliation(s)
- Weiqiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zihao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- School of Life SciencesUniversity of Science and Technology of ChinaAnhuiChina
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ran Tian
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Inge Seim
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Alaattin Kaya
- Department of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityChengduChina
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
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211
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Wang XF, Zhang YX, Niu YQ, Sha Y, Wang ZH, Zhang ZB, Yang J, Liu B, Li LF. Post-hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*-genome diploid species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1500-1513. [PMID: 37313760 DOI: 10.1111/tpj.16334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023]
Abstract
Understanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A-, B- and D-lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S-genome species (Aegilops speltoides) of the B-lineage and four S*-genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D-lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A-, B- and D-lineage species. Our estimates identified frequent genetic introgressions from A- and B-lineages to the D-lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A- and B-lineages along all the seven chromosomes to the extant D-lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B-lineage) and the other four S*-genome diploid species (D-lineage), while natural selection is a potential contributor to divergence among the four S*-genome species at telomeric regions. Our study provides a genome-wide view on how genetic introgression and natural selection acted together yet chromosome-regionally divided to promote genomic divergence among the five S- and S*-genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.
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Affiliation(s)
- Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, 130118, China
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
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212
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Chen K, Chen X, Lang C, Yuan X, Huang J, Li Z, Xu M, Wu K, Zhou C, Li Q, Zhu C, Liu L, Shang X. CircFam190a: a critical positive regulator of osteoclast differentiation via enhancement of the AKT1/HSP90β complex. Exp Mol Med 2023; 55:2051-2066. [PMID: 37653038 PMCID: PMC10545668 DOI: 10.1038/s12276-023-01085-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 09/02/2023] Open
Abstract
The identification of key regulatory factors that control osteoclastogenesis is important. Accumulating evidence indicates that circular RNAs (circRNAs) are discrete functional entities. However, the complexities of circRNA expression as well as the extent of their regulatory functions during osteoclastogenesis have yet to be revealed. Here, based on circular RNA sequencing data, we identified a circular RNA, circFam190a, as a critical regulator of osteoclast differentiation and function. During osteoclastogenesis, circFam190a is significantly upregulated. In vitro, circFam190a enhanced osteoclast formation and function. In vivo, overexpression of circFam190a induced significant bone loss, while knockdown of circFam190a prevented pathological bone loss in an ovariectomized (OVX) mouse osteoporosis model. Mechanistically, our data suggest that circFam90a enhances the binding of AKT1 and HSP90β, promoting AKT1 stability. Altogether, our findings highlight the critical role of circFam190a as a positive regulator of osteoclastogenesis, and targeting circFam190a might be a promising therapeutic strategy for treating pathological bone loss.
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Affiliation(s)
- Kun Chen
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Xi Chen
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Chuandong Lang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Xingshi Yuan
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Junming Huang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, 330000, Nanchang, Jiangxi, China
| | - Zhi Li
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Mingyou Xu
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Kerong Wu
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China
| | - Chenhe Zhou
- Department of Orthopedic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China
| | - Qidong Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China.
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, 230001, Hefei, Anhui, China.
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, 230001, Hefei, Anhui, China.
| | - Chen Zhu
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China.
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China.
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, 230001, Hefei, Anhui, China.
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, 230001, Hefei, Anhui, China.
| | - Xifu Shang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, China.
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213
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Yu P, Qu N, Zhu R, Hu J, Han P, Wu J, Tan L, Gan H, He C, Fang C, Lei Y, Li J, He C, Lan F, Shi X, Wei W, Wang Y, Ji Q, Yu FX, Wang YL. TERT accelerates BRAF mutant-induced thyroid cancer dedifferentiation and progression by regulating ribosome biogenesis. SCIENCE ADVANCES 2023; 9:eadg7125. [PMID: 37647391 PMCID: PMC10468137 DOI: 10.1126/sciadv.adg7125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023]
Abstract
TERT reactivation occurs frequently in human malignancies, especially advanced cancers. However, in vivo functions of TERT reactivation in cancer progression and the underlying mechanism are not fully understood. In this study, we expressed TERT and/or active BRAF (BRAF V600E) specifically in mouse thyroid epithelium. While BRAF V600E alone induced papillary thyroid cancer (PTC), coexpression of BRAF V600E and TERT resulted in poorly differentiated thyroid carcinoma (PDTC). Spatial transcriptome analysis revealed that tumors from mice coexpressing BRAF V600E and TERT were highly heterogeneous, and cell dedifferentiation was positively correlated with ribosomal biogenesis. Mechanistically, TERT boosted ribosomal RNA (rRNA) expression and protein synthesis by interacting with multiple proteins involved in ribosomal biogenesis. Furthermore, we found that CX-5461, an rRNA transcription inhibitor, effectively blocked proliferation and induced redifferentiation of thyroid cancer. Thus, TERT promotes thyroid cancer progression by inducing cancer cell dedifferentiation, and ribosome inhibition represents a potential strategy to treat TERT-reactivated cancers.
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Affiliation(s)
- Pengcheng Yu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Zhu
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqian Hu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peizhen Han
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiahao Wu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Licheng Tan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hualei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Cong He
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuantao Fang
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yubin Lei
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenxi He
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Lan
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjun Wei
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fa-Xing Yu
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Long Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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214
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Li H, Yuan L, Wang P, Sheng Y, Fu Z, Peng H. Clonal architecture and single-cell transcriptome landscape in Richter's syndrome. Br J Haematol 2023; 202:1055-1060. [PMID: 37401149 DOI: 10.1111/bjh.18952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Affiliation(s)
- Heng Li
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Lingli Yuan
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Peilong Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yue Sheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Zheng Fu
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
- MegaRobo Technologies Co., Ltd, Suzhou, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
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215
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Wang X, Li J, Han L, Liang C, Li J, Shang X, Miao X, Luo Z, Zhu W, Li Z, Li T, Qi Y, Li H, Lu X, Li L. QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize. Nat Commun 2023; 14:5232. [PMID: 37633966 PMCID: PMC10460418 DOI: 10.1038/s41467-023-41022-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
Genetic dissection of agronomic traits is important for crop improvement and global food security. Phenotypic variation of tassel branch number (TBN), a major breeding target, is controlled by many quantitative trait loci (QTLs). The lack of large-scale QTL cloning methodology constrains the systematic dissection of TBN, which hinders modern maize breeding. Here, we devise QTG-Miner, a multi-omics data-based technique for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. Using QTG-Miner, we clone and verify seven genes underlying seven TBN QTLs. Compared to conventional methods, QTG-Miner performs well for both major- and minor-effect TBN QTLs. Selection analysis indicates that a substantial number of genes and network modules have been subjected to selection during maize improvement. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups. In summary, QTG-Miner provides a large-scale approach for rapid cloning of QTGs in crops and dissects the genetic base of TBN for further maize breeding.
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Affiliation(s)
- Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengyong Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jiaxin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaoyang Shang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xinxin Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wanchao Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tianhuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yongwen Qi
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510325, Guangdong, China
| | - Huihui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Chen J, Ma S, Luo B, Hao H, Li Y, Yang H, Zhu F, Zhang P, Niu R, Pan P. Human umbilical cord mesenchymal stromal cell small extracellular vesicle transfer of microRNA-223-3p to lung epithelial cells attenuates inflammation in acute lung injury in mice. J Nanobiotechnology 2023; 21:295. [PMID: 37626408 PMCID: PMC10464265 DOI: 10.1186/s12951-023-02038-3] [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: 03/09/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Acute lung injury (ALI), manifested as strong pulmonary inflammation and alveolar epithelial damage, is a life-threatening disease with high morbidity and mortality. Small extracellular vesicles (sEVs), secreted by multiple types of cells, are critical cellular communication mediators and can inhibit inflammation by transferring bioactive molecules, such as microRNAs (miRNAs). Thus, we hypothesized that sEVs derived from mesenchymal stromal cells (MSC sEVs) could transfer miRNAs to attenuate inflammation of lung epithelial cells during ALI. METHODS C57BL/6 male mice were intratracheally administered LPS (10 mg/kg). Six hours later, the mice were randomly administered with MSC sEVs (40 µg per mouse in 150 µl of saline), which were collected by ultracentrifugation. Control group received saline administration. After 48 h, the mice were sacrificed to evaluate pulmonary microvascular permeability and inflammatory responses. In vitro, A549 cells and primary human small airway epithelial cells (SAECs) were stimulated with LPS with or without MSC sEVs treatment. RESULTS In vitro, MSC sEVs could also inhibit the inflammation induced by LPS in A549 cells and SAECs (reducing TNF-α, IL-1β, IL-6 and MCP-1). Moreover, MSC sEV treatment improved the survival rate, alleviated pulmonary microvascular permeability, and inhibited proinflammatory responses (reducing TNF-α, IL-1β, IL-6 and JE-1) in ALI mice. Notably, miR-223-3p was found to be served as a critical mediator in MSC sEV-induced regulatory effects through inhibition of poly (adenosine diphosphate-ribose) polymerase-1 (PARP-1) in lung epithelial cells. CONCLUSIONS Overall, these findings suggest that MSC sEVs may offer a novel promising strategy for ALI.
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Affiliation(s)
- Jie Chen
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China
| | - Shiyang Ma
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China
| | - Baihua Luo
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Haojie Hao
- Institute of Basic Medicine Science, Chinese People's Liberation Army General Hospital, Chinese People's Liberation Army Medical College, Beijing, China
| | - Yanqin Li
- Center of Pulmonary & Critical Care Medicine, Chinese People's Liberation Army (PLA) General Hospital, Chinese PLA Medical College, Beijing, China
| | - Hang Yang
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China
| | - Fei Zhu
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China
| | - Peipei Zhang
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China
| | - Ruichao Niu
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China.
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China.
- Department of Respiratory Medicine, The Second Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China.
| | - Pinhua Pan
- Department of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, No.28 Xiangya Road, Kai-Fu District, Changsha, 410008, Hunan, China.
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Chang-sha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, 410008, Hunan, P.R. China.
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Gong Z, Zhang J, Li Y, Li H, Zhang Z, Qin Y, Jiang Y, Duan Y, Li T, Miao J, Wu Y. Identification of Potential Gene Targets for Suppressing Oviposition in Holotrichia parallela Using Comparative Transcriptome Analysis. Int J Mol Sci 2023; 24:13138. [PMID: 37685945 PMCID: PMC10487570 DOI: 10.3390/ijms241713138] [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: 07/07/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Holotrichia parallela is an important plant pest. Comparative feeding experiments showed that the egg production, oviposition duration and survival rate of H. parallela beetles were significantly higher when they fed on elm leaves than when they fed on willow or purpus privet leaves. RNA sequencing was used to determine transcriptomic changes associated with oviposition. Comparative transcriptome analysis revealed that the beetles that fed on elm and willow had a total of 171 genes with differential expression. When the beetles fed on elm and purpus privet, 3568 genes had differential expression. The vitellogenesis, ovarian serine protease, odorant-binding proteins, acyl-CoA synthetase and follicle cell proteins were commonly upregulated genes in elm-fed beetles compared with those fed on willow/purpus privet leaves. The involvement of the follicle cell protein 3C gene in the regulation of oviposition was confirmed using RNA interference. The results provide insights into the molecular mechanisms underlying oviposition in H. parallela feeding on different host plants. This study also describes a method for identifying potentially effective genes for pest control.
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Affiliation(s)
- Zhongjun Gong
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Jing Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Yanmin Li
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Huiling Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Ziqi Zhang
- Institute of Plant Protection, Luoyang Academy of Agricultural and Forestry Sciences, Luoyang 471027, China
| | - Yifan Qin
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Yueli Jiang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Yun Duan
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Tong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Jin Miao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
| | - Yuqing Wu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Crop Integrated Pest Management of the Southern of North China, Ministry of Agriculture of the People’s Republic of China, Zhengzhou 450002, China; (Z.G.)
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218
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Wang X, Jin Z, Tang S, Huang X, Wang S, Ren X, Xu M. ATRX loss suppresses the type I interferon response in sarcoma cells through chromatin remodeling. Am J Cancer Res 2023; 13:3547-3558. [PMID: 37693131 PMCID: PMC10492102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/30/2023] [Indexed: 09/12/2023] Open
Abstract
Sarcomas constitute a heterogeneous group of mesenchymal cancers and are particularly common in children and adolescents, leading to significant lethality. Therefore, it is necessary to understand the underlying mechanisms by which genetic alterations promote sarcoma progression. Here, we demonstrate that loss-of-function of ATRX, a member of the SWI/SNF DNA-remodeling family, represses the interferon (IFN)-β response by inducing chromatin remodeling in sarcoma cells. We show that ATRX mutations are associated with worse prognosis and attenuate IFN-α/β response in patients with specific types of sarcomas. Using poly(I:C) as a stimulation model, we show that natural ATRX mutation or ATRX depletion via CRISPR/Cas9 or siRNA significantly suppresses the expression of IFNB1 and other cytokines in sarcoma cells. Moreover, RNA-seq data reveal that ATRX ablation globally influences the expression pattern of poly(I:C)-stimulated genes (PSGs). Through ATAC-seq, we show that ATRX loss enhance chromatin accessibility generally, which consistent with the heterochromatin modulating function of ATRX. However, a set of PSGs display a decrease of chromatin accessibility after ATRX depletion, indicating that ATRX promote the transcription of these genes through chromatin remodeling. Thus, we highlight that ATRX mutation plays critical roles in blocking Type I IFN signaling in sarcoma cells and point out the clinical importance of this effect on sarcoma treatment.
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Affiliation(s)
- Xinrui Wang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Zige Jin
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Shanshan Tang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Xiyu Huang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Shanshan Wang
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Xiaohe Ren
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
| | - Mafei Xu
- Department of Cell Biology, School of Life Sciences, Anhui Medical University Hefei 230032, Anhui, China
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219
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Zhao N, Yu Z, Cai Z, Chen W, He X, Huo Z, Lin X. Novel combinations of variations in KCNQ1 were associated with patients with long QT syndrome or Jervell and Lange-Nielsen syndrome. BMC Cardiovasc Disord 2023; 23:399. [PMID: 37568094 PMCID: PMC10422715 DOI: 10.1186/s12872-023-03417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
OBJECTIVES Long QT syndrome (LQTS) is one of the primary causes of sudden cardiac death (SCD) in youth. Studies have identified mutations in ion channel genes as key players in the pathogenesis of LQTS. However, the specific etiology in individual families remains unknown. METHODS Three unrelated Chinese pedigrees diagnosed with LQTS or Jervell and Lange-Nielsen syndrome (JLNS) were recruited clinically. Whole exome sequencing (WES) was performed and further validated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. RESULTS All of the probands in our study experienced syncope episodes and featured typically prolonged QTc-intervals. Two probands also presented with congenital hearing loss and iron-deficiency anemia and thus were diagnosed with JLNS. A total of five different variants in KCNQ1, encoding a subunit of the voltage-gated potassium channel, were identified in 3 probands. The heterozygous variants, KCNQ1 c.749T > C was responsible for LQTS in Case 1, transmitting in an autosomal dominant pattern. Two patterns of compound heterozygous variants were responsible for JLNS, including a large deletion causing loss of the exon 16 and missense variant c.1663 C > T in Case 2, and splicing variant c.605-2 A > G and frame-shift variant c.1265del in Case 3. To our knowledge, the compound heterozygous mutations containing a large deletion and missense variant were first reported in patients with JLNS. CONCLUSION Our study expanded the LQTS genetic spectrum, thus favoring disease screening and diagnosis, personalized treatment, and genetic consultation.
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Affiliation(s)
- Nongnong Zhao
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
- Yuyao People's Hospital of Zhejiang Province, Yuyao, Ningbo, 315400, Zhejiang, China
| | - Zhengyang Yu
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhejun Cai
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Wenai Chen
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Xiaopeng He
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhaoxia Huo
- Experimental Teaching Center, School of Basic Medical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
| | - Xiaoping Lin
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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220
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Han PJ, Luo LJ, Han Y, Song L, Zhen P, Han DY, Wei YH, Zhou X, Wen Z, Qiu JZ, Bai FY. Microbial Community Affects Daqu Quality and the Production of Ethanol and Flavor Compounds in Baijiu Fermentation. Foods 2023; 12:2936. [PMID: 37569205 PMCID: PMC10418397 DOI: 10.3390/foods12152936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Daqu is a traditional starter for Baijiu fermentation and is produced by spontaneous fermentation of ground and moistened barley or wheat. The quality of Daqu is traditionally evaluated based on physicochemical and subjective sensory parameters without microbiological analysis. Here, we compared the physicochemical characteristics of qualified (QD) and inferior (ID) Daqu, their microbial communities based on plate counting and PacBio SMRT sequencing of rRNA gene libraries, and their impacts on Baijiu fermentation. The results showed that the glucoamylase and α-amylase activities of QD were significantly higher than those of ID. The counts of yeasts and relative abundances of functional microbes, especially the amylolytic bacterium Bacillus licheniformis and fungi Saccharomycopsis fibuligera and Lichtheimia ramosa, were significantly higher in QD than in ID. The laboratory-scale Baijiu fermentation tests showed that the relative abundances of the amylolytic microbes were higher in the QD than the ID fermentation set, resulting in more efficient fermentation, as indicated by more weight loss and higher moisture content in the former. Consequently, more glycerol, acetic acid, ethanol, and other volatile compounds were produced in the QD than in the ID fermentation set. The results suggest that Daqu quality is determined by, and can be evaluated based on, its microbial community.
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Affiliation(s)
- Pei-Jie Han
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Lu-Jun Luo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Ying Han
- Technology Center, Shanxi Xinghuacun Fen Wine Factory Co., Ltd., Fenyang 032205, China
| | - Liang Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Pan Zhen
- Technology Center, Shanxi Xinghuacun Fen Wine Factory Co., Ltd., Fenyang 032205, China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Yu-Hua Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Zhang Wen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
| | - Jun-Zhi Qiu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.-J.L.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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221
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Wang R, Li W, He Q, Zhang H, Wang M, Zheng X, Liu Z, Wang Y, Du C, Du H, Xing L. The genome of okra ( Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content. HORTICULTURE RESEARCH 2023; 10:uhad120. [PMID: 37554345 PMCID: PMC10405168 DOI: 10.1093/hr/uhad120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/26/2023] [Indexed: 08/10/2023]
Abstract
Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.
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Affiliation(s)
- Ruyu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Xinyuan Zheng
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
| | - Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
- Hebei Basic Science Center for Biotic Interaction, Institute of Life Sciences and Green Development, Hebei University, Baoding 071000, China
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Miao M, Lyu M, Zhong C, Liu Y. Correlation Between MMP9 Promoter Methylation and Transient Ischemic Attack/Mild Ischemic Stroke with Early Cognitive Impairment. Clin Interv Aging 2023; 18:1221-1232. [PMID: 37547382 PMCID: PMC10404041 DOI: 10.2147/cia.s421830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
Background/Objective Dyskinesia caused by transient ischemic attack (TIA) and mild ischemic stroke (MIS) is mild and short-lived; however, cognitive impairment (CI) can occur in the acute phase and be easily overlooked. DNA methylation is an epigenetic phenomenon that can affect gene expression through gene silencing. Blood levels of matrix metalloproteinase (MMP) 9 are elevated in ischemic stroke patients and is associated with the destruction of the blood-brain barrier and the occurrence of CI. No studies have investigated the relationship between MMP9 gene methylation and TIA/MIS with early cognitive impairment (ECI). As such, the purpose of the present study was to investigate the correlation between MMP9 gene methylation and TIA/MIS with ECI. Methods Data from 112 subjects were collected, including 84 with TIA/MIS (National Institutes of Health Stroke Scale <5 points) and 28 non-stroke control subjects. Patients were evaluated within 7 days of TIA/MIS onset according to four single-domain cognitive scales. Whole blood DNA methylation was detected using MethylTarget sequencing technology. Comparison of MMP9 gene methylation levels among subgroups was performed using statistical methods. Results The site S33-79 in the TIA/MIS group was hypomethylated compared with the control group, and sites S33-25 and S33-30 in TIA/MIS with ECI was hypomethylated compared with TIA/MIS without ECI. Compared with the small artery occlusion group, MMP9 gene, S33-25, 30, 39, 53, 58, 73, 79, 113 and 131 sites in the large artery atherosclerosis group were hypomethylated. Conclusion MMP9 gene hypomethylation sites were associated with TIA/MIS and TIA/MIS with ECI, and there was a strong correlation between MMP9 gene hypomethylation and atherosclerotic TIA/MIS. MMP9 gene methylation can reflect the severity of TIA/MIS. MMP9 gene hypomethylation sites may be used as potential biomarkers and therapeutic targets for TIA/MIS and TIA/MIS with ECI.
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Affiliation(s)
- Meng Miao
- Department of Neurology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Mingyang Lyu
- Haihe Laboratory of Cell Ecosystem, Tianjin, People’s Republic of China
| | - Chi Zhong
- Department of Neurology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, People’s Republic of China
| | - Ying Liu
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, People’s Republic of China
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Zhang M, Lu Y, Zhu Y, Wu K, Chen S, Zhou L, Wang F, Peng Y, Li X, Pan J, Chen B, Liu Z, Wang X. Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Drug Resistance: A Retrospective Observational Study in Eastern China. Antibiotics (Basel) 2023; 12:1257. [PMID: 37627677 PMCID: PMC10451829 DOI: 10.3390/antibiotics12081257] [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: 06/09/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Pulmonary tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB). Whole-genome sequencing (WGS) holds great promise as an advanced technology for accurately predicting anti-TB drug resistance. The development of a reliable method for detecting drug resistance is crucial in order to standardize anti-TB treatments, enhance patient prognosis, and effectively reduce the risk of transmission. In this study, our primary objective was to explore and determine the potential of WGS for assessing drug resistance based on genetic variants recommended by the World Health Organization (WHO). A total of 1105 MTB strains were selected from samples collected from 2014-2018 in Zhejiang Province, China. Phenotypic drug sensitivity tests (DST) of the anti-TB drugs were conducted for isoniazid (INH), rifampicin (RFP), streptomycin, ethambutol, fluoroquinolones (levofloxacin and moxifloxacin), amikacin, kanamycin, and capreomycin, and the drug-resistance rates were calculated. The clean WGS data of the 1105 strains were acquired and analyzed. The predictive performance of WGS was evaluated by the comparison between genotypic and phenotypic DST results. For all anti-TB drugs, WGS achieved good specificity values (>90%). The sensitivity values for INH and RFP were 91.78% and 82.26%, respectively; however, they were ≤60% for other drugs. The positive predictive values for anti-TB drugs were >80%, except for ethambutol and moxifloxacin, and the negative predictive values were >90% for all drugs. In light of the findings from our study, we draw the conclusion that WGS is a valuable tool for identifying genome-wide variants. Leveraging the genetic variants recommended by the WHO, WGS proves to be effective in detecting resistance to RFP and INH, enabling the identification of multi-drug resistant TB patients. However, it is evident that the genetic variants recommended for predicting resistance to other anti-TB drugs require further optimization and improvement.
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Affiliation(s)
- Mingwu Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310020, China; (Y.L.); (X.L.)
| | - Yelei Zhu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Kunyang Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Songhua Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Lin Zhou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Fei Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Ying Peng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310020, China; (Y.L.); (X.L.)
| | - Junhang Pan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Bin Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Zhengwei Liu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
| | - Xiaomeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China; (M.Z.); (Y.Z.); (K.W.); (S.C.); (L.Z.); (F.W.); (Y.P.); (J.P.); (B.C.)
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Wu X, Jiao J, Xia Y, Yan X, Liu Z, Cao Y, Ma L. Case report: A Chinese patient with glutathione synthetase deficiency and a novel glutathione synthase mutation. Front Pediatr 2023; 11:1212405. [PMID: 37576147 PMCID: PMC10413980 DOI: 10.3389/fped.2023.1212405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
Glutathione synthetase deficiency (GSSD) is an autosomal-recessive metabolic disorder caused by glutathione synthetase (GSS) gene mutations. No more than 90 cases of GSSD have been reported worldwide; thus, the spectrum of GSS mutations and the genotype-phenotype association remain unclear. Here, we present a severely affected infant carrying a compound heterozygous GSS variation, c.491G > A, and a novel variant of c.1343_1348delTACTTC. We also summarize the clinical manifestations, treatment protocol, prognosis, and genetic characteristics of previously reported GSSD cases in China. In this case study, our patient presented with tachypnea, jaundice, intractable metabolic acidosis, and hemolytic anemia. Urinary-organic acid analysis revealed elevated 5-oxoproline levels. Further, this patient showed improved outcomes owing to early diagnosis and the timely administration of vitamins C and E. Therefore, our study indicates that in clinical cases of unexplained hemolytic anemia and metabolic acidosis, GSSD should be considered. Additionally, genetic testing and antioxidant application might help identify GSSD and improve the prognosis.
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Affiliation(s)
- Xiaojiao Wu
- Department of Neonatology, Children’s Hospital of Hebei Province, Shijiazhuang, China
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Jiancheng Jiao
- Department of Neonatology, Children’s Hospital of Hebei Province, Shijiazhuang, China
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Yaofang Xia
- Department of Neonatology, Children’s Hospital of Hebei Province, Shijiazhuang, China
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Xiaotong Yan
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Zehao Liu
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Yanyan Cao
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Li Ma
- Department of Neonatology, Children’s Hospital of Hebei Province, Shijiazhuang, China
- Pediatric Clinical Research Centre of Hebei Province, Children's Hospital of Hebei Province, Shijiazhuang, China
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Xing L, Wang M, He Q, Zhang H, Liang H, Zhou Q, Liu Y, Liu Z, Wang Y, Du C, Xiao Y, Liu J, Li W, Liu G, Du H. Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum. BMC Biol 2023; 21:161. [PMID: 37480118 PMCID: PMC10362693 DOI: 10.1186/s12915-023-01643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
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Affiliation(s)
- Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hanfei Liang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qinghong Zhou
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yao Xiao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Jianan Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Guixia Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
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226
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Prunier JG, Chevalier M, Raffard A, Loot G, Poulet N, Blanchet S. Genetic erosion reduces biomass temporal stability in wild fish populations. Nat Commun 2023; 14:4362. [PMID: 37474616 PMCID: PMC10359329 DOI: 10.1038/s41467-023-40104-4] [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: 02/13/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
Genetic diversity sustains species adaptation. However, it may also support key ecosystems functions and services, for example biomass production, that can be altered by the worldwide loss of genetic diversity. Despite extensive experimental evidence, there have been few attempts to empirically test whether genetic diversity actually promotes biomass and biomass stability in wild populations. Here, using long-term demographic wild fish data from two large river basins in southwestern France, we demonstrate through causal modeling analyses that populations with high genetic diversity do not reach higher biomasses than populations with low genetic diversity. Nonetheless, populations with high genetic diversity have much more stable biomasses over recent decades than populations having suffered from genetic erosion, which has implications for the provision of ecosystem services and the risk of population extinction. Our results strengthen the importance of adopting prominent environmental policies to conserve this important biodiversity facet.
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Affiliation(s)
- Jérôme G Prunier
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France.
| | - Mathieu Chevalier
- Department of Ecology and Evolution, University of Lausanne, Biophore, CH-1015, Lausanne, Switzerland
- Ifremer, DYNECO, F-29280, Plouzané, France
| | - Allan Raffard
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200, Thonon-les-Bains, France
| | - Géraldine Loot
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, cedex, 4, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400, Toulouse, France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200, Moulis, France.
- CNRS, UPS, École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, F-31062, Toulouse, cedex, 4, France.
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Chen X, Liu Y, Lv K, Wang M, Liu X, Li B. FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing. BIOINFORMATICS ADVANCES 2023; 3:vbad099. [PMID: 37521311 PMCID: PMC10375421 DOI: 10.1093/bioadv/vbad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Motivation Direct RNA-seq (dRNA-seq) using Oxford Nanopore Technology (ONT) has revolutionized transcript mapping by offering enhanced precision due to its long-read length. Unlike traditional techniques, dRNA-seq eliminates the need for PCR amplification, reducing the impact of GC bias, and preserving valuable base physical information, such as RNA modification and poly(A) length estimation. However, the rapid advancement of ONT devices has set higher standards for analytical software, resulting in potential challenges of software incompatibility and reduced efficiency. Results We present a novel workflow, called FASTdRNA, to manipulate dRNA-seq data efficiently. This workflow comprises two modules: a data preprocessing module and a data analysis module. The preprocessing data module, dRNAmain, encompasses basecalling, mapping, and transcript counting, which are essential for subsequent analyses. The data analysis module consists of a range of downstream analyses that facilitate the estimation of poly(A) length, prediction of RNA modifications, and assessment of alternative splicing events across different conditions with duplication. The FASTdRNA workflow is designed for the Snakemake framework and can be efficiently executed locally or in the cloud. Comparative experiments have demonstrated its superior performance compared to previous methods. This innovative workflow enhances the research capabilities of dRNA-seq data analysis pipelines by optimizing existing processes and expanding the scope of analysis. Availability and implementation The workflow is freely available at https://github.com/Tomcxf/FASTdRNA under an MIT license. Detailed install and usage guidance can be found in the GitHub repository.
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Affiliation(s)
- Xiaofeng Chen
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Yongqi Liu
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Kaiwen Lv
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Meiling Wang
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Xiaoqin Liu
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Bosheng Li
- Corresponding author. Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological Economic Development District, Weifang, Shandong 261000, China. E-mail:
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228
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Lian H, Song S, Chen W, Shi A, Jiang H, Hu S. Genetic characterization of dilated cardiomyopathy patients undergoing heart transplantation in the Chinese population by whole-exome sequencing. J Transl Med 2023; 21:476. [PMID: 37461109 PMCID: PMC10351148 DOI: 10.1186/s12967-023-04282-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/17/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is one of the most frequent causes of heart failure and heart transplantation (HTx). The genetic basis of DCM among patients undergoing HTx remains to be further studied. This study aimed to characterize the genetic basis of DCM HTx in the Chinese population. METHODS In total, 208 unrelated DCM patients who underwent HTx at Fuwai Hospital between June 2004 and June 2017 were included in this study. Whole-exome sequencing (WES) was performed for all patients. Gene burden analysis, variant classification, and genotype-phenotype correlation analysis were subsequently performed. RESULTS After completing the bioinformatics analysis, gene burden analysis suggested that titin (TTN), filamin C (FLNC) and lamin A/C (LMNA) were significantly enriched with rare protein-altering variants. The frequencies of TTN and FLNC truncating variants in our cohort were 18.8% and 8.7%, respectively. Among the 165 rare variants in high evidence DCM-related genes, 27 (16.4%) and 59 (35.8%) were interpreted as pathogenic (P) and likely pathogenic (LP), respectively. In addition, 41 (47.7%) and 16 (18.6%) of these 86 P/LP variants are located in TTN and FLNC, respectively. The FLNC group contained more patients with NYHA class IV than the P/LP-negative group (FLNC, 16/18 vs. P/LP-negative, 81/123, P = 0.049). CONCLUSIONS Based on WES, we provided a primary genetic spectrum of DCM patients undergoing HTx in the Chinese population. TTN and FLNC harbour the most P/LP variants. FLNC truncation may lead to severe clinical symptoms in DCM patients.
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Affiliation(s)
- Hong Lian
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Center, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Shen Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Wenzheng Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Anteng Shi
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Haobin Jiang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
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229
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Chang Y, Zhang R, Ma Y, Sun W. A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data. Sci Data 2023; 10:451. [PMID: 37438373 DOI: 10.1038/s41597-023-02362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Rhododendron vialii (subgen. Azaleastrum) is an evergreen shrub with high ornamental value. This species has been listed as a plant species with extremely small populations (PSESP) for urgent protection by China's Yunnan provincial government in 2021, due to anthropogenic habitat fragmentation. However, limited genomic resources hinder scientifically understanding of genetic threats that the species is currently facing. In this study, we assembled a high-quality haplotype-resolved genome of R. vialii based on PacBio HiFi long reads and Hi-C reads. The assembly contains two haploid genomes with sizes 532.73 Mb and 521.98 Mb, with contig N50 length of 35.67 Mb and 34.70 Mb, respectively. About 99.92% of the assembled sequences could be anchored to 26 pseudochromosomes, and 14 gapless assembled chromosomes were included in this assembly. Additionally, 60,926 protein-coding genes were identified, of which 93.82% were functionally annotated. This is the first reported genome of R. vialii, and hopefully it will lay the foundations for further research into the conservation genomics and horticultural domestication of this ornamentally important species.
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Affiliation(s)
- Yuhang Chang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China.
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, 650201, China.
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Ni P, Nie F, Zhong Z, Xu J, Huang N, Zhang J, Zhao H, Zou Y, Huang Y, Li J, Xiao CL, Luo F, Wang J. DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. Nat Commun 2023; 14:4054. [PMID: 37422489 PMCID: PMC10329642 DOI: 10.1038/s41467-023-39784-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.
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Affiliation(s)
- Peng Ni
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Fan Nie
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Zeyu Zhong
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Jinrui Xu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Neng Huang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Jun Zhang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Haochen Zhao
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - You Zou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Yuanfeng Huang
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410000, China
| | - Jinchen Li
- Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410000, China
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410000, China
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Tianhe District, Guangzhou, China.
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, 29634-0974, USA.
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
- Xiangjiang Laboratory, Changsha, 410205, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China.
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231
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Bian X, Cao Y, Zhi X, Ma N. Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family in Brassica napus and Its Role in Abiotic Stress Response. Int J Mol Sci 2023; 24:11242. [PMID: 37511002 PMCID: PMC10379087 DOI: 10.3390/ijms241411242] [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: 05/12/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Plant Cysteine Oxidase (PCO) is a plant O2-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were analyzed. In this study, 20, 7 and 8 PCO genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the PCOs were divided into five groups: PCO1, PCO2, PCO3, PCO4 and PCO5. Gene organization and motif distribution analysis suggested that the PCO gene family was relatively conserved during evolution. According to the public expression data, PCO genes were expressed in different tissues at different developmental stages. Moreover, qRT-PCR data showed that most of the Bna/Bra/BoPCO5 members were expressed in leaves, roots, flowers and siliques, suggesting an important role in both vegetative and reproductive development. Expression of BnaPCO was induced by various abiotic stress, especially waterlogging stress, which was consistent with the result of cis-element analysis. In this study, the PCO gene family of Brassicaceae was analyzed for the first time, which contributes to a comprehensive understanding of the origin and evolution of PCO genes in Brassicaceae and the function of BnaPCO in abiotic stress responses.
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Affiliation(s)
- Xiaohua Bian
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yifan Cao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Ximin Zhi
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Ma
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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232
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Han Y, Yang J, Wu H, Liu F, Qin B, Li R. Improving Rice Leaf Shape Using CRISPR/Cas9-Mediated Genome Editing of SRL1 and Characterizing Its Regulatory Network Involved in Leaf Rolling through Transcriptome Analysis. Int J Mol Sci 2023; 24:11087. [PMID: 37446265 DOI: 10.3390/ijms241311087] [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: 06/15/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Leaf rolling is a crucial agronomic trait to consider in rice (Oryza sativa L.) breeding as it keeps the leaves upright, reducing interleaf shading and improving photosynthetic efficiency. The SEMI-ROLLED LEAF 1 (SRL1) gene plays a key role in regulating leaf rolling, as it encodes a glycosylphosphatidylinositol-anchored protein located on the plasma membrane. In this study, we used CRISPR/Cas9 to target the second and third exons of the SRL1 gene in the indica rice line GXU103, which resulted in the generation of 14 T0 transgenic plants with a double-target mutation rate of 21.4%. After screening 120 T1 generation plants, we identified 26 T-DNA-free homozygous double-target mutation plants. We designated the resulting SRL1 homozygous double-target knockout as srl1-103. This line exhibited defects in leaf development, leaf rolling in the mature upright leaves, and a compact nature of the fully grown plants. Compared with the wild type (WT), the T2 generation of srl1-103 varied in two key aspects: the width of flag leaf (12.6% reduction compared with WT) and the leaf rolling index (48.77% increase compared with WT). In order to gain a deeper understanding of the involvement of SRL1 in the regulatory network associated with rice leaf development, we performed a transcriptome analysis for the T2 generation of srl1-103. A comparison of srl1-103 with WT revealed 459 differentially expressed genes (DEGs), including 388 upregulated genes and 71 downregulated genes. In terms of the function of the DEGs, there seemed to be a significant enrichment of genes associated with cell wall synthesis (LOC_Os08g01670, LOC_Os05g46510, LOC_Os04g51450, LOC_Os10g28080, LOC_Os04g39814, LOC_Os01g71474, LOC_Os01g71350, and LOC_Os11g47600) and vacuole-related genes (LOC_Os09g23300), which may partially explain the increased leaf rolling in srl1-103. Furthermore, the significant downregulation of BAHD acyltransferase-like protein gene (LOC_Os08g44840) could be the main reason for the decreased leaf angle and the compact nature of the mutant plants. In summary, this study successfully elucidated the gene regulatory network in which SRL1 participates, providing theoretical support for targeting this gene in rice breeding programs to promote variety improvement.
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Affiliation(s)
- Yue Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hu Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
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233
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Guo Z, Wei J, Xu Z, Lin C, Peng Y, Wang Q, Wang D, Yang X, Xu KW. HollyGTD: an integrated database for holly (Aquifoliaceae) genome and taxonomy. FRONTIERS IN PLANT SCIENCE 2023; 14:1220925. [PMID: 37469783 PMCID: PMC10352911 DOI: 10.3389/fpls.2023.1220925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Zhonglong Guo
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Junrong Wei
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Zhenxiu Xu
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Chenxue Lin
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ye Peng
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Qi Wang
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Dong Wang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- WeiRan Biotech, Beijing, China
| | - Xiaozeng Yang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ke-Wang Xu
- Co−Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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234
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An R, Liu Y, Pan C, Da Z, Zhang P, Qiao N, Zhao F, Ba S. Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163308. [PMID: 37028668 DOI: 10.1016/j.scitotenv.2023.163308] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/26/2023] [Accepted: 04/01/2023] [Indexed: 05/27/2023]
Abstract
Alpine wetland is a natural laboratory for studying the Earth's third polar ecosphere. Protist communities are key components of wetland ecosystems which are extremely vulnerable to environmental change. It is of great importance to study the protist community in relation to environment, which might be the key to understand the ecosystem of the alpine wetlands under global change. In this study, we investigated the composition of protist communities across the Mitika Wetland, a unique alpine wetland hosting tremendous endemic diversity. Using 18S rRNA gene high-throughput sequencing, we evaluated how protist taxonomic and functional group composition is structured by seasonal climate and environmental variation. We found a high relative abundance of Ochrophyta, Ciliophora, and Cryptophyta, each of which showcased a unique spatial pattern in the wet and dry seasons. The proportion of consumers, parasites and phototrophs groups were stable among the functional zones and also between the seasons, with consumers dominating communities in terms of richness, while phototrophic taxa dominated in terms of relative abundance. Protist and each functional group were rather regulated by deterministic than stochastic processes, with water quality having a strong control on communities. Salinity and pH were the most important environmental factors at shaping protistan community. The protist co-occurrence network dominated by the positive edge indicating the communities resisted extreme environmental conditions through close cooperation, and more consumers were determined as the keystones in wet season and more phototrophic taxa in dry season. Our results provided the baseline of the protist taxonomic and functional group composition in the highest wetland, and highlighted environmental selections drive protist distribution, implying the alpine wetland ecosystem are sensitive to climate changes and human activities.
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Affiliation(s)
- Ruizhi An
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Yang Liu
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Chengmei Pan
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Zhen Da
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Peng Zhang
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Nanqian Qiao
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Sang Ba
- Laboratory of Wetland and Catchments Ecology in Tibetan Plateau, School of Ecology and Environment, Tibet University, Lhasa 850000, China; Center for Carbon Neutrality in the Earth's Third Pole, Tibet University, Lhasa 850000, China.
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235
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Li Z, Chen Y, Li Y, Zeng Y, Li W, Ma X, Huang L, Shen Y. Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm. Int J Mol Sci 2023; 24:10970. [PMID: 37446145 DOI: 10.3390/ijms241310970] [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: 05/17/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli's genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources.
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Affiliation(s)
- Zhipeng Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Yiqiong Chen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Yangyan Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Ying Zeng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Wanying Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Xiaona Ma
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Lili Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Yanting Shen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100000, China
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236
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Yu JG, Tang JY, Wei R, Lan MF, Xiang RC, Zhang XC, Xiang QP. The first homosporous lycophyte genome revealed the association between the recent dynamic accumulation of LTR-RTs and genome size variation. PLANT MOLECULAR BIOLOGY 2023:10.1007/s11103-023-01366-0. [PMID: 37380791 DOI: 10.1007/s11103-023-01366-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
The contrasting genome size between homosporous and heterosporous plants is fascinating. Different from the heterosporous seed plants and mainly homosporous ferns, the lycophytes are either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). Many lycophytes are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer's disease. For the seed-free vascular plants, several high-quality genomes of heterosporous Selaginella, homosporous ferns (maidenhair fern, monkey spider tree fern), and heterosporous ferns (Azolla) have been published and provided important insights into the origin and evolution of early land plants. However, the homosporous lycophyte genome has not been decoded. Here, we assembled the first homosporous lycophyte genome and conducted comparative genomic analyses by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size of Lycopodium clavatum is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is long terminal repeat (LTR). This study disclosed a high birth rate and a low death rate of the LTR-RTs in homosporous lycophytes, but the opposite occurs in heterosporous lycophytes. we propose that the recent activity of LTR-RT is responsible for the immense genome size variation between homosporous and heterosporous lycophytes. By combing Ks analysis with a phylogenetic approach, we discovered two whole genome duplications (WGD). Morover, we identified all the five recognized key enzymes for the HupA biosynthetic pathway in the L. clavatum genome, but found this pathway incomplete in other major lineages of land plants. Overall, this study is of great importance for the medicinal utilization of lycophytes and the decoded genome data will be a key cornerstone to elucidate the evolution and biology of early vascular land plants.
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Affiliation(s)
- Ji-Gao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Jun-Yong Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, China
| | - Mei-Fang Lan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, China
| | - Rui-Chen Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, China.
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237
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Li M, Zhang H, Zhang W, Cao Y, Sun B, Jiang Q, Zhang Y, Liu H, Guo W, Chang C, Zhou N, Lv C, Guo C, Guo X, Shang J, Huang S, Zhu Y. One global disseminated 193 kb high-risk hybrid plasmid harboring tet(X4), mcr or bla NDM threatening public health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162807. [PMID: 36921865 DOI: 10.1016/j.scitotenv.2023.162807] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 05/10/2023]
Abstract
In Shanghai, the prevalence of tet(X4) and tet(X4)-carrying plasmid from food-producing -animal Enterobacteriales has not been intensively investigated. Here, five tet(X4)-positive swine-origin E. coli strains were characterized among 652 food-producing-animal E. coli isolates in Shanghai during 2018-2021 using long-term surveillance among poultry, swine and cattle, antimicrobial susceptibility testing, and tet(X4)-specific PCR. A combination of short- and long-read sequencing technologies demonstrated that the five strains with 4 STs carried a nearly identical 193 kb tet(X4)-bearing plasmid (p193k-tetX4) belonging to the same IncFIA(HI1)/IncHI1A/IncHIB plasmid family (p193k). Surprisingly, 34 of the 151 global tet(X4)-positive plasmids was the p193k members and exclusively pandemic in China. Other p193k members harboring many critically important ARGs (mcr or blaNDM) with particular genetic environment are widespread throughout human-animal-environmental sources, with 33.77 % human origin. Significantly, phylogenetic analysis of 203 p193k-tetX4 sequences revealed that human- and animal-origin plasmids clustered within the same phylogenetic subgroups. The largest lineage (173/203) comprised 161 E. coli, 6 Klebsiella, 3 Enterobacter, 2 Citrobacter, and 1 Leclercia spp. from animals (n = 143), humans (n = 18), and the environment (n = 9). Intriguingly, the earliest 2015 E. coli strain YA_GR3 from Malaysian river water and 2016 S. enterica Chinese clinical strain GX1006 in another lineage demonstrated that p193k-tetX4 have been widely spread from S. enterica or E. coli to other Enterobacterales. Furthermore, 180 E. coli p193k-tetX4 strains were widespread cross-sectorial transmission among food animals, pets, migratory birds, human and ecosystems. Our findings proved the extensive transmission of the high-risk p193k harboring crucial ARGs across multiple interfaces and species. Therefore, one-health-based systemic surveillance of these similar high-risk plasmids across numerous sources and bacterial species is extremely essential.
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Affiliation(s)
- Min Li
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Haoran Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Wengang Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Ying Cao
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Bingqing Sun
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Qin Jiang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Yu Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Haodong Liu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - WenNan Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Cheng Chang
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Nan Zhou
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Chao Lv
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Chaoyi Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Jun Shang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China.
| | - Shixin Huang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China.
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China.
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238
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Wang D, Xie D, Zhang J, Cai B, Yang B, Zhou L, Huang X. Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson's disease. Sci Rep 2023; 13:9252. [PMID: 37286730 DOI: 10.1038/s41598-023-36503-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Wilson's disease (WD) is an autosomal recessive disorder with a genetic basis. The predominant non-motor symptom of WD is cognitive dysfunction, although the specific genetic regulatory mechanism remains unclear. Tx-J mice, with an 82% sequence homology of the ATP7B gene to the human gene, are considered the most suitable model for WD. This study employs deep sequencing to investigate the differences in RNA transcript profiles, both coding and non-coding, as well as the functional characteristics of the regulatory network involved in WD cognitive impairment. The cognitive function of tx-J mice was evaluated using the Water Maze Test (WMT). Long non-coding RNA (lncRNA), circular RNA (circRNA), and messenger RNA (mRNA) profiles were analyzed in the hippocampal tissue of tx-J mice to identify differentially expressed RNAs (DE-RNAs). Subsequently, the DE-RNAs were used to construct protein-protein interaction (PPI) networks, as well as DE-circRNAs and lncRNAs-associated competing endogenous RNA (ceRNA) expression networks, and coding-noncoding co-expression (CNC) networks. To elucidate their biological functions and pathways, the PPI and ceRNA networks were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A total of 361 differentially expressed mRNAs (DE-mRNAs), comprising 193 up-regulated and 168 down-regulated mRNAs, 2627 differentially expressed long non-coding RNAs (DE-lncRNAs), consisting of 1270 up-regulated and 1357 down-regulated lncRNAs, and 99 differentially expressed circular RNAs (DE-circRNAs), consisting of 68 up-regulated and 31 down-regulated circRNAs, were observed in the tx-J mice group when compared to the control mice group. Gene Ontology (GO) and pathway analyses revealed that DE-mRNAs were enriched in cellular processes, calcium signaling pathways, and mRNA surveillance pathways. In contrast, the DE-circRNAs-associated competing endogenous RNA (ceRNA) network was enriched for covalent chromatin modification, histone modification, and axon guidance, whereas the DE-lncRNAs-associated ceRNA network was enriched for dendritic spine, regulation of cell morphogenesis involved in differentiation, and mRNA surveillance pathway. The study presented the expression profiles of lncRNA, circRNA, and mRNA in the hippocampal tissue of tx-J mice. Furthermore, the study constructed PPI, ceRNA, and CNC expression networks. The findings are significant in comprehending the function of regulatory genes in WD associated with cognitive impairment. These results also offer valuable information for the diagnosis and treatment of WD.
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Affiliation(s)
- Dan Wang
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, People's Republic of China
| | - Daojun Xie
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China.
| | - Juan Zhang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Biao Cai
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, People's Republic of China
| | - Bo Yang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Lei Zhou
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Xiaofeng Huang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
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239
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Zheng X, Zhao N, Peng L, Li Z, Liu C, You Q, Fang B. Biological characteristics of microRNAs secreted by exosomes of periodontal ligament stem cells due to mechanical force. Eur J Orthod 2023:7188171. [PMID: 37262013 DOI: 10.1093/ejo/cjad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND Orthodontic tooth movement (OTM) has previously been considered an inflammatory process. However, recent studies suggest that exosomes may play an important role in the cellular microenvironment of OTM. microRNAs (miRNAs) are one of the major constituents of exosomes. This study aims to investigate the biological characteristics of miRNAs secreted by exosomes of periodontal ligament stem cells (PDLSCs) due to mechanical forces. MATERIALS AND METHODS First, we established a mechanical stress model. The PDLSCs were loaded under different force values and exosomes were extracted after 48 h. High-throughput sequencing of exosomal miRNAs was performed to further evaluate their biological functions and underlying mechanisms. RESULTS The morphology and functions of exosomes were not significantly different between the loading and non-loading PDLSC groups. The optimal loading time and force were 48 h and 1 g/cm2, respectively. After sequencing, gene ontology (GO) and Kyoto encyclopaedia of genes and genomes (KEGG) pathway and network analyses were performed and 10 differentially expressed miRNAs were identified according to a literature search. These are miR-99a-5p, miR-485-3P, miR-29a-3p,miR-21-5p, miR-146a-5p, miR140-3p, miR-1306-5p, miR-126-5p, miR-125a-5p, and miR-23a-3p. LIMITATIONS Extracting exosomes needs a large amount of PDLSCs. More functional experiments need to be done to confirm the exact mechanism of exosomal miRNAs of PDLSCs due to mechanical force. CONCLUSIONS The expression levels of miRNAs secreted by PDLSC-derived exosomes due to mechanical force were very different compared to PDLSC-derived exosomes under nonmechanical stress. The function of many of the identified exosomal miRNAs was found to be related to osteoblasts and osteoclasts. Further validation is required. A functional investigation of these miRNA could provide novel insights into their mechanism.
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Affiliation(s)
- Xiaowen Zheng
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ning Zhao
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Liying Peng
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Zhenxia Li
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Chao Liu
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Qingling You
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Bing Fang
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
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240
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Zhao Z, Zhao H, Zhang L, Huang Z, Ke H, Liu Y, Duan Y, Li H, Wang X, Li Q. Integrated analysis of how gender and body weight affect the intestinal microbial diversity of Gymnocypris chilianensis. Sci Rep 2023; 13:8811. [PMID: 37258553 DOI: 10.1038/s41598-023-35600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/20/2023] [Indexed: 06/02/2023] Open
Abstract
Intestinal microorganisms that living in the mucosa and contents of the gastrointestinal tract of animals, have close links with their hosts over a long evolutionary history. The community structure of the fish intestinal microbiota is associated with food, living environment, and the growth stage. To screen for potential probiotics that can be used for regulating breeding behaviors, this study focused on the diversity of fish intestinal microorganisms. This study aimed to investigate the effects of sex and body weight on the intestinal microbial diversity of Gymnocypris chilianensis in the wild. The results showed that the significant high diversity and richness of intestinal microbiota were fould in heavier individuals, and males. The dominant bacterial phyla of G. chilianensis were Proteobacteria, Firmicutes, and Bacteroidetes. In addition, the abundance of Firmicutes varied significantly among different body weights. The genus profile revealed that small individuals were dominated by Weissella, while females were dominated by Aeromonas, and both large individuals and males were dominated by other genera. Phylogenetic relationships and UPGMA clustering analysis showed significant differences among the groups. In general, the two main factors that have an effect on the intestinal microbiota diversity of wild G. chilianensis are sex and body weight.
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Affiliation(s)
- Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Hongyu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Ya Liu
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Huadong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China
| | - Xiongyan Wang
- Sichuan Water Conservancy Vocational College, Chongzhou, Sichuan, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, 1611 Xiyuan Avenue, Chengdu, Sichuan, China.
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241
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Loghry HJ, Kwon H, Smith RC, Sondjaja NA, Minkler SJ, Young S, Wheeler NJ, Zamanian M, Bartholomay LC, Kimber MJ. Extracellular vesicles secreted by Brugia malayi microfilariae modulate the melanization pathway in the mosquito host. Sci Rep 2023; 13:8778. [PMID: 37258694 PMCID: PMC10232515 DOI: 10.1038/s41598-023-35940-9] [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: 03/04/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
Vector-borne, filarial nematode diseases cause significant disease burdens in humans and domestic animals worldwide. Although there is strong direct evidence of parasite-driven immunomodulation of mammalian host responses, there is less evidence of parasite immunomodulation of the vector host. We have previously reported that all life stages of Brugia malayi, a filarial nematode and causative agent of Lymphatic filariasis, secrete extracellular vesicles (EVs). Here we investigate the immunomodulatory effects of microfilariae-derived EVs on the vector host Aedes aegypti. RNA-seq analysis of an Ae. aegypti cell line treated with B. malayi microfilariae EVs showed differential expression of both mRNAs and miRNAs. AAEL002590, an Ae. aegypti gene encoding a serine protease, was shown to be downregulated when cells were treated with biologically relevant EV concentrations in vitro. Injection of adult female mosquitoes with biologically relevant concentrations of EVs validated these results in vivo, recapitulating the downregulation of AAEL002590 transcript. This gene was predicted to be involved in the mosquito phenoloxidase (PO) cascade leading to the canonical melanization response and correspondingly, both suppression of this gene using RNAi and parasite EV treatment reduced PO activity in vivo. Our data indicate that parasite-derived EVs interfere with critical immune responses in the vector host, including melanization.
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Affiliation(s)
- Hannah J Loghry
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
| | - Hyeogsun Kwon
- Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, USA
| | - Ryan C Smith
- Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, USA
| | - Noelle A Sondjaja
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Sarah J Minkler
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Sophie Young
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Nicolas J Wheeler
- Department of Biology, College of Arts and Sciences, University of Wisconsin-Eau Claire, Eau Claire, WI, USA
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Lyric C Bartholomay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael J Kimber
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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242
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Li N, Ye Y, Wu Y, Li L, Hu J, Luo D, Li Y, Yang J, Gao Y, Hai W, Xie Y, Jiang L. Alterations in histology of the aging salivary gland and correlation with the glandular inflammatory microenvironment. iScience 2023; 26:106571. [PMID: 37124415 PMCID: PMC10131127 DOI: 10.1016/j.isci.2023.106571] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/29/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Aging-related salivary dysfunction typically causes reduced saliva volumes, which leads to debilitating consequences, even affecting patient quality of life. Understanding the respective clinicopathological characteristics and molecular mechanisms underlying salivary gland functioning during aging is vital for therapeutic purposes. Here, we provide a detailed atlas of the salivary gland microenvironment during aging, and we identified several phenotypes characteristic of aging salivary glands, including acini atrophy, increased inflammatory cells, altered immune responses, and accumulation of lysosomes and autophagosomes in aging cells, which may reflect progressive degeneration of salivary gland function. Furthermore, our analyses suggested significant enrichment of metabolic pathways in aging glands. Our results revealed complex cellular cross-talk among aging acinar cells, inflammatory factors, and immune responses. A natural aging animal model was established to verify these findings. This study provides mechanistic insights into age-related clinicopathogenesis, important implications for early diagnosis, and identification of new targets for improving salivary gland dysfunction.
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Affiliation(s)
- Ning Li
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yulin Ye
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yicheng Wu
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Lei Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiawei Hu
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Danyang Luo
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yusi Li
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Yang
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yiming Gao
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Wangxi Hai
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Corresponding author
| | - Yinyin Xie
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Corresponding author
| | - Liting Jiang
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- Corresponding author
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243
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Wang Z, Deng Q, Gu Y, Li M, Chen Y, Wang J, Zhang Y, Zhang J, Hu Q, Zhang S, Chen W, Chen Z, Li J, Wang X, Liang H. Integrated single-nucleus sequencing and spatial architecture analysis identified distinct injured-proximal tubular types in calculi rats. Cell Biosci 2023; 13:92. [PMID: 37208718 DOI: 10.1186/s13578-023-01041-3] [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: 10/31/2022] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Urolithiasis with high prevalence and recurrence rate, has impacts on kidney injury in patients, becomes a socioeconomic and healthcare problem in worldwide. However, the biology of kidney with crystal formation and proximal tubular injury remains essentially unclear. The present study aims to evaluate the cell biology and immune-communications in urolithiasis mediated kidney injury, to provide new insights in the kidney stone treatment and prevention. RESULTS We identified 3 distinct injured-proximal tubular cell types based on the differentially expression injury markers (Havcr1 and lcn2) and functional solute carriers (slc34a3, slc22a8, slc38a3 and slc7a13), and characterized 4 main immune cell types in kidney and one undefined cell population, where F13a1+/high/CD163+/high monocyte & macrophage and Sirpa/Fcgr1a/Fcgr2a+/high granulocyte were the most enriched. We performed intercellular crosstalk analysis based on the snRNA-seq data and explored the potential immunomodulation of calculi stone formation, and founded that the interaction between ligand Gas6 and its receptors (Gas6-Axl, Gas6-Mertk) was specifically observed in the injured-PT1 cells, but not injured-PT2 and -PT3 cells. The interaction of Ptn-Plxnb2 was only observed between the injured-PT3 cells and its receptor enriched cells. CONCLUSIONS Present study comprehensively characterized the gene expression profile in the calculi rat kidney at single nucleus level, identified novel marker genes for all cell types of rat kidney, and determined 3 distinct sub-population of injured-PT clusters, as well as intercellular communication between injured-PTs and immune cells. Our collection of data provides a reliable resource and reference for studies on renal cell biology and kidney disease.
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Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Yanli Gu
- Central Laboratory, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Min Li
- Department of Pathology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Yeda Chen
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Jieyan Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Qiyi Hu
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Shenping Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Zhenhua Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Jiaying Li
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Xisheng Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China.
- Department of Urology, People's Hospital of Longhua, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong, 518109, P.R. China.
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China.
- Department of Urology, People's Hospital of Longhua, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong, 518109, P.R. China.
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Ying F, Guo J, Gao X, Huang L, Gao L, Cai J, Wang Z. Establishment of highly metastatic ovarian cancer model with omental tropism via in vivo selection. iScience 2023; 26:106719. [PMID: 37197325 PMCID: PMC10183668 DOI: 10.1016/j.isci.2023.106719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/15/2023] [Accepted: 04/18/2023] [Indexed: 05/19/2023] Open
Abstract
Epithelial ovarian cancer (OC) is often diagnosed at an advanced stage with peritoneal metastasis, and preclinical models mimicking the natural course of OC peritoneal metastasis are essential to improve treatment. We implanted ES2 and ID8 cells in the ovaries of mice and obtained highly metastatic (HM) sublines from their omental metastases after three cycles in vivo selection. Orthotopic xenografts derived from the HM sublines showed enhanced omental tropism and more extensive metastasis with earlier onset. The HM cells exhibited increased in vitro migration and invasion properties, and RNA sequencing revealed that the genes related to epithelial-mesenchymal transition and extracellular matrix regulation were significantly altered in the HM cells. Among them, the upregulated genes were significantly associated with poorer survival in OC patients. In conclusion, these HM sublines can be leveraged to establish spontaneous metastatic OC mouse models, which may serve as ideal preclinical models for anti-metastasis therapy for OC patients.
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Affiliation(s)
- Feiquan Ying
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jing Guo
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xuejiao Gao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lin Huang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lingling Gao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jing Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Corresponding author
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Corresponding author
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Ran L, Zhang S, Wang G, Zhao P, Sun J, Zhou J, Gan H, Jeon R, Li Q, Herrmann J, Wang F. Mitochondrial pyruvate carrier-mediated metabolism is dispensable for the classical activation of macrophages. Nat Metab 2023; 5:804-820. [PMID: 37188821 DOI: 10.1038/s42255-023-00800-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/05/2023] [Indexed: 05/17/2023]
Abstract
Glycolysis is essential for the classical activation of macrophages (M1), but how glycolytic pathway metabolites engage in this process remains to be elucidated. Glycolysis leads to production of pyruvate, which can be transported into the mitochondria by the mitochondrial pyruvate carrier (MPC) followed by utilization in the tricarboxylic acid cycle. Based on studies that used the MPC inhibitor UK5099, the mitochondrial route has been considered to be of significance for M1 activation. Using genetic approaches, here we show that the MPC is dispensable for metabolic reprogramming and activation of M1 macrophages. In addition, MPC depletion in myeloid cells has no impact on inflammatory responses and macrophage polarization toward the M1 phenotype in a mouse model of endotoxemia. While UK5099 reaches maximal MPC inhibitory capacity at approximately 2-5 μM, higher concentrations are required to inhibit inflammatory cytokine production in M1 and this is independent of MPC expression. Taken together, MPC-mediated metabolism is dispensable for the classical activation of macrophages and UK5099 inhibits inflammatory responses in M1 macrophages due to effects other than MPC inhibition.
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Affiliation(s)
- Linyu Ran
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- Medical College, Tongji University, Shanghai, China
| | - Song Zhang
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA
| | - Guosheng Wang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Pei Zhao
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- Medical College, Tongji University, Shanghai, China
| | - Jiaxing Sun
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiaqi Zhou
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haiyun Gan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ryounghoon Jeon
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (KMEDIhub), Daegu, Republic of Korea
| | - Qiang Li
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Joerg Herrmann
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Feilong Wang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
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Gao H, Jiang S, Wang Y, Hu M, Xue Y, Cao B, Dou H, Li R, Yi X, Jiang L, Zhang B, Li Y. Comparison of gut bacterial communities of Hyphantriacunea Drury (Lepidoptera, Arctiidae), based on 16S rRNA full-length sequencing. Biodivers Data J 2023; 11:e98143. [PMID: 38327372 PMCID: PMC10848398 DOI: 10.3897/bdj.11.e98143] [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: 11/29/2022] [Accepted: 04/14/2023] [Indexed: 02/09/2024] Open
Abstract
There are a large number of microorganisms in the gut of insects, which form a symbiotic relationship with the host during the long-term co-evolution process and have a significant impact on the host's nutrition, physiology, development, immunity, stress tolerance and other aspects. However, the composition of the gut microbes of Hyphantriacunea remains unclear. In order to investigate the difference and diversity of intestinal microbiota of H.cunea larvae feeding on different host plants, we used PacBio sequencing technology for the first time to sequence the 16S rRNA full-length gene of the intestinal microbiota of H.cunea. The species classification, β diversity and function of intestinal microflora of the 5th instar larvae of four species of H.cunea feeding on apricot, plum, redbud and Chinese ash were analysed. The results showed that a total of nine phyla and 65 genera were identified by PacBio sequencing, amongst which Firmicutes was the dominant phylum and Enterococcus was the dominant genus, with an average relative abundance of 59.29% and 52.16%, respectively. PERMANOVA analysis and cluster heat map showed that the intestinal microbiomes of H.cunea larvae, fed on different hosts, were significantly different. LEfSe analysis confirmed the effect of host diet on intestinal community structure and PICRUSt2 analysis showed that most of the predictive functions were closely related to material transport and synthetic, metabolic and cellular processes. The results of this study laid a foundation for revealing the interaction between the intestinal microorganisms of H.cunea and its hosts and provided ideas for exploring new green prevention and control strategies of H.cunea.
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Affiliation(s)
- Hui Gao
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
- School of Life Sciences, Shandong University, Qingdao, ChinaSchool of Life Sciences, Shandong UniversityQingdaoChina
| | - Sai Jiang
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Yinan Wang
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Meng Hu
- Forestry Protection and Development Service Center of Jining City, Jining, ChinaForestry Protection and Development Service Center of Jining CityJiningChina
| | - Yuyan Xue
- Qufu Bureau of Natural Resources and Planning, Qufu, ChinaQufu Bureau of Natural Resources and PlanningQufuChina
| | - Bing Cao
- Animal Husbandry and Fisheries Development Centre of Tengzhou, Tengzhou, ChinaAnimal Husbandry and Fisheries Development Centre of TengzhouTengzhouChina
| | - Hailong Dou
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Ran Li
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Xianfeng Yi
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Lina Jiang
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Bin Zhang
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot, Inner Mongolia Autonomous Region, ChinaCollege of Life Sciences and Technology, Inner Mongolia Normal UniversityHohhot, Inner Mongolia Autonomous RegionChina
| | - Yujian Li
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
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Zhang Y, Liu L, Wei C, Wang X, Li R, Xu X, Zhang Y, Geng G, Dang K, Ming Z, Tao X, Xu H, Yan X, Zhang J, Hu J, Li Y. Vitamin K2 supplementation improves impaired glycemic homeostasis and insulin sensitivity for type 2 diabetes through gut microbiome and fecal metabolites. BMC Med 2023; 21:174. [PMID: 37147641 PMCID: PMC10163743 DOI: 10.1186/s12916-023-02880-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND There is insufficient evidence for the ability of vitamin K2 to improve type 2 diabetes mellitus symptoms by regulating gut microbial composition. Herein, we aimed to demonstrate the key role of the gut microbiota in the improvement of impaired glycemic homeostasis and insulin sensitivity by vitamin K2 intervention. METHODS We first performed a 6-month RCT on 60 T2DM participants with or without MK-7 (a natural form of vitamin K2) intervention. In addition, we conducted a transplantation of the MK-7-regulated microbiota in diet-induced obesity mice for 4 weeks. 16S rRNA sequencing, fecal metabolomics, and transcriptomics in both study phases were used to clarify the potential mechanism. RESULTS After MK-7 intervention, we observed notable 13.4%, 28.3%, and 7.4% reductions in fasting serum glucose (P = 0.048), insulin (P = 0.005), and HbA1c levels (P = 0.019) in type 2 diabetes participants and significant glucose tolerance improvement in diet-induced obesity mice (P = 0.005). Moreover, increased concentrations of secondary bile acids (lithocholic and taurodeoxycholic acid) and short-chain fatty acids (acetic acid, butyric acid, and valeric acid) were found in human and mouse feces accompanied by an increased abundance of the genera that are responsible for the biosynthesis of these metabolites. Finally, we found that 4 weeks of fecal microbiota transplantation significantly improved glucose tolerance in diet-induced obesity mice by activating colon bile acid receptors, improving host immune-inflammatory responses, and increasing circulating GLP-1 concentrations. CONCLUSIONS Our gut-derived findings provide evidence for a regulatory role of vitamin K2 on glycemic homeostasis, which may further facilitate the clinical implementation of vitamin K2 intervention for diabetes management. TRIAL REGISTRATION The study was registered at https://www.chictr.org.cn (ChiCTR1800019663).
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Affiliation(s)
- Yuntao Zhang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Lin Liu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Chunbo Wei
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xuanyang Wang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Ran Li
- Department of Nutrition, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoqing Xu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Yingfeng Zhang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Guannan Geng
- Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Keke Dang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Zhu Ming
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xinmiao Tao
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Huan Xu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xuemin Yan
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Jia Zhang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Jinxia Hu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Ying Li
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China.
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248
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Nakandala U, Masouleh AK, Smith MW, Furtado A, Mason P, Constantin L, Henry RJ. Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes. HORTICULTURE RESEARCH 2023; 10:uhad058. [PMID: 37213680 PMCID: PMC10199705 DOI: 10.1093/hr/uhad058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/27/2023] [Indexed: 05/23/2023]
Abstract
Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus. Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased, with the available genomes of varying accuracy and completeness. We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species; Citrus australis (round lime) using highly accurate PacBio HiFi long reads, complemented with Hi-C scaffolding. Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C. australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness (BUSCO). Repeat analysis showed that more than 50% of the genome contained interspersed repeats. Among them, LTR elements were the predominant type (21.0%), of which LTR Gypsy (9.8%) and LTR copia (7.7%) elements were the most abundant repeats. A total of 29 464 genes and 32 009 transcripts were identified in the genome. Of these, 28 222 CDS (25 753 genes) had BLAST hits and 21 401 CDS (75.8%) were annotated with at least one GO term. Citrus specific genes for antimicrobial peptides, defense, volatile compounds and acidity regulation were identified. The synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2, 4, 7 and 8. This chromosome scale, and haplotype resolved C. australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.
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Affiliation(s)
- Upuli Nakandala
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
| | - Ardashir Kharabian Masouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
| | - Malcolm W Smith
- Department of Agriculture and Fisheries, Bundaberg Research Station, Bundaberg, Queensland 4670, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
| | - Patrick Mason
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
| | - Lena Constantin
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
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249
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Wang Z, Li Y, Zhao W, Jiang S, Huang Y, Hou J, Zhang X, Zhai Z, Yang C, Wang J, Zhu J, Pan J, Jiang W, Li Z, Ye M, Tan M, Jiang H, Dang Y. Integrative multi-omics and drug-response characterization of patient-derived prostate cancer primary cells. Signal Transduct Target Ther 2023; 8:175. [PMID: 37121942 PMCID: PMC10149505 DOI: 10.1038/s41392-023-01393-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 05/02/2023] Open
Abstract
Prostate cancer (PCa) is the second most prevalent malignancy in males across the world. A greater knowledge of the relationship between protein abundance and drug responses would benefit precision treatment for PCa. Herein, we establish 35 Chinese PCa primary cell models to capture specific characteristics among PCa patients, including gene mutations, mRNA/protein/surface protein distributions, and pharmaceutical responses. The multi-omics analyses identify Anterior Gradient 2 (AGR2) as a pre-operative prognostic biomarker in PCa. Through the drug library screening, we describe crizotinib as a selective compound for malignant PCa primary cells. We further perform the pharmacoproteome analysis and identify 14,372 significant protein-drug correlations. Surprisingly, the diminished AGR2 enhances the inhibition activity of crizotinib via ALK/c-MET-AKT axis activation which is validated by PC3 and xenograft model. Our integrated multi-omics approach yields a comprehensive understanding of PCa biomarkers and pharmacological responses, allowing for more precise diagnosis and therapies.
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Affiliation(s)
- Ziruoyu Wang
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Yanan Li
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Wensi Zhao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shuai Jiang
- Department of Urology, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
- Department of Urology, Zhongshan Hospital Wusong Branch, Fudan University, 200032, Shanghai, China
| | - Yuqi Huang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jun Hou
- Department of Urology, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Xuelu Zhang
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, 400016, Chongqing, China
| | - Zhaoyu Zhai
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, 400016, Chongqing, China
| | - Chen Yang
- Department of Urology, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Jiaqi Wang
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Jiying Zhu
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Jianbo Pan
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, 400016, Chongqing, China
| | - Wei Jiang
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Zengxia Li
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China.
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China.
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, 400016, Chongqing, China.
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250
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Zeng X, Wang Y, Liu B, Rao X, Cao C, Peng F, Zhi W, Wu P, Peng T, Wei Y, Chu T, Xu M, Xu Y, Ding W, Li G, Lin S, Wu P. Multi-omics data reveals novel impacts of human papillomavirus integration on the epigenomic and transcriptomic signatures of cervical tumorigenesis. J Med Virol 2023; 95:e28789. [PMID: 37212325 DOI: 10.1002/jmv.28789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023]
Abstract
Integration of human papilloma virus (HPV) DNA into the human genome may progressively contribute to cervical carcinogenesis. To explore how HPV integration affects gene expression by altering DNA methylation during carcinogenesis, we analyzed a multiomics dataset for cervical cancer. We obtained multiomics data by HPV-capture sequencing, RNA sequencing, and Whole Genome Bisulfite Sequencing from 50 patients with cervical cancer. We detected 985 and 485 HPV-integration sites in matched tumor and adjacent paratumor tissues. Of these, LINC00486 (n = 19), LINC02425 (n = 11), LLPH (n = 11), PROS1 (n = 5), KLF5 (n = 4), LINC00392 (n = 3), MIR205HG (n = 3) and NRG1 (n = 3) were identified as high-frequency HPV-integrated genes, including five novel recurrent genes. Patients at clinical stage II had the highest number of HPV integrations. E6 and E7 genes of HPV16 but not HPV18 showed significantly fewer breakpoints than random distribution. HPV integrations occurring in exons were associated with altered gene expression in tumor tissues but not in paratumor tissues. A list of HPV-integrated genes regulated at transcriptomic or epigenetic level was reported. We also carefully checked the candidate genes with regulation pattern correlated in both levels. HPV fragments integrated at MIR205HG mainly came from the L1 gene of HPV16. RNA expression of PROS1 was downregulated when HPV integrated in its upstream region. RNA expression of MIR205HG was elevated when HPV integrated into its enhancer. The promoter methylation levels of PROS1 and MIR205HG were all negatively correlated with their gene expressions. Further experimental validations proved that upregulation of MIR205HG could promote the proliferative and migrative abilities of cervical cancer cells. Our data provides a new atlas for epigenetic and transcriptomic regulations regarding HPV integrations in cervical cancer genome. We demonstrate that HPV integration may affect gene expression by altering methylation levels of MIR205HG and PROS1. Our study provides novel biological and clinical insights into HPV-induced cervical cancer.
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Affiliation(s)
- Xi Zeng
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuyouye Wang
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Binghan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinjie Rao
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Canhui Cao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fang Peng
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wenhua Zhi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ye Wei
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Chu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yashi Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wencheng Ding
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guoliang Li
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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