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Peng L, Liu Z, Liu P, Guo W, Liu T, Lei Z, Chang Q, Zhang M, Lin X, Wang F, Wu S. Genome-wide association analysis to search for new loci associated with stroke risk in Northwestern Chinese population. Gene 2024; 928:148807. [PMID: 39094715 DOI: 10.1016/j.gene.2024.148807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND AND PURPOSE Genetic factors play an important role in the pathogenesis of stroke(S). This study aimed to screen the loci associated with S risk in northwestern Chinese population by genome-wide association analysis (GWAS). METHODS A total of 1394 subjects, including 682 S patients and 692 controls, were enrolled in this study. SPSS 25.0 software was used for statistical analysis, and the independent sample t-test as well as Chi-square test were used to analyze the differences in age and gender between the case and control groups. The Precision Medicine Diversity Array (PMDA) genotyping chip was used in this study. The genotyping platform was the Gene Titan multi-channel instrument, and the Axiom Analysis Suite 6.0 software was used for the data analyzing. Besides, the LASSO analysis, SNP-SNP and GO/KEGG analysis were conducted to analyze the association between significant loci and S risk. RESULTS A total of 30 SNPs were found to be associated with the S risk based on additive model (p < 5 × 10-8). After the LASSO screening, 22 SNPs showed the diagnostic value in S. The SNPs interaction analysis further screened the SNP-SNP interaction groups associated with the S risk(p < 0.05). Finally, the GO/KEGG analysis discovered the suggestive significance loci could be involved in the S development mainly by immune-related functions and pathways. CONCLUSION This study discovered 30 S related SNPs and analyzed the potential pathways associated with genes located on the 30 SNPs, which were beneficial for enriching the genetic mechanism analysis of S in northwestern Chinese population.
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Affiliation(s)
- Linna Peng
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Zhongzhong Liu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China; Department of Epidemiology and Biostatistics, School of Public Health of Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Pei Liu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Weiyan Guo
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Tong Liu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Zhen Lei
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Qiaoqiao Chang
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Mi Zhang
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Xuemei Lin
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Fang Wang
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Songdi Wu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China; College of Life Science, Northwest University, Xi'an 710069, China.
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Pawar P, Akolkar K, Saxena V. An integrated bioinformatics approach reveals the potential role of microRNA-30b-5p and let-7a-5p during SARS CoV-2 spike-1 mediated neuroinflammation. Int J Biol Macromol 2024; 277:134329. [PMID: 39098684 DOI: 10.1016/j.ijbiomac.2024.134329] [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: 04/01/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
SARS-CoV-2 induced neuroinflammation contributing to neurological sequelae is one of the critical outcomes of long-COVID, however underlying regulatory mechanisms involved therein are poorly understood. We deciphered the profile of dysregulated microRNAs, their targets, associated pathways, protein-protein interactions (PPI), transcription factor-hub genes interaction networks, hub genes-microRNA co-regulatory networks in SARS-CoV-2 Spike-1 (S1) stimulated microglial cells along with candidate drug prediction using RNA-sequencing and multiple bioinformatics approaches. We identified 11 dysregulated microRNAs in the S1-stimulated microglial cells (p < 0.05). KEGG analysis revealed involvement of important neuroinflammatory pathways such as MAPK signalling, PI3K-AKT signalling, Ras signalling and axon guidance. PPI analysis further identified 11 hub genes involved in these pathways. Real time PCR validation confirmed a significant upregulation of microRNA-30b-5p and let-7a-5p; proinflammatory cytokines- IL-6, TNF-α, IL-1β, GM-CSF; and inflammatory genes- PIK3CA and AKT in the S1-stimulated microglial cells, while PTEN and SHIP1 expression was decreased as compared to the non-stimulated cells. Drug prediction analysis further indicated resveratrol, diclofenac and rapamycin as the potential drugs based on their degree of interaction with hub genes. Thus, targeting of these microRNAs and/or their intermediate signalling molecules would be a prospective immunotherapeutic approach in alleviating SARS-CoV-2-S1 mediated neuroinflammation; and needs further investigations.
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Affiliation(s)
- Puja Pawar
- Division of Immunology and Serology, ICMR-National Institute of Translational Virology & AIDS Research (NITVAR), MIDC, Bhosari, Pune, Maharashtra, India
| | - Kadambari Akolkar
- Division of Immunology and Serology, ICMR-National Institute of Translational Virology & AIDS Research (NITVAR), MIDC, Bhosari, Pune, Maharashtra, India
| | - Vandana Saxena
- Division of Immunology and Serology, ICMR-National Institute of Translational Virology & AIDS Research (NITVAR), MIDC, Bhosari, Pune, Maharashtra, India.
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3
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Guinard I, Brassard-Jollive N, Ruch L, Weber J, Eckly A, Boscher J, Léon C. Mechanical confinement prevents ectopic platelet release. Proc Natl Acad Sci U S A 2024; 121:e2407829121. [PMID: 39236232 DOI: 10.1073/pnas.2407829121] [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: 04/19/2024] [Accepted: 08/03/2024] [Indexed: 09/07/2024] Open
Abstract
Blood platelets are produced by megakaryocytes (MKs), their parent cells, which are in the bone marrow. Once mature, MK pierces through the sinusoid vessel, and the initial protrusion further elongates as proplatelet or buds to release platelets. The mechanisms controlling the decision to initiate proplatelet and platelet formation are unknown. Here, we show that the mechanical properties of the microenvironment prevent proplatelet and platelet release in the marrow stroma while allowing this process in the bloodstream. Loss of marrow confinement following myelosuppression led to inappropriate proplatelet and platelet release into the extravascular space. We further used an inert viscoelastic hydrogel to evaluate the impact of compressive stress. Transcriptional analysis showed that culture in three-dimensional gel induced upregulation of genes related to the Rho-GTPase pathway. We found higher Rho-GTPase activation, myosin light chain phosphorylation and F-actin under mechanical constraints while proplatelet formation was inhibited. The use of latrunculin-A to decrease F-actin promoted microtubule-dependent budding and proplatelet extension inside the gel. Additionally, ex vivo exposure of intact bone marrow to latrunculin-A triggered proplatelet extensions in the interstitial space. In vivo, this confinement-mediated high intracellular tension is responsible for the formation of the peripheral zone, a unique actin-rich structure. Cytoskeleton reorganization induces the disappearance of the peripheral zone upon reaching a liquid milieu to facilitate proplatelet and platelet formation. Hence, our data provide insight into the mechanisms preventing ectopic platelet release in the marrow stroma. Identifying such pathways is especially important for understanding pathologies altering marrow mechanics such as chemotherapy or myelofibrosis.
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Affiliation(s)
- Ines Guinard
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
| | - Noémie Brassard-Jollive
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
| | - Laurie Ruch
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
| | - Josiane Weber
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
| | - Anita Eckly
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
| | - Julie Boscher
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
| | - Catherine Léon
- University of Strasbourg, INSERM, Etablissement Français du Sang (EFS) Grand-Est, UMR_S1255 Biologie et Pharmacologie des Plaquettes Sanguines (BPPS), FMTS, Strasbourg F-67065, France
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Müller MN, Vicente Ferreira Junior A, Zanardi Lamardo E, Yogui GT, Flores Montes MDJ, Silva MA, Lima EJAC, Rojas LAV, Jannuzzi LGDS, Cunha MDGGDS, Melo PAMDC, Carvalho VPCD, Carneiro YMM, Carreira RDS, Araujo M, Santos LPDS. Finding the needle in a haystack: Evaluation of ecotoxicological effects along the continental shelf break during the Brazilian mysterious oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124422. [PMID: 38914197 DOI: 10.1016/j.envpol.2024.124422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/01/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Oceanic oil spills present significant ecological risks that have the potential to contaminate extensive areas, including coastal regions. The occurrence of the 2019 oil spill event in Brazil resulted in over 3000 km of contaminated beaches and shorelines. While assessing the impact on benthic and beach ecosystems is relatively straightforward due to direct accessibility, evaluating the ecotoxicological effects of open ocean oil spills on the pelagic community is a complex task. Difficulties are associated with the logistical challenges of responding promptly and, in case of the Brazilian mysterious oil spill, to the subsurface propagation of the oil that impeded remote visual detection. An oceanographic expedition was conducted in order to detect and evaluate the impact of this oil spill event along the north-eastern Brazilian continental shelf. The pursuit of dissolved and dispersed oil compounds was accomplished by standard oceanographic methods including seawater polycyclic aromatic hydrocarbons (PAHs) analysis, biomass stable carbon isotope (δ13C), particulate organic carbon to particulate organic nitrogen (POC:PON) ratios, nutrient analysis and ecotoxicological bioassays using the naupliar phase of the copepod Tisbe biminiensis. Significant ecotoxicological effects, reducing naupliar development by 20-40 %, were indicated to be caused by the presence of dispersed oil in the open ocean. The heterogeneous distribution of oil droplets aggravated the direct detection and biochemical indicators for oil are presented and discussed. Our findings serve as a case study for identifying and tracing subsurface propagation of oil, demonstrating the feasibility of utilizing standard oceanographic and ecotoxicological methods to assess the impacts of oil spill events in the open ocean. Ultimately, it encourages the establishment of appropriate measures and responses regarding the liability and regulation of entities to be held accountable for oil spills in the marine environment.
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Affiliation(s)
- Marius Nils Müller
- Department of Oceanography, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil; Macau Environmental Research Institute, Macau University of Science and Technology, Macau SAR, 999078, China.
| | | | - Eliete Zanardi Lamardo
- Department of Oceanography, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Gilvan Takeshi Yogui
- Department of Oceanography, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | | | - Marcus André Silva
- Department of Oceanography, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | | | | | | | | | | | | | | | - Renato da Silva Carreira
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, RJ, 22451-900, Brazil
| | - Moacyr Araujo
- Department of Oceanography, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
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Liang H, Yin G, Feng D, Chen H, Liu X, Li J. Research trends on nanomaterials in triple negative breast cancer (TNBC): a bibliometric analysis from 2010 to 2024. Drug Deliv Transl Res 2024:10.1007/s13346-024-01704-9. [PMID: 39242466 DOI: 10.1007/s13346-024-01704-9] [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] [Accepted: 08/26/2024] [Indexed: 09/09/2024]
Abstract
Breast cancer (BC) is an important cause of cancer-related death in the world. As a subtype of BC with the worst prognosis, triple-negative breast cancer (TNBC) is a serious threat to human life and health. In recent years, there has been an increasing amount of research aimed at designing and developing nanomaterials for the diagnosis and treatment of TNBC. The purpose of this study was to comprehensively evaluate the current status and trend of the application of nanomaterials in TNBC through bibliometric analysis. Studies focusing on nanomaterials and cancer were searched from the Web of Science core collection (WOSCC) database, and relevant literature meeting the inclusion criteria was selected for inclusion in the study. VOSviewer and CiteSpace were used to perform bibliometric and visual analysis of the included publications. A total of 2338 studies were included. Annual publications have increased from 2010 to 2024. China, the United States and India were the leading countries in the field, accounting for 66.1%, 11.5% and 7.2% of publications, respectively. The Chinese Academy of Sciences and Li Yaping were the most influential institutions and authors, respectively. Journal of Controlled Release was considered the most productive journal. Cancer Research was considered to be the most co-cited journal. Drug delivery and anti-cancer mechanisms related to nanomaterials were considered to be the most widely studied aspects, and green synthesis and anti-cancer mechanisms were also recent research hotspots. In this study, the characteristics of publications were summarized, and the most influential countries, institutions, authors, journals, hot spots and trends in the application of nanomaterials in cancer were identified. These findings provide valuable insights into the current state and future direction of this dynamic field.
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Affiliation(s)
- Hongyi Liang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, China
| | - Guoliang Yin
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, China
| | - Dandan Feng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, China
| | - Hanhan Chen
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Jinan, Shandong, 250014, China
| | - Xiaofei Liu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Jinan, Shandong, 250014, China
| | - Jingwei Li
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 16369 Jingshi Road, Jinan, Shandong, 250014, China.
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6
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Jang Y, Kang S, Han H, Kang CM, Cho NH, Kim BG. Fibrosis-Encapsulated Tumoroid, A Solid Cancer Assembloid Model for Cancer Research and Drug Screening. Adv Healthc Mater 2024:e2402391. [PMID: 39233539 DOI: 10.1002/adhm.202402391] [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: 06/30/2024] [Revised: 08/12/2024] [Indexed: 09/06/2024]
Abstract
Peritumoral fibrosis is known to promote cancer progression and confer treatment resistance in various solid tumors. Consequently, developing accurate cancer research and drug screening models that replicate the structure and function of a fibrosis-surrounded tumor mass is imperative. Previous studies have shown that self-assembly three-dimensional (3D) co-cultures primarily produce cancer-encapsulated fibrosis or maintain a fibrosis-encapsulated tumor mass for a short period, which is inadequate to replicate the function of fibrosis, particularly as a physical barrier. To address this limitation, a multi-layer spheroid formation method is developed to create a fibrosis-encapsulated tumoroid (FET) structure that maintains structural stability for up to 14 days. FETs exhibited faster tumor growth, higher expression of immunosuppressive cytokines, and equal or greater resistance to anticancer drugs compared to their parental tumoroids. Additionally, FETs serve as a versatile model for traditional cancer research, enabling the study of exosomal miRNA and gene functions, as well as for mechanobiology research when combined with alginate hydrogel. Our findings suggest that the FET represents an advanced model that more accurately mimics solid cancer tissue with peritumoral fibrosis. It may show potential superiority over self-assembly-based 3D co-cultures for cancer research and drug screening, and holds promise for personalized drug selection in cancer treatment.
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Affiliation(s)
- Yeonsue Jang
- Department of Urological Science Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Suki Kang
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyunho Han
- Department of Urological Science Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Chang Moo Kang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Nam Hoon Cho
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Baek Gil Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
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7
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Shahzad K, Zhang M, Mubeen I, Zhang X, Guo L, Qi T, Feng J, Tang H, Qiao X, Wu J, Xing C. Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton. Funct Integr Genomics 2024; 24:156. [PMID: 39230785 DOI: 10.1007/s10142-024-01420-0] [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: 07/10/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 09/05/2024]
Abstract
The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced GI isoform Gh_A02G0645_N17 significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene ELF in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.
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Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Meng Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Iqra Mubeen
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Liping Guo
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Huini Tang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Jianyong Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
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8
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McGowan EC, Storry JR, Olsson ML. An intronic polymorphism associated with 2,3-bisphosphoglycerate levels in human red cells is linked to expression of RhCE blood groups. Proc Natl Acad Sci U S A 2024; 121:e2412585121. [PMID: 39172775 DOI: 10.1073/pnas.2412585121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Affiliation(s)
- Eunike C McGowan
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Biomedical Center C14, Lund University, Lund SE-221 84, Sweden
| | - Jill R Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Biomedical Center C14, Lund University, Lund SE-221 84, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund SE-221 85, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Biomedical Center C14, Lund University, Lund SE-221 84, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund SE-221 85, Sweden
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Li J, Wang D, Hao X, Li Y, Gao H, Fan Y, Fang B, Guo Y. Exploring the high-quality ingredients and mechanisms of Da Chuanxiong Formula in the treatment of neuropathic pain based on network pharmacology, molecular docking, and molecular dynamics simulation. Biomed Pharmacother 2024; 178:117195. [PMID: 39068852 DOI: 10.1016/j.biopha.2024.117195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
Da Chuanxiong Formula (DCXF) is a traditional herbal prescription used for pain management. It consists of Chuanxiong Rhizoma (CR) and Gastrodiae Rhizoma (GR). Despite its long history of use, the underlying therapeutic mechanism of DCXF remains insufficiently understood. Therefore, in this study, key target genes were obtained through network pharmacology research methods and molecular docking techniques, including transient receptor potential vanilloid 1 (TRPV1), adenosine A2a receptor (ADORA2A), nuclear receptor subfamily 3 group C member 1 (NR3C1), and protein kinase C beta (PRKCB). Molecular dynamics simulations demonstrated the favorable binding between all four key genes and their corresponding compounds. Notably, chronic constriction injury (CCI) treatment resulted in a significant decrease in mechanical threshold and thermal latency period for rat foot contraction, which was ameliorated upon administration of DCXF. Furthermore, real-time quantitative reverse transcription PCR (RT-qPCR) and western blot (WB) analyses indicated an upregulation of TRPV1, ADORA2A, NR3C1, and PRKCB expression in the rat dorsal root ganglion following CCI, which was attenuated by treatment with DCXF. The expressions of inflammatory factors, including tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6), in the rat dorsal root ganglion were assessed using ELISA, confirming consistent trends with the aforementioned findings. The results of this study offer a promising theoretical foundation for the utilization of DCXF in the treatment of neuropathic pain (NP).
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Affiliation(s)
- Jinshi Li
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Dongxu Wang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Xiaotong Hao
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Yuan Li
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Hairong Gao
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Yiting Fan
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Bo Fang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China.
| | - Yang Guo
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, China.
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Feehan J, Tripodi N, Kondrikov D, Wijeratne T, Gimble J, Hill W, Apostolopoulos V, Duque G. Differential Responses to Aging Among the Transcriptome and Proteome of Mesenchymal Progenitor Populations. J Gerontol A Biol Sci Med Sci 2024; 79:glae147. [PMID: 38837176 PMCID: PMC11369222 DOI: 10.1093/gerona/glae147] [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: 12/29/2023] [Indexed: 06/06/2024] Open
Abstract
The biological aging of stem cells (exhaustion) is proposed to contribute to the development of a variety of age-related conditions. Despite this, little is understood about the specific mechanisms which drive this process. In this study, we assess the transcriptomic and proteomic changes in 3 different populations of mesenchymal progenitor cells from older (50-70 years) and younger (20-40 years) individuals to uncover potential mechanisms driving stem cell exhaustion in mesenchymal tissues. To do this, we harvested primary bone marrow mesenchymal stem and progenitor cells (MPCs), circulating osteoprogenitors (COP), and adipose-derived stem cells (ADSCs) from younger and older donors, with an equal number of samples from men and women. These samples underwent RNA sequencing and label-free proteomic analysis, comparing the younger samples to the older ones. There was a distinct transcriptomic phenotype in the analysis of pooled older stem cells, suggestive of suppressed proliferation and differentiation; however, these changes were not reflected in the proteome of the cells. Analyzed independently, older MPCs had a distinct phenotype in both the transcriptome and proteome consistent with altered differentiation and proliferation with a proinflammatory immune shift in older adults. COP cells showed a transcriptomic shift to proinflammatory signaling but no consistent proteomic phenotype. Similarly, ADSCs displayed transcriptomic shifts in physiologies associated with cell migration, adherence, and immune activation but no proteomic change with age. These results show that there are underlying transcriptomic changes with stem cell aging that may contribute to a decline in tissue regeneration. However, the proteome of the cells was inconsistently regulated.
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Affiliation(s)
- Jack Feehan
- Department of Medicine—Western Health, University of Melbourne, Melbourne, Victoria, Australia
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Nicholas Tripodi
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Western Health, Victoria University and University of Melbourne, Melbourne, Victoria, Australia
| | - Dmitry Kondrikov
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tissa Wijeratne
- Department of Medicine—Western Health, University of Melbourne, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Western Health, Victoria University and University of Melbourne, Melbourne, Victoria, Australia
| | - Jeffrey Gimble
- Center for Stem Cell Research and Regenerative Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - William Hill
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center, Charleston, South Carolina, USA
- Center for Healthy Aging, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Western Health, Victoria University and University of Melbourne, Melbourne, Victoria, Australia
| | - Gustavo Duque
- Bone, Muscle & Geroscience Research Group, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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11
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Li W, Wang Y, Gao J, Wang A. Antimicrobial resistance and its risks evaluation in wetlands on the Qinghai-Tibetan Plateau. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116699. [PMID: 38981389 DOI: 10.1016/j.ecoenv.2024.116699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/11/2024]
Abstract
Amidst the global antimicrobial resistance (AMR) crisis, antibiotic resistance has permeated even the most remote environments. To understand the dissemination and evolution of AMR in minimally impacted ecosystems, the resistome and mobilome of wetlands across the Qinghai-Tibetan Plateau and its marginal regions were scrutinized using metagenomic sequencing techniques. The composition of wetland microbiomes exhibits significant variability, with dominant phyla including Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Notably, a substantial abundance of Antibiotic Resistance Genes (ARGs) and Mobile Genetic Elements (MGEs) was detected, encompassing 17 ARG types, 132 ARG subtypes, and 5 types of MGEs (Insertion Sequences, Insertions Sequences, Genomic Islands, Transposons, and Integrative Conjugative Elements). No significant variance was observed in the prevalence of resistome and mobilome across different wetland types (i.e., the Yellow River, other rivers, lakes, and marshes) (R=-0.5882, P=0.607). The co-occurrence of 74 ARG subtypes and 22 MGEs was identified, underscoring the pivotal role of MGEs in shaping ARG pools within the Qinghai-Tibetan Plateau wetlands. Metagenomic binning and analysis of assembled genomes (MAGs) revealed that 93 out of 206 MAGs harbored ARGs (45.15 %). Predominantly, Burkholderiales, Pseudomonadales, and Enterobacterales were identified as the primary hosts of these ARGs, many of which represent novel species. Notably, a substantial proportion of ARG-carrying MAGs also contained MGEs, reaffirming the significance of MGEs in AMR dissemination. Furthermore, utilizing the arg_ranker framework for risk assessment unveiled severe contamination of high-risk ARGs across most plateau wetlands. Moreover, some prevalent human pathogens were identified as potential hosts for these high-risk ARGs, posing substantial transmission risks. This study aims to investigate the prevalence of resistome and mobilome in wetlands, along with evaluating the risk posed by high-risk ARGs. Such insights are crucial for informing environmental protection strategies and facilitating the management of water resources on the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Weiwei Li
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Yanfang Wang
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Jianxin Gao
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Ailan Wang
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China.
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12
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Anagnostou E, Kouvli M, Karagianni E, Gamvroula A, Kalamatianos T, Stranjalis G, Skoularidou M. Romberg's test revisited: Changes in classical and advanced sway metrics in patients with pure sensory neuropathy. Neurophysiol Clin 2024; 54:102999. [PMID: 39042993 DOI: 10.1016/j.neucli.2024.102999] [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: 04/27/2024] [Revised: 06/09/2024] [Accepted: 06/19/2024] [Indexed: 07/25/2024] Open
Abstract
OBJECTIVES The Romberg test, undoubtedly a classical and well-established method in physical neurological assessment of patients with sensory ataxia, has long been suspected to be prone to several limitations. Here, we quantified upright stance before and after visual deprivation in a selected cohort of patients with pure sensory neuropathy. METHODS Static balance was assessed in sensory neuropathy patients during quiet stance on a force platform under different visual and proprioceptive feedback conditions. Sural nerve neurography was employed to evaluate the severity of peripheral neuropathy. Conventional and advanced postural sway metrics were investigated to draw a quantitative analogy to the clinical Romberg test. RESULTS Posturographic analyses showed that patients displayed Romberg and vestibular Romberg quotient values around 2, indicating an approximately twofold increase in body sway in the absence of vision. However, the diagnostic discrimination ability between patients and controls was only modest. Even less impactful were the diagnostic contributions of frequency domain and non-linear sway analyses. This was primarily attributed to the heightened body sway exhibited by patients with sensory neuropathy under 'eyes open' conditions, diminishing the contrast with the 'eyes closed' condition as assessed in the classical Romberg test. CONCLUSION We conclude that the Romberg test, even in its quantitative form with the aid of an apparatus, had an unsatisfactory classification value in terms of distinguishing patients from healthy controls. Instead, it should be interpreted within the comprehensive context of the broader neurological examination and the electrodiagnosis of peripheral nerve function.
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Affiliation(s)
- Evangelos Anagnostou
- Department of Neurology, University of Athens, Eginition Hospital, Athens, Greece.
| | - Maria Kouvli
- Department of Neurology, University of Athens, Eginition Hospital, Athens, Greece
| | - Evangelia Karagianni
- Department of Neurology, University of Athens, Eginition Hospital, Athens, Greece
| | - Anastasia Gamvroula
- Department of Neurology, University of Athens, Eginition Hospital, Athens, Greece
| | | | - George Stranjalis
- Department of Neurosurgery, University of Athens, Evangelismos Hospital, Athens, Greece
| | - Maria Skoularidou
- Department of Neurology, University of Athens, Eginition Hospital, Athens, Greece; The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
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13
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Shu X, Hua G, Zheng X, Chen Z, Zhang J, Zhuang W, Chen J. Screening of reliable reference genes for the normalization of RT-qPCR in chicken oviduct tract. Poult Sci 2024; 103:103980. [PMID: 38959666 PMCID: PMC11269787 DOI: 10.1016/j.psj.2024.103980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Utilizing publicly available RNA-seq data to screen for ideal reference genes is more efficient and accurate than traditional methods. Previous studies have identified optimal reference genes in various chicken tissues, but none have specifically focused on the oviduct (including the infundibulum, magnum, isthmus, uterus, and vagina), which is crucial for egg production. Identifying stable reference genes in the oviduct is essential for improving research on gene expression levels. This study investigated genes with consistent expression patterns in the chicken oviduct, encompassing both individual oviduct tract tissues and the entire oviduct, by utilizing multiple RNA-seq datasets. The screening results revealed the discovery of 100 novel reference genes in each segment of oviduct tissues, primarily associated with cell cycle regulation and RNA binding. Moreover, the majority of housekeeping genes (HKGs) showed inconsistent expression levels across distinct samples, suggesting their lack of stability under varying conditions. The stability of the newly identified reference genes was assessed in comparison to previously validated stable reference genes in chicken oviduct and commonly utilized HKGs, employing traditional reference gene screening methods. HERPUD2, CSDE1, VPS35, PBRM1, LSM14A, and YWHAB were identified to be suitable novel reference gene for different parts of the oviduct. HERPUD2 and YWHAB were reliable for gene expression normalization throughout the oviduct tract. Furthermore, overexpression and interference assays in DF1 cells showed LSM14A and YWHAB play a crucial role in cell proliferation, highlighting the importance of these newly reference genes for further research. Overall, this study has expanded the options for reference genes in RT-qPCR experiments in different segments of the chicken oviduct and the entire oviduct.
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Affiliation(s)
- Xin Shu
- Jiangsu Key Laboratory of Sericultural Biology and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaotong Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Ziwei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Jilong Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Wuchao Zhuang
- Jiangsu Key Laboratory of Sericultural Biology and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jianfei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.
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14
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Zeng H, Lai J, Liu Z, Liu W, Zhang Y. Specific blood metabolite associations with Gout: a Mendelian randomization study. Eur J Clin Nutr 2024:10.1038/s41430-024-01497-7. [PMID: 39215202 DOI: 10.1038/s41430-024-01497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE Gout, common metabolic disorders, have poorly understood links with blood metabolites. Exploring these relationships could enhance clinical prevention and treatment strategies. METHODS We applied bidirectional two-sample Mendelian randomization (MR) analysis, using data from a genome-wide association (GWAS) study of 486 blood metabolites. Gout data was obtained from FinnGen R8 (7461 gout and 221,323 control cases). We implemented the inverse variance-weighted (IVW) method for main analytical approach. Extensive heterogeneity, pleiotropy tests, leave-one-out analysis, and reverse MR were conducted to validate the robustness of our findings. Both Bonferroni and False Discovery Rate (FDR) corrections were used to adjust for multiple comparisons, ensuring stringent validation of our results. RESULTS Initial MR identified 31 candidate metabolites with potential genetic associations to gout. Following rigorous sensitivity analysis, 23 metabolites as potential statistical significance after final confirmation. These included metabolites enhancing gout risk such as X-11529 (OR = 1.225, 95% CI 1.112-1.350, P < 0.001), as well as others like piperine and stachydrine, which appeared to confer protective effects. The analysis was strengthened by reverse MR analysis. Additionally, an enrichment analysis was conducted, suggesting that 1-methylxanthine may be involved in the metabolic process of gout through the caffeine metabolism pathway. CONCLUSION Identifying causal metabolites offers new insights into the mechanisms influencing gout, suggesting pathways for future research and potential therapeutic targets.
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Affiliation(s)
- Huiqiong Zeng
- Traditional Chinese Medicine Department of Immunology, Women & Children Health Institute Futian Shenzhen, #2002 Jintian Road, Shenzhen, 518000, China
| | - Junda Lai
- Department of Human Life Sciences, Beijing Sport University, Haidian district, Beijing, #48 Xinxi Road, 100029, China
| | - Zhihang Liu
- Department of National Cybersecurity Center, Wuhan University, Wuchang District, #299 Bayi Road, Wuhan, 430072, Hubei, China
| | - Wei Liu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine; National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, #314 Anshanxi Road, Tianjin, 300381, China.
| | - Ye Zhang
- Traditional Chinese Medicine Department of Immunology, Women & Children Health Institute Futian Shenzhen, #2002 Jintian Road, Shenzhen, 518000, China.
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15
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He S, Hao L, Chen Y, Gong B, Xu X. Chinese herbal Jianpi Jiedu formula suppressed colorectal cancer growth in vitro and in vivo via modulating hypoxia-inducible factor 1 alpha-mediated fibroblasts activation. JOURNAL OF ETHNOPHARMACOLOGY 2024; 337:118753. [PMID: 39209001 DOI: 10.1016/j.jep.2024.118753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/16/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Jianpi Jiedu Formula (JPJDF) is a traditional Chinese medicinal decoction clinically used for its anti-cancer properties, particularly in colorectal cancer (CRC). AIM OF THE STUDY This study aims to investigate the therapeutic effects of JPJDF on CRC and elucidate its potential molecular mechanisms, with a focus on its impact on hypoxia-inducible factor 1 alpha (HIF1α) and cancer-associated fibroblasts (CAFs) both in vitro and in vivo. MATERIALS AND METHODS UPLC-Q-TOF-MS was used to identify the constituents of JPJDF. A chemical-induced colorectal cancer model was established and treated with JPJDF to evaluate its effects. Tumor size was measured, and histopathological analyses were performed to examine JPJDF's regulatory potential on CRC. The functional mechanism of JPJDF was predicted through network pharmacology, molecular docking, and transcriptomics. Co-culture techniques involving CRC cells and CCD-18Co fibroblasts were used to assess JPJDF's impact on fibroblast activation. The effects of HIF1α on CAFs were evaluated using CCK-8 proliferation, clonal formation, and apoptotic assays, with differential marker expression quantified via qPCR and Western blotting. RESULTS Pharmacodynamic assessment demonstrated that JPJDF reduced tumor size without affecting body weight, indicating its safety in the chemical-induced murine CRC model. Network pharmacology analysis, combined with molecular docking and transcriptomics, revealed that JPJDF regulates HIF-1 signaling pathways and identified HIF1α as a potential target for JPJDF's anti-CRC effect. JPJDF effectively suppressed CRC growth in vivo by attenuating fibroblast activation, reducing α-SMA expression and POSTN secretion through HIF1α inhibition. HIF1α knockdown in CRC cells inhibited fibroblast proliferation and clonal formation, while overexpression promoted these processes. Additionally, downregulating HIF1α suppressed α-SMA and POSTN expression in fibroblasts, whereas overexpression enhanced fibroblast activation. CONCLUSION JPJDF emerges as a promising therapeutic candidate for inhibiting CAFs activation by targeting HIF1α, offering potential avenues for modulating fibroblast activation towards CAFs in CRC therapy.
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Affiliation(s)
- Shenglan He
- Department of Digestive Endoscopy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Lixiao Hao
- Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Youlan Chen
- Institute of Integrated Traditional Chinese and Western Medicine Digestive Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Biao Gong
- Department of Digestive Endoscopy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Department of Gastroenterology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Xiaowen Xu
- Department of Digestive Endoscopy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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16
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Cheng C, Wu F, Xu Y, Ren C, Chen T, Li S, Shen P, Jiang F. Proteome analysis provides insights into sex differences in Holothuria Scabra. PLoS One 2024; 19:e0301884. [PMID: 39208133 PMCID: PMC11361572 DOI: 10.1371/journal.pone.0301884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Sex-determining mechanism is still ambiguous for sea cucumber Holothuria scabra which only manifests gonochorism in gonad. In this study, proteomic analysis was employed to delineate sex-related proteins and genes in gonads of H. scabra, subsequently validated through Quantitative real-time polymerase chain reaction (qRT-PCR). A total of 5,313 proteins were identified via proteome sequencing. Among these, 817 proteins exhibited expression in both the ovary and testis, with 445 proteins displaying up-regulation and 372 proteins showing down-regulation (ovary vs testis). Furthermore, 136 and 69 proteins were identified as ovary-specific and testis-specific Differentially Abundant Proteins (DAPs), respectively. And 9 DAP coding genes which play crucial role in ovary and testis were verified by qRT-PCR. Notably, 24 ovary-bias proteins enriched in ribosome pathway strongly indicated the crucial role of ribosome in ovary. This study serves to furnish novel evidence pertaining to sex differences in H. scabra.
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Affiliation(s)
- Chuhang Cheng
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
- College of Life Science and Technology of Guangxi University, Nanning, China
| | - FeiFei Wu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yizhi Xu
- School of Biological Sciences, University of Edinburgh, Edinburgh, England
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB) / Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB) / Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shella Li
- BASIS International School, Guangzhou, China
| | - Peihong Shen
- College of Life Science and Technology of Guangxi University, Nanning, China
| | - Fajun Jiang
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
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Zhou J, Yuan H, Park S. Predicting structure-targeted food bioactive compounds for middle-aged and elderly Asians with myocardial infarction: insights from genetic variations and bioinformatics-integrated deep learning analysis. Food Funct 2024. [PMID: 39207263 DOI: 10.1039/d4fo00591k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Myocardial infarction (MI) is a significant global health issue. Despite the advances in genome-wide association studies, a complete genetic and molecular understanding of MI is elusive and needs to be fully explored. This study aimed to elucidate the genetic framework of MI and explore the potential health benefits of natural compounds (NCs). The genetic architecture of MI was explored using data from the Korean Genome and Epidemiology Study. We pinpointed crucial protein-coding genes related to MI by multi-marker analysis of genomic annotation for gene-based analysis. The bioinformatics-integrated deep neural analysis of NCs (BioDeepNat), a novel disease discovery application, was utilized to assess the influence of NCs on MI-related target proteins and validated with molecular docking analysis. The BioDeepNat application revealed significant NCs on MI-related target proteins, such as E-resveratrol, epicatechin 3-gallate, and kaempferol. The E3 region of RNF213 protein with a point mutation (Arg4810Lys) had different binding energies with NCs, such as ursolic acid and olean-12-en-28-oic acid, compared to the wild type. However, ginsenosides, eleutheroside, oleanolic acid, and hederagenin showed similar binding energies to wild and mutated types of RNF213 protein. The predicted NCs were primarily sourced from foods such as common grapes and teas. Aromatic hydrocarbons are frequently observed as the prevalent functional groups with high binding affinity for NCs in a molecular docking analysis. In conclusion, the proteins encoded by these genes identified by gene-based analysis interacted with several NCs with health promotion found in day-to-day foods, particularly E-resveratrol and kaempferol. This understanding offers promising directions for precision nutrition strategies in MI.
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Affiliation(s)
- Junyu Zhou
- Department of Bioconvergence, Hoseo University, Asan 31499, Korea
| | - Heng Yuan
- Department of Bioconvergence, Hoseo University, Asan 31499, Korea
| | - Sunmin Park
- Department of Bioconvergence, Hoseo University, Asan 31499, Korea
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan 31499, Korea.
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18
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Macur K, Roszkowska A, Czaplewska P, Miękus-Purwin N, Klejbor I, Moryś J, Bączek T. Pressure Cycling Technology Combined With MicroLC-SWATH Mass Spectrometry for the Analysis of Sex-Related Differences Between Male and Female Cerebella: A Promising Approach to Investigating Proteomics Differences in Psychiatric and Neurodegenerative Diseases. Proteomics Clin Appl 2024:e202400001. [PMID: 39205462 DOI: 10.1002/prca.202400001] [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: 01/03/2024] [Revised: 07/19/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE Pressure cycling technology (PCT) coupled with data-independent sequential window acquisition of all theoretical mass spectra (SWATH-MS) can be a powerful tool for identifying and quantifying biomarkers (e.g., proteins) in complex biological samples. Mouse models are frequently used in brain studies, including those focusing on different neurodevelopmental and psychiatric disorders. More and more pieces of evidence have suggested that sex-related differences in the brain impact the rates, clinical manifestations, and therapy outcomes of these disorders. However, sex-based differences in the proteomic profiles of mouse cerebella have not been widely investigated. EXPERIMENTAL DESIGN In this pilot study, we evaluate the applicability of coupling PCT sample preparation with microLC-SWATH-MS analysis to map and identify differences in the proteomes of two female and two male mice cerebellum samples. RESULTS We identified and quantified 174 proteins in mice cerebella. A comparison of the proteomic profiles revealed that the levels of 11 proteins in the female and male mice cerebella varied significantly. CONCLUSIONS AND CLINICAL RELEVANCE Although this study utilizes a small sample, our results indicate that the studied male and female mice cerebella possessed differing proteome compositions, mainly with respect to energy metabolism processes.
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Affiliation(s)
- Katarzyna Macur
- Core Facility Laboratories, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Anna Roszkowska
- Department of Pharmaceutical Chemistry, Medical University of Gdańsk, Gdańsk, Poland
| | - Paulina Czaplewska
- Core Facility Laboratories, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Natalia Miękus-Purwin
- Department of Pharmaceutical Chemistry, Medical University of Gdańsk, Gdańsk, Poland
| | - Ilona Klejbor
- Department of Anatomy, Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Janusz Moryś
- Department of Normal Anatomy, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Medical University of Gdańsk, Gdańsk, Poland
- Department of Nursing and Medical Rescue, Institute of Health Sciences, Pomeranian University in Słupsk, Słupsk, Poland
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Van der Auwera S, Ameling S, Wittfeld K, Bülow R, Nauck M, Völzke H, Völker U, Grabe HJ. Circulating miRNAs modulating systemic low-grade inflammation and affecting neurodegeneration. Prog Neuropsychopharmacol Biol Psychiatry 2024; 135:111130. [PMID: 39209100 DOI: 10.1016/j.pnpbp.2024.111130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE AND DESIGN Inflammatory processes are an important part of the etiology of many chronic diseases across various medical domains, including neurodegeneration. Understanding their regulation on the molecular level represents a major challenge. Regulatory microRNAs (miRNAs), have been recognized for their role in post-transcriptionally modulating immune-related pathways serving as biomarkers for numerous diseases. SUBJECTS AND METHODS This study aims to investigate the association between 176 plasma-circulating miRNAs and the blood-based immune markers C-reactive protein and fibrinogen within the general population-based SHIP-TREND-0 cohort (N = 801) and assess their impact on neurodegeneration in linear regression and moderation analyses. RESULTS We provide strong evidence for miRNA-mediated regulation, particularly in relation to fibrinogen, identifying 48 significant miRNAs with a pronounced over-representation in chronic inflammatory and neurological diseases. Additional moderation analyses explored the influence of the APOE ε4 genotype and brain white matter neurodegeneration on the association between miRNAs and inflammation. Again, significant associations were observed for fibrinogen with special emphasize on hsa-miR-148a-3p, known to impact on neuroinflammation. CONCLUSIONS Our study suggests the involvement of several plasma-circulating miRNAs in regulating immunological markers while also being linked to neurodegeneration. The strong interplay between miRNAs and inflammation holds promising potential for clinical application in many immune-related neurodegenerative diseases.
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Affiliation(s)
- Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany; German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Greifswald, Germany.
| | - Sabine Ameling
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Robin Bülow
- Institute for Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Matthias Nauck
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Henry Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany; Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany; German Centre for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17475 Greifswald, Germany
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20
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Peerapen P, Boonmark W, Chantarasaka S, Thongboonkerd V. Trigonelline prevents high-glucose-induced endothelial-to-mesenchymal transition, oxidative stress, mitochondrial dysfunction, and impaired angiogenic activity in human endothelial EA.hy926 cells. Biomed Pharmacother 2024; 179:117320. [PMID: 39191024 DOI: 10.1016/j.biopha.2024.117320] [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: 06/14/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
Trigonelline (TRIG) is a natural compound in an alkaloid family found in diverse plants. This compound exerts anti-inflammatory, anti-allergic, anti-oxidative and anti-fibrotic activities in several disease models. However, its beneficial role in endothelial injury, especially induced by diabetes, is unclear. We, therefore, evaluated the effects of TRIG on the cellular proteome of human endothelial (EA.hy926) cells followed by functional validation in high-glucose (HG)-induced endothelial deteriorations. Label-free quantification using nanoLC-ESI-Qq-TOF MS/MS revealed 40 downregulated and 29 upregulated proteins induced by TRIG. Functional enrichment analysis using DAVID and REVIGO tools suggested the involvement of these altered proteins in several biological processes and molecular functions, particularly cell-cell adhesion, ATP metabolic process, cell redox homeostasis, cadherin binding, and ATP hydrolysis activity. Experimental validation showed that HG triggered endothelial-to-mesenchymal transition (EndMT) (as demonstrated by increased spindle index and mesenchymal markers, i.e., fibronectin and vimentin, and decreased endothelial markers, i.e., PECAM-1 and VE-cadherin), increased oxidized proteins, and reduced intracellular ATP, active mitochondria, endothelial tube/mesh formation and VEGF secretion. However, TRIG successfully abolished all these defects induced by HG. These data indicate that TRIG prevents HG-induced EndMT, oxidative stress, mitochondrial dysfunction, and impaired angiogenic activity in human endothelial cells.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanida Boonmark
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Suwichaya Chantarasaka
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Department of Dermatology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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21
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Campos M, Pérez-Collazos E, Díaz-Pérez A, López-Alvarez D, Oumouloud A, Mur LAJ, Vogel JP, Catalán P. Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei. Mol Ecol 2024:e17513. [PMID: 39188107 DOI: 10.1111/mec.17513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 07/24/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
Brachypodium stacei is the most ancestral lineage in the genus Brachypodium, a model system for grass functional genomics. B. stacei shows striking and sometimes contradictory biological and evolutionary features, including a high selfing rate yet extensive admixture, an ancient Miocene origin yet with recent evolutionary radiation, and adaptation to different dry climate conditions in its narrow distribution range. Therefore, it constitutes an ideal system to study these life history traits. We studied the phylogeography of 17 native circum-Mediterranean B. stacei populations (39 individuals) using genome-wide RADseq SNP data and complete plastome sequences. Nuclear SNP data revealed the existence of six distinct genetic clusters, low levels of intra-population genetic diversity and high selfing rates, albeit with signatures of admixture. Coalescence-based dating analysis detected a recent split between crown lineages in the Late Quaternary. Plastome sequences showed incongruent evolutionary relationships with those recovered by the nuclear data, suggesting interbreeding and chloroplast capture events between genetically distant populations. Demographic and population dispersal coalescent models identified an ancestral origin of B. stacei in the western-central Mediterranean islands, followed by an early colonization of the Canary Islands and two independent colonization events of the eastern Mediterranean region through long-distance dispersal and bottleneck events as the most likely evolutionary history. Climate niche data identified three arid niches of B. stacei in the southern Mediterranean region. Our findings indicate that the phylogeography of B. stacei populations was shaped by recent radiations, frequent extinctions, long-distance dispersal events, occasional interbreeding, and adaptation to local climates.
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Affiliation(s)
- Miguel Campos
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Ernesto Pérez-Collazos
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
| | - Antonio Díaz-Pérez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- GESPLAN S.A. C, Las Palmas de Gran Canaria, Spain
- Instituto de Genética, Facultad de Agronomía, Universidad Central de Venezuela, Maracay, Venezuela
| | - Diana López-Alvarez
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Facultad de Ciencias Agropecuarias, Departamento de Ciencias Biológicas, Universidad Nacional de Colombia, Palmira, Colombia
| | - Ali Oumouloud
- Institute Agronomique et Vétérinaire Hassan II, Agadir, Morocco
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - John P Vogel
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pilar Catalán
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain
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22
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Ye Z, Fu L, Li S, Chen Z, Ouyang J, Shang X, Liu Y, Gao L, Wang Y. Synergistic collaboration between AMPs and non-direct antimicrobial cationic peptides. Nat Commun 2024; 15:7319. [PMID: 39183339 PMCID: PMC11345435 DOI: 10.1038/s41467-024-51730-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024] Open
Abstract
Non-direct antimicrobial cationic peptides (NDACPs) are components of the animal innate immune system. But their functions and association with antimicrobial peptides (AMPs) are incompletely understood. Here, we reveal a synergistic interaction between the AMP AW1 and the NDACP AW2, which are co-expressed in the frog Amolops wuyiensis. AW2 enhances the antibacterial activity of AW1 both in vitro and in vivo, while mitigating the development of bacterial resistance and eradicating biofilms. AW1 and AW2 synergistically damage bacterial membranes, facilitating cellular uptake and interaction of AW2 with the intracellular target bacterial genomic DNA. Simultaneously, they trigger the generation of ROS in bacteria, contributing to cell death upon reaching a threshold level. Moreover, we demonstrate that this synergistic antibacterial effect between AMPs and NDACPs is prevalent across diverse animal species. These findings unveil a robust and previously unknown correlation between AMPs and NDACPs as a widespread antibacterial immune defense strategy in animals.
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Affiliation(s)
- Zifan Ye
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuangyu Li
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Ziying Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Jianhong Ouyang
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Xinci Shang
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Yanli Liu
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
| | - Yipeng Wang
- Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.
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23
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Rosenkranz RRE, Vraggalas S, Keller M, Sankaranarayanan S, McNicoll F, Löchli K, Bublak D, Benhamed M, Crespi M, Berberich T, Bazakos C, Feldbrügge M, Schleiff E, Müller-McNicoll M, Zarnack K, Fragkostefanakis S. A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato. Nucleic Acids Res 2024:gkae730. [PMID: 39180404 DOI: 10.1093/nar/gkae730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Global warming poses a threat for crops, therefore, the identification of thermotolerance mechanisms is a priority. In plants, the core factors that regulate transcription under heat stress (HS) are well described and include several HS transcription factors (HSFs). Despite the relevance of alternative splicing in HS response and thermotolerance, the core regulators of HS-sensitive alternative splicing have not been identified. In tomato, alternative splicing of HSFA2 is important for acclimation to HS. Here, we show that several members of the serine/arginine-rich family of splicing factors (SRSFs) suppress HSFA2 intron splicing. Individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) combined with RNA-Seq revealed that RS2Z35 and RS2Z36, which make up a plant-specific clade of SR proteins, not only regulate HSFA2 but approximately 50% of RNAs that undergo HS-sensitive alternative splicing, with preferential binding to purine-rich RNA motifs. Single and double CRISPR rs2z mutant lines show a dysregulation of splicing and exhibit lower basal and acquired thermotolerance compared to wild type plants. Our results suggest that RS2Z35 and RS2Z36 have a central role in mitigation of the negative effects of HS on RNA splicing homeostasis, and their emergence might have contributed to the increased capacity of plants to acclimate to high temperatures.
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Affiliation(s)
- Remus R E Rosenkranz
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stavros Vraggalas
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute of Molecular Life Sciences & Institute of Molecular Biosciences, Computational RNA Biology, Goethe University Frankfurt, Frankfurt, Germany
| | | | - François McNicoll
- Institute of Molecular Biosciences, RNA Regulation in Higher Eukaryotes, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Daniela Bublak
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay-CNRS, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay-CNRS, Orsay, France
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Frankfurt, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute of Plant Breeding and Genetic Resources, ELGO DEMETER, Thessaloniki, Greece
| | - Michael Feldbrügge
- Institute of Microbiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Enrico Schleiff
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Institute of Molecular Biosciences, RNA Regulation in Higher Eukaryotes, Goethe University Frankfurt, Frankfurt, Germany
- Max-Planck Institute for Biophysics, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute of Molecular Life Sciences & Institute of Molecular Biosciences, Computational RNA Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - Sotirios Fragkostefanakis
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
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24
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Yao S, Zhu Y, He F, Yuan M, Jiang R, Zhang H, Fu Y, Wei K. JAK activity regulates mesoderm cell fate by controlling MESP1 expression. Eur J Cell Biol 2024; 103:151452. [PMID: 39182311 DOI: 10.1016/j.ejcb.2024.151452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/13/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024] Open
Abstract
Cardiac development requires precise gene expression programs at each developmental stage guided by multiple signaling pathways and transcription factors (TFs). MESP1 is transiently expressed in mesoderm, and is essential for subsequent cardiac development, while the precise mechanism regulating its own transcription and mesoderm cell fate is not fully understood. Therefore, we developed a high content screen assay to identify regulators of MESP1 expression in mesodermal cells differentiated from human pluripotent stem cells (hPSCs). The screen identified CYT387, a JAK1/JAK2 kinase inhibitor, as a potent activator of MESP1 expression, which was also found to promote cardiomyocyte differentiation in vitro. Mechanistic studies found that JAK inhibition promotes MESP1 expression by reducing cytoplasmic calcium concentration and subsequently activating canonical WNT signaling. Our study identified a role of JAK signaling in early mesodermal cells, and sheds light on the connection between the JAK-STAT pathway and transcriptional regulation of MESP1, which expands our understanding of mesoderm and cardiac development.
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Affiliation(s)
- Su Yao
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yalin Zhu
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Fenglian He
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Min Yuan
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Rui Jiang
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hongjie Zhang
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanbin Fu
- Shanghai Cancer Institute, Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ke Wei
- Institute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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25
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Hashem J, Alkhalaileh L, Abushukair H, Ayesh M. miRNA Profiles in Patients with Hematological Malignancy at Different Stages of the Disease: A Preliminary Study. Biomedicines 2024; 12:1924. [PMID: 39200388 PMCID: PMC11351647 DOI: 10.3390/biomedicines12081924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/02/2024] Open
Abstract
The dysregulation of miRNA expression has been shown to impact cellular physiology and tumorigenesis. Studies have reported several miRNA regulatory elements and pathways that play a significant role in the diagnosis, prognosis, and treatment of hematological malignancies. This is the first study to test the differential expression of miRNAs at crucial stages of the disease, specifically newly diagnosed, resistant to treatment, and remission. Circulating miRNAs extracted from the blood samples of 18 patients diagnosed with leukemia or lymphoma at different stages and 2 healthy controls were quantified by qPCR using a panel of 96 tumorigenic miRNAs. An enrichment analysis was performed to understand the mechanisms through which differential miRNA expression affects cellular and molecular functions. Significant upregulation of hsa-miR-1, hsa-miR-20a-5p, hsa-miR-23a-3p, hsa-miR-92b3p, and hsa-miR-196a-5p was detected among the different stages of leukemia and lymphoma. mir-1 and mir-196a-5p were upregulated in the remission stage of leukemia, while mir-20a-5p, mir-23a-3p, and mir-92b-3p were upregulated during the resistant stage of lymphoma. The enrichment analysis revealed these miRNAs' involvement in the RAS signaling pathway, TGF-β signaling, and apoptotic pathways, among others. This study highlights new biomarkers that could be used as potential targets for disease diagnosis, prognosis, and treatment, therefore enhancing personalized treatments and survival outcomes for patients.
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Affiliation(s)
- Jood Hashem
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Lujain Alkhalaileh
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Hassan Abushukair
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (H.A.); (M.A.)
| | - Mahmoud Ayesh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan; (H.A.); (M.A.)
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26
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Han Z, Gong L, Xue Y, Wang R, Liu J, Wang X, Zhao W, Liao H, Li R. Effects of Inonotus obliquus on ameliorating podocyte injury in ORG mice through TNF pathway and prediction of active compounds. Front Pharmacol 2024; 15:1426917. [PMID: 39234117 PMCID: PMC11371614 DOI: 10.3389/fphar.2024.1426917] [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: 05/02/2024] [Accepted: 08/06/2024] [Indexed: 09/06/2024] Open
Abstract
Background Podocyte injury is a common pathologic mechanism in diabetic kidney disease (DKD) and obesity-related glomerulopathy (ORG). Our previous study confirmed that Inonotus obliquus (IO) improved podocyte injury on DKD rats. The current study explored the pharmacological effects, related mechanisms and possible active components of IO on ORG mice. Methods Firstly, by combining ultra-high performance liquid chromatography tandem mass spectrometry analysis (UPLC-Q-TOF-MS) with network pharmacology to construct the human protein-protein interaction mechanism and enrich the pathway, which led to discover the crucial mechanism of IO against ORG. Then, ORG mice were established by high-fat diet and biochemical assays, histopathology, and Western blot were used to explore the effects of IO on obesity and podocyte injury. Finally, network pharmacology-based findings were confirmed by immunohistochemistry. The compositions of IO absorbed in mice plasma were analyzed by UPLC-Q-TOF-MS and molecular docking was used to predict the possible active compounds. Results The network pharmacology result suggested that IO alleviated the inflammatory response of ORG by modulating TNF signal. The 20-week in vivo experiment confirmed that IO improved glomerular hypertrophy, podocyte injury under electron microscopy, renal nephrin, synaptopodin, TNF-α and IL-6 expressions with Western blotting and immunohistochemical staining. Other indicators of ORG such as body weight, kidney weight, serum total cholesterol, liver triglyceride also improved by IO intervention. The components analysis showed that triterpenoids, including inoterpene F and trametenolic acid, might be the pharmacodynamic basis. Conclusion The research based on UPLC-Q-TOF-MS analysis, network pharmacology and in vivo experiment suggested that the amelioration of IO on podocyte injury in ORG mice via its modulation on TNF signal. Triterpenoids were predicated as acting components.
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Affiliation(s)
- Zhaodi Han
- Drug Clinical Trial Institution, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Le Gong
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Yani Xue
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Rui Wang
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Jing Liu
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Xinyu Wang
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Wenyan Zhao
- School of Pharmacy, Shanxi Medical University, Taiyuan, China
| | - Hui Liao
- Drug Clinical Trial Institution, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Rongshan Li
- Department of Nephrology, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University, Taiyuan, China
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27
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Giovannuzzi S, Shyamal SS, Bhowmik R, Ray R, Manaithiya A, Carta F, Parrkila S, Aspatwar A, Supuran CT. Physiological modeling of the metaverse of the Mycobacterium tuberculosis β-CA inhibition mechanism. Comput Biol Med 2024; 181:109029. [PMID: 39173489 DOI: 10.1016/j.compbiomed.2024.109029] [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: 05/29/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
Tuberculosis (TB) is an infectious disease that primarily affects the lungs of humans and accounts for Mycobacterium tuberculosis (Mtb) bacteria as the etiologic agent. In this study, we introduce a computational framework designed to identify the important chemical features crucial for the effective inhibition of Mtb β-CAs. Through applying a mechanistic model, we elucidated the essential features pivotal for robust inhibition. Using this model, we engineered molecules that exhibit potent inhibitory activity and introduce relevant novel chemistry. The designed molecules were prioritized for synthesis based on their predicted pKi values via the QSAR (Quantitative Structure-Activity Relationship) model. All the rationally designed and synthesized compounds were evaluated in vitro against different carbonic anhydrase isoforms expressed from the pathogen Mtb; moreover, the off-target and widely human-expressed CA I and II were also evaluated. Among the reported derivatives, 2, 4, and 5 demonstrated the most valuable in vitro activity, resulting in promising candidates for the treatment of TB infection. All the synthesized molecules exhibited favorable pharmacokinetic and toxicological profiles based on in silico predictions. Docking analysis confirmed that the zinc-binding groups bind effectively into the catalytic triad of the Mtb β-Cas, supporting the in vitro outcomes with these binding interactions. Furthermore, molecules with good prediction accuracies according to previously established mechanistic and QSAR models were utilized to delve deeper into the realm of systems biology to understand their mechanism in combating tuberculotic pathogenesis. The results pointed to the key involvement of the compounds in modulating immune responses via NF-κβ1, SRC kinase, and TNF-α to modulate granuloma formation and clearance via T cells. This dual action, in which the pathogen's enzyme is inhibited while modulating the human immune machinery, represents a paradigm shift toward more effective and comprehensive treatment approaches for combating tuberculosis.
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Affiliation(s)
- Simone Giovannuzzi
- Department of Neuroscience, Psychology, Drug Research, and Child's Health, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Sagar Singh Shyamal
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ratul Bhowmik
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Rajarshi Ray
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ajay Manaithiya
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Fabrizio Carta
- Department of Neuroscience, Psychology, Drug Research, and Child's Health, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Seppo Parrkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Ltd, Tampere University Hospital, Tampere, Finland
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Claudiu T Supuran
- Department of Neuroscience, Psychology, Drug Research, and Child's Health, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy.
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28
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Lind J, Aksoy O, Prchal-Murphy M, Fan F, Fulciniti M, Stoiber D, Bakiri L, Wagner EF, Zwickl-Traxler E, Sattler M, Kollmann K, Vallet S, Podar K. Dual therapeutic targeting of MYC and JUNB transcriptional programs for enhanced anti-myeloma activity. Blood Cancer J 2024; 14:138. [PMID: 39160158 PMCID: PMC11333473 DOI: 10.1038/s41408-024-01117-4] [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: 04/13/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/21/2024] Open
Abstract
Deregulation of transcription factors (TFs) leading to uncontrolled proliferation of tumor cells within the microenvironment represents a hallmark of cancer. However, the biological and clinical impact of transcriptional interference, particularly in multiple myeloma (MM) cells, remains poorly understood. The present study shows for the first time that MYC and JUNB, two crucial TFs implicated in MM pathogenesis, orchestrate distinct transcriptional programs. Specifically, our data revealed that expression levels of MYC, JUNB, and their respective downstream targets do not correlate and that their global chromatin-binding patterns are not significantly overlapping. Mechanistically, MYC expression was not affected by JUNB knockdown, and conversely, JUNB expression and transcriptional activity were not affected by MYC knockdown. Moreover, suppression of MYC levels in MM cells via targeting the master regulator BRD4 by either siRNA-mediated knockdown or treatment with the novel proteolysis targeting chimera (PROTAC) MZ-1 overcame bone marrow (BM) stroma cell/IL-6-induced MYC- but not MEK-dependent JUNB-upregulation and transcriptional activity. Consequently, targeting of the two non-overlapping MYC- and JUNB-transcriptoms by MZ-1 in combination with genetic or pharmacological JUNB-targeting approaches synergistically enhanced MM cell death, both in 2D and our novel dynamic 3D models of the BM milieu as well as in murine xenografts. In summary, our data emphasize the opportunity to employ MYC and JUNB dual-targeting treatment strategies in MM as another exciting approach to further improve patient outcomes.
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Affiliation(s)
- Judith Lind
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Osman Aksoy
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Michaela Prchal-Murphy
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Dagmar Stoiber
- Division of Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Latifa Bakiri
- Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
| | - Erwin F Wagner
- Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
- Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria
| | | | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Karoline Kollmann
- Pharmacology and Toxicology, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Sonia Vallet
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
- Division of Internal Medicine 2, University Hospital Krems, Krems/ Donau, Austria
| | - Klaus Podar
- Division of Molecular Oncology and Hematology, Department of Basic and Translational Oncology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.
- Division of Internal Medicine 2, University Hospital Krems, Krems/ Donau, Austria.
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Li X, Mills WT, Jin DS, Meffert MK. Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. CELL REPORTS METHODS 2024; 4:100836. [PMID: 39127045 DOI: 10.1016/j.crmeth.2024.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024]
Abstract
Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types.
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Affiliation(s)
- Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William T Mills
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel S Jin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mollie K Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Vela S, Wolf ESA, Rollins JA, Cuevas HE, Vermerris W. Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1437344. [PMID: 39220294 PMCID: PMC11362643 DOI: 10.3389/ffunb.2024.1437344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/19/2024] [Indexed: 09/04/2024]
Abstract
In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen Colletotrichum sublineola, the causal agent of anthracnose, a problematic disease of sorghum (Sorghum bicolor (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum-C. sublineola interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and C. sublineola can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with C. sublineola. Approximately 0.3% and 93% of the reads mapped to the genomes of C. sublineola and Sorghum bicolor, respectively. Expression profiling of in vitro versus in planta C. sublineola at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by C. sublineola were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of C. sublineola but also supports the long-term goal of developing resistant sorghum cultivars.
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Affiliation(s)
- Saddie Vela
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Emily S. A. Wolf
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Jeffrey A. Rollins
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Hugo E. Cuevas
- United States Department of Agriculture, Agricultural Research Service, Tropical Agriculture Research Station, Mayagüez, PR, United States
| | - Wilfred Vermerris
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL, United States
- University of Florida Genetics Institute, Gainesville, FL, United States
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31
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Ding Y, Liu G, Li Q, Zou L, Dai J, Chongsuvivatwong V. Distribution characteristics of human herpes viruses in the lower respiratory tract and their impact on 30-day mortality in community-acquired pneumonia patients. Front Cell Infect Microbiol 2024; 14:1436509. [PMID: 39220283 PMCID: PMC11362831 DOI: 10.3389/fcimb.2024.1436509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
Human herpes viruses (HHVs) are commonly detected in community-acquired pneumonia (CAP) patients, particularly those with complex complications, attracting increased attention from clinical practitioners. However, the significance of detecting HHVs in bronchoalveolar lavage fluid (BALF) with CAP patients is still unclear. This study retrospectively analyzed BALF samples from 64 CAP patients at the Kunming Third People's Hospital between August 2021 and December 2023. Metagenomic next generation sequencing (mNGS) was conducted on BALF samples during CAP onset. Multivariate Cox regression models were used to identify independent risk factors for 30-day all-cause mortality in CAP. HHVs were found in 84.4% of CAP patients, which were the most common pathogens (45.1%), followed by bacteria (30.2%) and fungi (11.5%). Bacterial-viral co-infections were most common, occurring in 39 patients. Notably, there was no significant difference in HHV presence between severe and non-severe CAP patients (EBV: P = 0.431, CMV: P = 0.825), except for HHV-7 (P = 0.025). In addition, there was no significant difference in the 30-day mortality between HHV positive and HHV negative groups (P = 0.470), as well as between the HHV-7 positive and HHV-7 negative groups (P = 0.910). However, neither HHVs nor HHV-7 was independent risk factors for 30-day mortality in CAP patients (HHVs: HR 1.171, P = 0.888; HHV-7: HR 1.947, P = 0.382). In summary, among the prevalent presence of multiple HHVs, EBV and CMV were the most prevalent in CAP patients. Patients with sCAP were more susceptible to HHV-7 than those with non-sCAP. These results provide valuable insights for clinicians in guiding appropriate interventions for CAP treatment.
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Affiliation(s)
- Yadi Ding
- Department of Public Laboratory, The Third People's Hospital of Kunming City, Infectious Disease Clinical Medical Center of Yunnan Province, Kunming, Yunnan, China
| | - Guiming Liu
- Department of Public Laboratory, The Third People's Hospital of Kunming City, Infectious Disease Clinical Medical Center of Yunnan Province, Kunming, Yunnan, China
| | - Qiujing Li
- Department of Public Laboratory, The Third People's Hospital of Kunming City, Infectious Disease Clinical Medical Center of Yunnan Province, Kunming, Yunnan, China
| | - Lingqing Zou
- Department of Public Laboratory, The Third People's Hospital of Kunming City, Infectious Disease Clinical Medical Center of Yunnan Province, Kunming, Yunnan, China
| | - Jingyi Dai
- Department of Public Laboratory, The Third People's Hospital of Kunming City, Infectious Disease Clinical Medical Center of Yunnan Province, Kunming, Yunnan, China
- International Research Fellow, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Chai Y, Sun X, Zhou Q, Li H, Xi Y. Exploration of the mechanism of fraxetin in treating acute myeloid leukemia based on network pharmacology and experimental verification. Heliyon 2024; 10:e34717. [PMID: 39166080 PMCID: PMC11334658 DOI: 10.1016/j.heliyon.2024.e34717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 08/22/2024] Open
Abstract
Objective To explore the pharmacological mechanism of the effect of fraxetin in treating acute myeloid leukemia (AML) by the network pharmacology method combined with experimental validation. Methods The targets of fraxetin were identified through Swisstarget prediction, PhammerMap, and CTDBASE. Disease-related targets of AML were explored using GeneCards and DisGenet databases, and the intersected targets were analyzed in the String website to construct a protein-protein interaction (PPI) network. Subsequently, gene ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were conducted using the DAVID database. Molecular docking of core proteins with drugs was performed using Auto Dock Vina software. Finally, the effect of fraxetin on AML was evaluated by in vitro experiments. The effect of fraxetin on AML cell proliferation was assessed by CCK8, the effect of fraxetin on AML cell apoptosis was assessed by flow cytometry, and the expression of relevant protein targets was detected by Western blotting to evaluate the anti-AML effect of fraxetin. Results In this study, fraxetin exerts its effect against AML through 101 intersecting genes. The pathway enrichment analysis revealed that the pharmacological effects of fraxetin on AML were related to the Adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway, and the molecular docking results indicated that fraxetin had an excellent binding affinity to both the core target and AMPK. In vitro experiments have demonstrated that fraxetin inhibited the proliferation and induced apoptosis of THP1 and HL60 cells, and the western blotting results indicated that the p-AMPK of the fraxetin intervention group was significantly changed in a dose-dependent manner. Conclusion Fraxetin may modulate the AMPK signal pathway by interactine with the core target, thereby potentially therapeutic effect on AML.
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Affiliation(s)
- Yihong Chai
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
| | - Xiaohong Sun
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
| | - Qi Zhou
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
| | - Hongxing Li
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
| | - Yaming Xi
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
- Department of Hematology, First Hospital of Lanzhou University, Lanzhou 730000, Gansu, People's Republic of China
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Bérubé M, Abedini A, Lapointe E, Gusscott S, Brind'Amour J, Zamberlam G, Boerboom D. SFRP4 promotes autophagy and blunts FSH responsiveness through inhibition of AKT signaling in ovarian granulosa cells. Cell Commun Signal 2024; 22:396. [PMID: 39138534 PMCID: PMC11323480 DOI: 10.1186/s12964-024-01736-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Secreted frizzled-related proteins (SFRPs) comprise a family of WNT signaling antagonists whose roles in the ovary are poorly understood. Sfrp4-null mice were previously found to be hyperfertile due to an enhanced granulosa cell response to gonadotropins, leading to decreased antral follicle atresia and enhanced ovulation rates. The present study aimed to elucidate the mechanisms whereby SFRP4 antagonizes FSH action. METHODS Primary cultures of granulosa cells from wild-type mice were treated with FSH and/or SFRP4, and effects of treatment on gene expression were evaluated by RT-qPCR and RNAseq. Bioinformatic analyses were conducted to analyse the effects of SFRP4 on the transcriptome, and compare them to those of FSH or a constitutively active mutant of FOXO1. Additional granulosa cell cultures from wild-type or Sfrp4-null mice, some pretreated with pharmacologic inhibitors of specific signaling effectors, were used to examine the effects of FSH and/or SFRP4 on signaling pathways, autophagy and apoptosis by western blotting and TUNEL. RESULTS Treatment of cultured granulosa cells with recombinant SFRP4 was found to decrease basal and FSH-stimulated mRNA levels of FSH target genes. Unexpectedly, this effect was found to occur neither via a canonical (CTNNB1-dependent) nor non-canonical WNT signaling mechanism, but was found to be GSK3β-dependent. Rather, SFRP4 was found to antognize AKT activity via a mechanism involving AMPK. This lead to the hypophosphorylation of FOXO1 and a decrease in the expression of a portion of the FSH and FOXO1 transcriptomes. Conversely, FSH-stimulated AMPK, AKT and FOXO1 phosphorylation levels were found to be increased in the granulosa cells of Sfrp4-null mice relative to wild-type controls. SFRP4 treatement of granulosa cells also induced autophagy by signaling via AKT-mTORC1-ULK1, as well as apoptosis. CONCLUSIONS This study identifies a novel GSK3β-AMPK-AKT signaling mechanism through which SFPR4 antagonizes FSH action, and further identifies SFRP4 as a novel regulator of granulosa cell autophagy. These findings provide a mechanistic basis for the phenotypic changes previously observed in Sfrp4-null mice, and broaden our understanding of the physiological roles of WNT signaling processes in the ovary.
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Affiliation(s)
- Michael Bérubé
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Atefeh Abedini
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Evelyne Lapointe
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Samuel Gusscott
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Julie Brind'Amour
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Gustavo Zamberlam
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada
| | - Derek Boerboom
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, J2S 2M2, Canada.
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Chen M, Fu Z, Wu C. Tumor-derived exosomal ICAM1 promotes bone metastasis of triple-negative breast cancer by inducing CD8+ T cell exhaustion. Int J Biochem Cell Biol 2024; 175:106637. [PMID: 39147124 DOI: 10.1016/j.biocel.2024.106637] [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: 04/30/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
Exosomes, which are nanosized extracellular vesicles, have emerged as crucial mediators of the crosstalk between tumor cells and the immune system. Intercellular adhesion molecule 1 (ICAM1) plays a crucial role in multiple immune functions as well as in the occurrence, development and metastasis of cancer. As a glycoprotein expressed on the cell membrane, ICAM1 is secreted extracellularly on exosomes and regulates the immunosuppressive microenvironment. However, the role of exosomal ICAM1 in the immune microenvironment of breast cancer bone metastases remains unclear. This study aimed to elucidated the role of exosomal ICAM1 in facilitating CD8+ T cell exhaustion and subsequent bone metastasis in triple-negative breast cancer (TNBC). We demonstrated that TNBC cells release ICAM1-enriched exosomes, and the binding of ICAM1 to its receptor is necessary for the suppressive effect of CD8 T cell proliferation and function. This pivotal engagement not only inhibits CD8+ T cell proliferation and activation but also initiates the development of an immunosuppressive microenvironment that is conducive to TNBC tumor growth and bone metastasis. Moreover, ICAM1 blockade significantly impairs the ability of tumor exosomes to bind to CD8+ T cells, thereby inhibiting their immunosuppressive effects. The present study elucidates the complex interaction between primary tumors and the immune system that is mediated by exosomes and provides a foundation for the development of novel cancer immunotherapies that target ICAM1 with the aim of mitigating TNBC bone metastasis.
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Affiliation(s)
- Mingcang Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China; Metabolic Disease Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
| | - Chunyu Wu
- Department of Breast Surgery (Integrated Traditional and Western Medicine), Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Wang X, Zhang Z, Qi Y, Zhang Z, Zhang Y, Meng K, Yuan J, Quan F. Study of the uptake mechanism of two small extracellular vesicle subtypes by granulosa cells. Anim Reprod Sci 2024; 270:107576. [PMID: 39178587 DOI: 10.1016/j.anireprosci.2024.107576] [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: 04/11/2024] [Revised: 07/25/2024] [Accepted: 08/10/2024] [Indexed: 08/26/2024]
Abstract
As a new mechanism of intercellular communication, the uptake of extracellular vesicles (EVs) by receptor cells has become a hot topic in the field. Previously, research on the uptake of EVs has focused on the mechanism of small EVs (sEVs, also known as exosomes). As sEVs represent a mixed heterogeneous population, the issue of whether there are different uptake mechanisms for different subsets of sEVs by recipient cells urgently need to be addressed. There are EVs in follicular fluid, which play an important role in the communication between follicular cells and the development of oocytes. Previously, we isolated two subtypes of sEVs in follicular fluid: low density-sEVs (LD-sEVs) and high density-sEVs (HD-sEVs). The current study aimed to explore the uptake characteristics of these two subtypes of sEVs by granulosa cells. First, PKH67 was used to label the two sEVs subtypes, and we observed their uptake by granulosa cells using confocal microscopy and flow cytometry. We then explored the specific mechanisms underlying uptake of these two sEV subtypes by granulosa cells using specific inhibitors and RNA interference. The results showed that granulosa cells took up both kinds of sEVs through a clathrin-independent pathway. In addition to requiring caveolin, cholesterol, and Na+/H+ exchange, the uptake of HD-sEVs also depended on the activity of tyrosine kinase and phosphoinositide 3-kinase. A better understanding of the mechanism of granulosa cell uptake of different subtypes of sEVs in follicular fluid is of considerable significance leading to more accurate use of EVs for targeted treatment of infertility and other related diseases.
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Affiliation(s)
- Xiaomei Wang
- College of Basic Medicine, Jining Medical University, Jining 272000, China; College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zihan Zhang
- College of Second Clinical Medical, Jining Medical University, Jining 272000, China
| | - Yuanmin Qi
- College of Clinical Medicine, Jining Medical University, Jining 272000, China
| | - Zhimin Zhang
- College of Clinical Medicine, Jining Medical University, Jining 272000, China
| | - Yixin Zhang
- College of Second Clinical Medical, Jining Medical University, Jining 272000, China
| | - Kai Meng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China; Lin He's Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining 272000, China
| | - Jinxiang Yuan
- Lin He's Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining 272000, China.
| | - Fusheng Quan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Vivarelli S, Spatari G, Costa C, Giambò F, Fenga C. Computational Analyses Reveal Deregulated Clock Genes Associated with Breast Cancer Development in Night Shift Workers. Int J Mol Sci 2024; 25:8659. [PMID: 39201344 PMCID: PMC11355052 DOI: 10.3390/ijms25168659] [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: 07/15/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Breast cancer (BC) is the leading cause of cancer death among women worldwide. Women employed in shift jobs face heightened BC risk due to prolonged exposure to night shift work (NSW), classified as potentially carcinogenic by the International Agency for Research on Cancer (IARC). This risk is linked to disruptions in circadian rhythms governed by clock genes at the cellular level. However, the molecular mechanisms are unclear. This study aimed to assess clock genes as potential BC biomarkers among women exposed to long-term NSW. Clock gene expression was analysed in paired BC and normal breast tissues within Nurses' Health Studies I and II GEO datasets. Validation was performed on additional gene expression datasets from healthy night shift workers and women with varying BC susceptibility, as well as single-cell sequencing datasets. Post-transcriptional regulators of clock genes were identified through miRNA analyses. Significant alterations in clock gene expression in BC compared to normal tissues were found. BHLHE40, CIART, CLOCK, PDPK1, and TIMELESS were over-expressed, while HLF, NFIL3, NPAS3, PER1, PER3, SIM1, and TEF were under-expressed. The downregulation of PER1 and TEF and upregulation of CLOCK correlated with increased BC risk in healthy women. Also, twenty-six miRNAs, including miR-10a, miR-21, miR-107, and miR-34, were identified as potential post-transcriptional regulators influenced by NSW. In conclusion, a panel of clock genes and circadian miRNAs are suggested as BC susceptibility biomarkers among night shift workers, supporting implications for risk stratification and early detection strategies.
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Affiliation(s)
- Silvia Vivarelli
- Department of Biomedical and Dental Sciences, Morphological and Functional Imaging, Section of Occupational Medicine, University of Messina, 78712 Messina, Italy; (G.S.); (F.G.); (C.F.)
| | - Giovanna Spatari
- Department of Biomedical and Dental Sciences, Morphological and Functional Imaging, Section of Occupational Medicine, University of Messina, 78712 Messina, Italy; (G.S.); (F.G.); (C.F.)
| | - Chiara Costa
- Department of Clinical and Experimental Medicine, University of Messina, 78712 Messina, Italy;
| | - Federica Giambò
- Department of Biomedical and Dental Sciences, Morphological and Functional Imaging, Section of Occupational Medicine, University of Messina, 78712 Messina, Italy; (G.S.); (F.G.); (C.F.)
| | - Concettina Fenga
- Department of Biomedical and Dental Sciences, Morphological and Functional Imaging, Section of Occupational Medicine, University of Messina, 78712 Messina, Italy; (G.S.); (F.G.); (C.F.)
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Mészár Z, Erdei V, Szücs P, Varga A. Epigenetic Regulation and Molecular Mechanisms of Burn Injury-Induced Nociception in the Spinal Cord of Mice. Int J Mol Sci 2024; 25:8510. [PMID: 39126078 PMCID: PMC11313498 DOI: 10.3390/ijms25158510] [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: 07/21/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Epigenetic mechanisms, including histone post-translational modifications (PTMs), play a critical role in regulating pain perception and the pathophysiology of burn injury. However, the epigenetic regulation and molecular mechanisms underlying burn injury-induced pain remain insufficiently explored. Spinal dynorphinergic (Pdyn) neurons contribute to heat hyperalgesia induced by severe scalding-type burn injury through p-S10H3-dependent signaling. Beyond p-S10H3, burn injury may impact various other histone H3 PTMs. Double immunofluorescent staining and histone H3 protein analyses demonstrated significant hypermethylation at H3K4me1 and H3K4me3 sites and hyperphosphorylation at S10H3 within the spinal cord. By analyzing Pdyn neurons in the spinal dorsal horn, we found evidence of chromatin activation with a significant elevation in p-S10H3 immunoreactivity. We used RNA-seq analysis to compare the effects of burn injury and formalin-induced inflammatory pain on spinal cord transcriptomic profiles. We identified 98 DEGs for burn injury and 86 DEGs for formalin-induced inflammatory pain. A limited number of shared differentially expressed genes (DEGs) suggest distinct central pain processing mechanisms between burn injury and formalin models. KEGG pathway analysis supported this divergence, with burn injury activating Wnt signaling. This study enhances our understanding of burn injury mechanisms and uncovers converging and diverging pathways in pain models with different origins.
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Affiliation(s)
- Zoltán Mészár
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (Z.M.); (P.S.)
| | - Virág Erdei
- Department of Radiology, Central Hospital of Northern Pest—Military Hospital, H-1134 Budapest, Hungary;
| | - Péter Szücs
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (Z.M.); (P.S.)
- HUN-REN-DE Neuroscience Research Group, H-4032 Debrecen, Hungary
| | - Angelika Varga
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (Z.M.); (P.S.)
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Dalal K, Yang W, Tian E, Chernish A, McCluggage P, Lara AJ, Ten Hagen KG, Tabak LA. In vivo mapping of the mouse Galnt3-specific O-glycoproteome. J Biol Chem 2024; 300:107628. [PMID: 39098533 DOI: 10.1016/j.jbc.2024.107628] [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: 01/22/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
The UDP-N-acetylgalactosamine polypeptide:N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes initiates O-linked glycosylation by catalyzing the addition of the first GalNAc sugar to serine or threonine on proteins destined to be membrane-bound or secreted. Defects in individual isoforms of the GalNAc-T family can lead to certain congenital disorders of glycosylation (CDG). The polypeptide N-acetylgalactosaminyltransferase 3 (GALNT)3-CDG, is caused by mutations in GALNT3, resulting in hyperphosphatemic familial tumoral calcinosis due to impaired glycosylation of the phosphate-regulating hormone fibroblast growth factor 23 (FGF23) within osteocytes of the bone. Patients with hyperphosphatemia present altered bone density, abnormal tooth structure, and calcified masses throughout the body. It is therefore important to identify all potential substrates of GalNAc-T3 throughout the body to understand the complex disease phenotypes. Here, we compared the Galnt3-/- mouse model, which partially phenocopies GALNT3-CDG, with WT mice and used a multicomponent approach using chemoenzymatic conditions, a product-dependent method constructed using EThcD triggered scans in a mass spectrometry workflow, quantitative O-glycoproteomics, and global proteomics to identify 663 Galnt3-specific O-glycosites from 269 glycoproteins across multiple tissues. Consistent with the mouse and human phenotypes, functional networks of glycoproteins that contain GalNAc-T3-specific O-glycosites involved in skeletal morphology, mineral level maintenance, and hemostasis were identified. This library of in vivo GalNAc-T3-specific substrate proteins and O-glycosites will serve as a valuable resource to understand the functional implications of O-glycosylation and to unravel the underlying causes of complex human GALNT3-CDG phenotypes.
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Affiliation(s)
- Kruti Dalal
- Biological Chemistry Section and Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Weiming Yang
- Biological Chemistry Section and Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - E Tian
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Aliona Chernish
- Biological Chemistry Section and Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Peggy McCluggage
- Biological Chemistry Section and Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexander J Lara
- Biological Chemistry Section and Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelly G Ten Hagen
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Lawrence A Tabak
- Biological Chemistry Section and Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA.
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Pei J, Zhang J, Yu C, Luo J, Hua Y, Wei G. APOD: A biomarker associated with oxidative stress in acute rejection of kidney transplants based on multiple machine learning algorithms and animal experimental validation. Transpl Immunol 2024; 86:102101. [PMID: 39096939 DOI: 10.1016/j.trim.2024.102101] [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: 03/12/2024] [Revised: 07/16/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
BACKGROUND Oxidative stress is an unavoidable process in kidney transplantation and is closely related to the development of acute rejection after kidney transplantation. This study aimed to investigate the biomarkers associated with oxidative stress and their potential biological functions during acute rejection of kidney transplants. METHODS We identified Hub genes using five machine learning algorithms based on differentially expressed genes (DEGs) in the kidney transplant acute rejection dataset GSE50058 and oxidative stress-related genes (OS) obtained from the MSigDB database, and validated them with the datasets GSE1563 and GSE9493, as well as with animal experiments; Subsequently, we explored the potential biological functions of Hub genes using single-gene GSEA enrichment analysis; The Cibersort algorithm was used to explore the altered levels of infiltration of 22 immune cells during acute rejection of renal transplantation, and a correlation analysis between Hub genes and immune cells was performed; Finally, we also explored transcription factors (TFs), miRNAs, and potential drugs that regulate Hub genes. RESULTS We obtained a total of 57 genes, which we defined as oxidative stress-associated differential genes (DEOSGs), after intersecting DEGs during acute rejection of kidney transplants with OSs obtained from the MSigDB database; The results of enrichment analysis revealed that DEOSGs were mainly enriched in response to oxidative stress, response to reactive oxygen species, and regulation of oxidative stress and reactive oxygen species; Subsequently, we identified one Hub gene as APOD using five machine learning algorithms, which were validated by validation sets and animal experiments; The results of single-gene GSEA enrichment analysis revealed that APOD was closely associated with the regulation of immune signaling pathways during acute rejection of kidney transplants; The Cibersort algorithm found that the infiltration levels of a total of 10 immune cells were altered in acute rejection, while APOD was found to correlate with the expression of multiple immune cells; Finally, we also identified 154 TFs, 12 miRNAs, and 12 drugs or compounds associated with APOD regulation. CONCLUSION In this study, APOD was identified as a biomarker associated with oxidative stress during acute rejection of kidney transplants using multiple machine learning algorithms, which provides a potential therapeutic target for mitigating oxidative stress injury and reducing the incidence of acute rejection in kidney transplantation.
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Affiliation(s)
- Jun Pei
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Jie Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Chengjun Yu
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Jin Luo
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China
| | - Yi Hua
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China.
| | - Guanghui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, China; Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, China.
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Xiong Z, Li Z, Sima X, Zeng Z. Astaxanthin reduces TBPH-induced neurobehavioral deficits in mice by the ROS-ERK1/2-FOS pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 281:116674. [PMID: 38964056 DOI: 10.1016/j.ecoenv.2024.116674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/15/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The persistence of the novel brominated flame retardant, bis(2-ethylhexyl)-3,4,5,6-tetrabromophthalate (TBPH), in the environment and its potential for bioaccumulation in living organisms, including humans, further exacerbate its health risks. Therefore, ongoing research is crucial for fully understanding the extent of TBPH's neurotoxicity and for developing effective mitigation strategies. This study aims to investigate the potential neurotoxicity of TBPH on mouse neurobehavior and to evaluate the protective effects of the natural antioxidant astaxanthin (AST) against TBPH-induced neurotoxicity. The results indicate that exposure to TBPH can lead to a decline in learning and memory abilities and abnormal behaviors in mice, which may be associated with oxidative stress responses and apoptosis in the hippocampus. TBPH may disrupt the normal function of hippocampal neurons by activating the extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway. Mice exposed to TBPH treated with AST showed improved learning and memory abilities in the Morris water maze (MWM) and Step-down test (SDT). AST, through its antioxidant action, was able to significantly reduce the increase in reactive oxygen species (ROS) levels induced by TBPH, the increased expression of apoptosis markers, and the activation of the ERK1/2-FOS signaling pathway, alleviating TBPH-induced apoptosis in hippocampal neurons and improving neurobehavioral outcomes. These findings suggest that AST may alleviate the neurotoxicity of TBPH by modulating molecular events related to apoptosis and the ERK1/2-FOS signaling pathway. Thus, this study provides evidence for AST as a potential interventional strategy for the prevention or treatment of cognitive decline associated with environmental neurotoxicant exposure.
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Affiliation(s)
- Zhenkun Xiong
- Department of Neurosurgery, Jiujiang City Key Laboratory of Cell Therapy, Jiujiang NO.1 People's Hospital, Jiangxi 332000, PR China
| | - Zhenhua Li
- Department of Cardiothoracic Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, PR China
| | - Xueqin Sima
- Department of Histology and Embryology, School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning 437100, PR China.
| | - Zhi Zeng
- Department of Pathology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, PR China.
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Zhao J, Ge X, Li T, Yang M, Zhao R, Yan S, Wu H, Liu Y, Wang K, Xu Z, Jia J, Liu L, Dou T. Integrating metabolomics and transcriptomics to analyze the differences of breast muscle quality and flavor formation between Daweishan mini chicken and broiler. Poult Sci 2024; 103:103920. [PMID: 38909504 PMCID: PMC11253666 DOI: 10.1016/j.psj.2024.103920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/25/2024] Open
Abstract
The quality and flavor of chicken are affected by muscle metabolites and related regulatory genes, and the molecular regulation mechanism of meat quality is different among different breeds of chicken. In this study, 40 one-day-old Daweishan mini chicken (DM) and Cobb broiler (CB) were selected from each group, with 4 replicates and 10 chickens in each replicate. The chickens were reared until 90 d of age under the same management conditions. Then, metabolomics and transcriptomics data of 90-day-old DM (n = 4) and CB (n = 4) were integrated to analyze metabolites affecting breast muscle quality and flavor, and to explore the important genes regulating meat quality and flavor related metabolites. The results showed that a total of 38 significantly different metabolites (SDMs) and 420 differentially expressed genes (DEGs) were detected in the breast muscle of the 2 breeds. Amino acid and lipid metabolism may be the cause of meat quality and flavor difference between DM and CB chickens, involving metabolites such as L-methionine, betaine, N6, N6, N6-Trimethyl-L-lysine, L-anserine, glutathione, glutathione disulfide, L-threonine, N-Acetyl-L-aspartic acid, succinate, choline, DOPC, SOPC, alpha-linolenic acid, L-palmitoylcarnitine, etc. Important regulatory genes with high correlation with flavor amino acids (GATM, GSTO1) and lipids (PPARG, LPL, PLIN1, SCD, ANGPTL4, FABP7, GK, B4GALT6, UGT8, PLPP4) were identified by correlation analysis, and the gene-metabolite interaction network of breast muscle mass and flavor formation in DM chicken was constructed. This study showed that there were significant differences in breast metabolites between DM and CB chickens, mainly in amino acid and lipid metabolites. These 2 kinds of substances may be the main reasons for the difference in breast muscle quality and flavor between the 2 breeds. In general, this study could provide a theoretical basis for further research on the molecular regulatory mechanism of the formation of breast muscle quality and flavor differences between DM and CB chickens, and provide a reference for the development, utilization and genetic breeding of high-quality meat chicken breeds.
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Affiliation(s)
- Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuehai Ge
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tao Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Min Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ruohan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Institute of Science and Technology, Chuxiong Normal University, Chuxiong 675099, China
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
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Peng TL, Syazwan SA, Hamdan RH, Najwa NS, Ramli MF, Harshiny N, Ishak IH. Virulence and proteomic responses of Metarhizium anisopliae against Aedes albopictus larvae. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 203:105982. [PMID: 39084787 DOI: 10.1016/j.pestbp.2024.105982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 08/02/2024]
Abstract
The tropical climate in Malaysia provides an ideal environment for the rapid proliferation of Aedes mosquitoes, notably Aedes aegypti and Aedes albopictus, prominent vectors of dengue fever. Alarmingly, these species are increasingly developing resistance to conventional pesticides. This study aimed to evaluate the efficacy of Metarhizium anisopliae isolate HSAH5 spores, specifically on conidia (CO) and blastospores (BL), against Ae. albopictus larvae. The study centered on evaluating their pathogenic effects and the resultant changes in protein expression. Spore suspensions with varying concentrations were prepared for larvicidal bioassays, and protein expressions were analysed using liquid chromatography-mass spectrometry. Subsequently, protein annotation and network analysis were conducted to elucidate infection mechanisms and the proteomic response. Based on the lethal concentrations and time frames, CO exhibited faster larval mortality than BL at lower concentrations. Despite this, both spore types demonstrated comparable overall pathogenic effects. Results from the proteomic profiling revealed 150 proteins with varied expressions following exposure to Ae. albopictus extract, shedding light on distinct infection strategies between the spores. Gene Ontology enrichment and network analysis illustrated the diverse metabolic adaptations of M. anisopliae and interactions with mosquito larvae. This highlighted the complexity of host-pathogen dynamics and the significance of biosynthetic processes, energy storage, and cellular interaction pathways in disease progression. The BL network, consisting 80 proteins and 74 connections, demonstrates the intricate fungal mechanisms triggered by host stimuli. Conversely, the CO network, though smaller, displayed notable interconnectivity and concentrated involvement at the cell periphery, suggesting a deliberate strategy for initial host contact. This study offers valuable insights into proteome dynamics of M. anisopliae's BL and CO for managing mosquito populations and combating disease transmission, thereby significantly advancing public health and environmental conservation efforts.
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Affiliation(s)
- Tan Li Peng
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia.
| | - Samsuddin Ahmad Syazwan
- Mycology and Pathology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia; Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia
| | - Ruhil Hayati Hamdan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Nurainun Sofea Najwa
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Muhammad Fahmi Ramli
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Nalliah Harshiny
- Mycology and Pathology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia; Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia
| | - Intan Haslina Ishak
- School of Biological Science, Universiti Sains Malaysia, Persiaran Sains, 11800 Gelugor, Pulau Pinang, Malaysia
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Mehta P, Liu CSC, Sinha S, Mohite R, Arora S, Chattopadhyay P, Budhiraja S, Tarai B, Pandey R. Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing. Life Sci Alliance 2024; 7:e202402683. [PMID: 38830771 PMCID: PMC11147948 DOI: 10.26508/lsa.202402683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Dengue fever, a neglected tropical arboviral disease, has emerged as a global health concern in the past decade. Necessitating a nuanced comprehension of the intricate dynamics of host-virus interactions influencing disease severity, we analysed transcriptomic patterns using bulk RNA-seq from 112 age- and gender-matched NS1 antigen-confirmed hospital-admitted dengue patients with varying severity. Severe cases exhibited reduced platelet count, increased lymphocytosis, and neutropenia, indicating a dysregulated immune response. Using bulk RNA-seq, our analysis revealed a minimal overlap between the differentially expressed gene and transcript isoform, with a distinct expression pattern across the disease severity. Severe patients showed enrichment in retained intron and nonsense-mediated decay transcript biotypes, suggesting altered splicing efficiency. Furthermore, an up-regulated programmed cell death, a haemolytic response, and an impaired interferon and antiviral response at the transcript level were observed. We also identified the potential involvement of the RBM39 gene among others in the innate immune response during dengue viral pathogenesis, warranting further investigation. These findings provide valuable insights into potential therapeutic targets, underscoring the importance of exploring transcriptomic landscapes between different disease sub-phenotypes in infectious diseases.
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Affiliation(s)
- Priyanka Mehta
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chinky Shiu Chen Liu
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sristi Sinha
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Ramakant Mohite
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Smriti Arora
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Partha Chattopadhyay
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sandeep Budhiraja
- https://ror.org/00e7r7m66 Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Bansidhar Tarai
- https://ror.org/00e7r7m66 Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Rajesh Pandey
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Ma M, Ma G, Zhang C, Wang Y, He X, Kang X. Identification of Autophagy-Related Genes Involved in Intervertebral Disc Degeneration by Microarray Data Analysis. World Neurosurg 2024; 188:e1-e17. [PMID: 38782255 DOI: 10.1016/j.wneu.2023.12.012] [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: 07/23/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 05/25/2024]
Abstract
BACKGROUND Nucleus pulposus cells survive in a hypoxic, acidic, nutrient-poor, and hypotonic microenvironment. Consequently, they maintain low proliferation and undergo autophagy to protect themselves from cellular stress. Therefore, we aimed to identify autophagy-related biomarkers involved in intervertebral disc degeneration pathogenesis. METHODS Autophagy-related differentially expressed genes were derived from the intersection between the public GSE147383 microarray data set to identify differentially expressed genes and online databases to identify autophagy-related genes. Furthermore, we assessed their biological functions with gene annotation and enrichment analysis in the Metscape portal. Then, the STRING database and Cytoscape software allowed inferring a protein-protein interaction (PPI) network and identifying hub genes. In addition, to predict transcription factors that may regulate the hub genes, we used the GeneMANIA website. Finally, the competing endogenous RNA prediction tools and Cytoscape were also used to construct an mRNA-miRNA-lncRNA network. RESULTS A total of 123 autophagy-related differentially expressed genes were identified, they were mainly involved in phosphoinositide 3-kinase-Akt signaling, autophagy animal, and apoptosis pathways. Nine were identified as hub genes (PTEN, MYC, CTNNB1, JUN, BECN1, ERBB2, FOXO3, ATM, and FN1) and 36 transcription factors were associated with them. Finally, an autophagy-associated competing endogenous RNA network was constructed based on the 9 hub genes. CONCLUSIONS Nine hub genes were identified and a network of competing endogenous RNA associated with autophagy was established. They can be used as autophagy-related biomarkers of intervertebral disc degeneration and for further exploration.
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Affiliation(s)
- Miao Ma
- Department of Orthopedics, The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China; Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Guifu Ma
- Department of Orthopedics, Gansu Provincial People's Hospital, Lanzhou, China
| | - Chao Zhang
- Department of Orthopedics, Gansu Provincial People's Hospital, Lanzhou, China
| | - Yajun Wang
- Breast Department, Zhangye People's Hospital Affiliated to Hexi University, Zhangye, China
| | - Xuegang He
- Department of Orthopedics, The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China; Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Xuewen Kang
- Department of Orthopaedics, Lanzhou University Second Hospital, Lanzhou, China.
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Tanwar N, Hasija Y. Explicate molecular landscape of combined pulmonary fibrosis and emphysema through explainable artificial intelligence: a comprehensive analysis of ILD and COPD interactions using RNA from whole lung homogenates. Med Biol Eng Comput 2024; 62:2557-2570. [PMID: 38644448 DOI: 10.1007/s11517-024-03099-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/14/2024] [Indexed: 04/23/2024]
Abstract
Combined pulmonary fibrosis and emphysema (CPFE) presents a unique challenge in respiratory disorders, merging features of interstitial lung disease (ILD) and chronic obstructive pulmonary disease (COPD). Using the random forest algorithm, our study thoroughly examines the molecular details of CPFE. Analyzing gene expression datasets from GSE47460 (ILD: 254, COPD: 220, control: 108), we identify key genes namely ADRB2, CDH3, IRS2, MATN3, CD38, PDIA4, VEGFC, and among twenty others, crucial in airway regulation, lung function, and apoptosis, shaping the complex pathogenesis of CPFE. Additionally, miRNAs (hsa-mir-101-3p, hsa-mir-1343-3p, hsa-mir-27a-3p, and miR-16-5p) showcase regulatory impacts on CPFE-related molecular pathways. Our machine learning model unveils these intricate interactions, offering a comprehensive insight into CPFE's molecular mechanisms. This research not only pinpoints potential therapeutic targets and biomarkers but also opens avenues for innovative approaches in managing CPFE, linking ILD and COPD within this complex respiratory condition.
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Affiliation(s)
- Nakul Tanwar
- Department of Biotechnology, Delhi Technological University (DTU), Delhi, 110042, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University (DTU), Delhi, 110042, India.
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Chen Z, Hua G, Shu X, Zhuang W, Zhang J, Zhu R, Zheng X, Chen J. Screening of reliable reference genes for the normalization of RT-qPCR in chicken liver tissues and LMH cells. Sci Rep 2024; 14:17828. [PMID: 39090210 PMCID: PMC11294616 DOI: 10.1038/s41598-024-68752-6] [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: 03/07/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
The liver plays a vital role in lipid synthesis and metabolism in poultry. To study the functional genes more effectively, it is essential to screen of reliable reference genes in the chicken liver, including females, males, embryos, as well as the Leghorn Male Hepatoma (LMH) cell line. Traditional reference gene screening involves selecting commonly used housekeeping genes (HKGs) for RT-qPCR experiments and using different algorithms to identify the most stable ones. However, this approach is limited in selecting the best reference gene from a small pool of HKGs. High-throughput sequencing technology may offer a solution to this limitation. This study aimed to identify the most consistently expressed genes by utilizing multiple published RNA-seq data of chicken liver and LMH cells. Subsequently, the stability of the newly identified reference genes was assessed in comparison to previously validated stable poultry liver expressed reference genes and the commonly employed HKGs using RT-qPCR. The findings indicated that there is a higher degree of similarity in stable expression genes between female and male liver (such as LSM14A and CDC40). In embryonic liver, the optimal new reference genes were SUDS3, TRIM33, and ERAL1. For LMH cells, the optimal new reference genes were ALDH9A1, UGGT1, and C21H1orf174. However, it is noteworthy that most HKGs did not exhibit stable expression across multiple samples, indicating potential instability under diverse conditions. Furthermore, RT-qPCR experiments proved that the stable expression genes identified from RNA-seq data outperformed commonly used HKGs and certain validated reference genes specific to poultry liver. Over all, this study successfully identified new stable reference genes in chicken liver and LMH cells using RNA-seq data, offering researchers a wider range of reference gene options for RT-qPCR in diverse situations.
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Affiliation(s)
- Ziwei Chen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xin Shu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Wuchao Zhuang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Jilong Zhang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Runbang Zhu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Xiaotong Zheng
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Jianfei Chen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China.
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Zakutansky PM, Ku L, Zhang G, Shi L, Li Y, Yao B, Bassell GJ, Read RD, Feng Y. Isoform balance of the long noncoding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts cell migration. J Biol Chem 2024; 300:107595. [PMID: 39032650 PMCID: PMC11367543 DOI: 10.1016/j.jbc.2024.107595] [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: 04/19/2024] [Revised: 07/02/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024] Open
Abstract
The long noncoding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) is involved in a variety of human cancers. Two overlapping NEAT1 isoforms, NEAT1_1 and NEAT1_2, are produced through mutually exclusive alternative 3' end formation. Previous studies extensively investigated NEAT1 dysregulation in tumors, but often failed to achieve distinct quantification of the two NEAT1 isoforms. Moreover, molecular mechanisms governing the biogenesis of NEAT1 isoforms and the functional impacts of their dysregulation in tumorigenesis remain poorly understood. In this study, we employed an isoform-specific quantification assay and found differential dysregulation of NEAT1 isoforms in patient-derived glioblastoma multiforme cells. We further showed usage of the NEAT1 proximal polyadenylation site (PAS) is a critical mechanism that controls glioma NEAT1 isoform production. CRISPR-Cas9-mediated PAS deletion reduced NEAT1_1 and reciprocally increased NEAT1_2, which enhanced nuclear paraspeckle formation in human glioma cells. Moreover, the utilization of the NEAT1 PAS is facilitated by the RNA-binding protein quaking (QKI), which binds to the proximal QKI recognition elements. Functionally, we identified transcriptomic changes and altered biological pathways caused by NEAT1 isoform imbalance in glioma cells, including the pathway for the regulation of cell migration. Finally, we demonstrated the forced increase of NEAT1_2 upon NEAT1 PAS deletion is responsible for driving glioma cell migration and promoting the expression of genes implicated in the regulation of cell migration. Together, our studies uncovered a novel mechanism that regulates NEAT1 isoforms and their functional impacts on the glioma transcriptome, which affects pathological pathways of glioma, represented by migration.
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Affiliation(s)
- Paul M Zakutansky
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell, and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Li Ku
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Guannan Zhang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Liang Shi
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Renee D Read
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA; Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Yue Feng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA.
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Oñate MK, Oon C, Bhattacharyya S, Low V, Chen C, Zhao X, Yan Z, Hang Y, Kim SK, Xia Z, Sherman MH. Stromal KITL/SCF promotes pancreas tissue homeostasis and restrains tumor progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605485. [PMID: 39131374 PMCID: PMC11312444 DOI: 10.1101/2024.07.29.605485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Components of normal tissue architecture serve as barriers to tumor progression. Inflammatory and wound-healing programs are requisite features of solid tumorigenesis, wherein alterations to immune and non-immune stromal elements enable loss of homeostasis during tumor evolution. The precise mechanisms by which normal stromal cell states limit tissue plasticity and tumorigenesis, and which are lost during tumor progression, remain largely unknown. Here we show that healthy pancreatic mesenchyme expresses the paracrine signaling molecule KITL, also known as stem cell factor, and identify loss of stromal KITL during tumorigenesis as tumor-promoting. Genetic inhibition of mesenchymal KITL in the contexts of homeostasis, injury, and cancer together indicate a role for KITL signaling in maintenance of pancreas tissue architecture, such that loss of the stromal KITL pool increased tumor growth and reduced survival of tumor-bearing mice. Together, these findings implicate loss of mesenchymal KITL as a mechanism for establishing a tumor-permissive microenvironment.
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Affiliation(s)
- M. Kathrina Oñate
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Chet Oon
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Sohinee Bhattacharyya
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Vivien Low
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Canping Chen
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Xiaofan Zhao
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Ziqiao Yan
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Zheng Xia
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Mara H. Sherman
- Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
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49
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Zheng YQ, Huang HH, Chen SX, Xu XE, Li ZM, Li YH, Chen SZ, Luo WX, Guo Y, Liu W, Li EM, Xu LY. Discovery and validation of combined biomarkers for the diagnosis of esophageal intraepithelial neoplasia and esophageal squamous cell carcinoma. J Proteomics 2024; 304:105233. [PMID: 38925350 DOI: 10.1016/j.jprot.2024.105233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Early diagnosis and intervention of esophageal squamous cell carcinoma (ESCC) can improve the prognosis. The purpose of this study was to identify biomarkers for ESCC and esophageal precancerous lesions (intraepithelial neoplasia, IEN). Based on the proteomic and genomic data of esophageal tissue including previously reported data, up-regulated proteins with copy number amplification in esophageal cancer were screened as candidate biomarkers. Five proteins, including KDM2A, RAD9A, ECT2, CYHR1 and TONSL, were confirmed by immunohistochemistry on ESCC and normal esophagus (NE). Then, we investigated the expression of 5 proteins in 236 participants (60 NEs, 93 IENs and 83 ESCCs) which were randomly divided into training set and test set. When distinguishing ESCC from NE, the area under curve (AUC) of the multiprotein model was 0.940 in the training set, while the lowest AUC of a protein was 0.735. In the test set, the results were similar. When distinguishing ESCC from IEN or distinguishing IEN from NE, the diagnostic efficiency of the multi-protein models were also improved compared with that of single protein. Our findings suggest that combined detection of KDM2A, RAD9A, ECT2, CYHR1 and TONSL can be used as potential biomarkers for the early diagnosis of ESCC and precancerous lesion development prediction. SIGNIFICANCE: Candidate biomarkers including KDM2A, RAD9A, ECT2, CYHR1 and TONSL screened by integrating genomic and proteomic data from the esophagus can be used as potential biomarkers for the early diagnosis of esophageal squamous cell carcinoma and precancerous lesion development prediction.
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Affiliation(s)
- Ya-Qi Zheng
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China; Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Hai-Hua Huang
- Department of Pathology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Shu-Xian Chen
- Department of Digestive Endoscopy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xiu-E Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhi-Mao Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yue-Hong Li
- Department of Digestive Endoscopy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Su-Zuan Chen
- Department of Digestive Endoscopy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wen-Xiong Luo
- Department of Endoscopy, Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Yi Guo
- Department of Endoscopy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wei Liu
- College of Science, Heilongjiang Institute of Technology, Harbin, Heilongjiang 150000, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041, China.
| | - Li-Yan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China.
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50
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Iqbal Z, Zahoor T, Pasha I, Shahid M. Eco-safe hot water dip alleviates antioxidant level and sensory quality of Indian jujube fruits. Heliyon 2024; 10:e34400. [PMID: 39114000 PMCID: PMC11304006 DOI: 10.1016/j.heliyon.2024.e34400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Indian jujube (Ber) is highly perishable climacteric fruit owing to high decay index limiting its marketability and demands interventions to prolong shelf life. Fungicides are normally used to control rot during postharvest storage, however, residues left necessitate eco-safe alternatives like hot water dipping. Mature, pre-climacteric jujubes were dipped in 45, 50 or 55 °C water for 8, 6 or 4 min, respectively and then stored at 5 °C for periodic quality evaluation. Dipping fruits in 55 °C water resulted in 32.69 and 35.27, 64.21 and 58.57, 30.41 and 30.42, 38.50 and 52.20 % lower weight loss, decay index, malondialdehyde (MDA) and electrolyte leakage, whereas 15.40 and 16.77, 19.51 and 20.48 % greater antioxidant activity and ascorbic acid respectively for Umran and Pakwhite compared to 25 °C water dip. The highest glucose, fructose, malic, citric, and tartaric acids were 23.44 ± 1.04 and 29.9 ± 0.95, 30.68 ± 1.72 and 41.17 ± 2.34 mg/100 g, 138.1 ± 6.45 and 112.97 ± 6.16, 57.49 ± 1.71 and 53.78 ± 1.90, 79.58 ± 5.1 and 65.3 ± 4.83 μg/100 g whereas lower sucrose 12.34 ± 0.94 and 16.33 ± 1.05 mg/100 g were respectively recorded in 55 °C water dipped Umran and Pakwhite fruits. High dip water temperature (55 °C) exhibited better quality with the lowest decay index and weight loss, greater membrane integrity, bioactives content and sensory acceptance scores. Hence, hot water dipping was shown to be an effective residue-free option to extend the marketable period of jujubes to capture distant markets.
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Affiliation(s)
- Zafar Iqbal
- National Institute of Food Science and Technology (NIFSAT), University of Agriculture, Faisalabad (UAF), Pakistan
- Food Technology Section, Post Harvest Research Centre, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Tahir Zahoor
- National Institute of Food Science and Technology (NIFSAT), University of Agriculture, Faisalabad (UAF), Pakistan
| | - Imran Pasha
- National Institute of Food Science and Technology (NIFSAT), University of Agriculture, Faisalabad (UAF), Pakistan
| | - Muhammad Shahid
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
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