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Lee CK, Huan PT, Chai CN, Ng LJ, Koay ESC, Lee OF, Tan M, Loh TP. Novel thiopurine S-methyltransferase ( TPMT) variant identified in Malay individuals. Clin Chem Lab Med 2024; 0:cclm-2024-0494. [PMID: 38661453 DOI: 10.1515/cclm-2024-0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Chun Kiat Lee
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
| | - Pei Tee Huan
- Department of Paediatrics, Yong Loo Lin School of Medicine, 37580 National University of Singapore , Singapore, Singapore
| | - Chean Nee Chai
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
| | - Li Jie Ng
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
| | - Evelyn Siew-Chuan Koay
- Department of Pathology, Yong Loo Lin School of Medicine, 37580 National University of Singapore , Singapore, Singapore
| | - Ogestelli Fabia Lee
- School of Life and Physical Sciences, 464889 PSB Academy , Singapore, Singapore
| | - Malcolm Tan
- Department of Gastroenterology and Hepatology, 37581 Singapore General Hospital , Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, 150744 National University Health System , Singapore, Singapore
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Han X, Weng M, Shi W, Wen Y, Long Y, Hu X, Ji G, Zhu Y, Wen X, Zhang F, Wu S. The Neurotranscriptome of Monochamus alternatus. Int J Mol Sci 2024; 25:4553. [PMID: 38674138 PMCID: PMC11050616 DOI: 10.3390/ijms25084553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
The Japanese pine sawyer Monochamus alternatus serves as the primary vector for pine wilt disease, a devastating pine disease that poses a significant threat to the sustainable development of forestry in the Eurasian region. Currently, trap devices based on informational compounds have played a crucial role in monitoring and controlling the M. alternatus population. However, the specific proteins within M. alternatus involved in recognizing the aforementioned informational compounds remain largely unclear. To elucidate the spatiotemporal distribution of M. alternatus chemosensory-related genes, this study conducted neural transcriptome analyses to investigate gene expression patterns in different body parts during the feeding and mating stages of both male and female beetles. The results revealed that 15 genes in the gustatory receptor (GR) gene family exhibited high expression in the mouthparts, most genes in the odorant binding protein (OBP) gene family exhibited high expression across all body parts, 22 genes in the odorant receptor (OR) gene family exhibited high expression in the antennae, a significant number of genes in the chemosensory protein (CSP) and sensory neuron membrane protein (SNMP) gene families exhibited high expression in both the mouthparts and antennae, and 30 genes in the ionotropic receptors (IR) gene family were expressed in the antennae. Through co-expression analyses, it was observed that 34 genes in the IR gene family were co-expressed across the four developmental stages. The Antenna IR subfamily and IR8a/Ir25a subfamily exhibited relatively high expression levels in the antennae, while the Kainate subfamily, NMDA subfamily, and Divergent subfamily exhibited predominantly high expression in the facial region. MalIR33 is expressed only during the feeding stage of M. alternatus, the MalIR37 gene exhibits specific expression in male beetles, the MalIR34 gene exhibits specific expression during the feeding stage in male beetles, the MalIR8 and MalIR39 genes exhibit specific expression during the feeding stage in female beetles, and MalIR8 is expressed only during two developmental stages in male beetles and during the mating stage in female beetles. The IR gene family exhibits gene-specific expression in different spatiotemporal contexts, laying the foundation for the subsequent selection of functional genes and facilitating the full utilization of host plant volatiles and insect sex pheromones, thereby enabling the development of more efficient attractants.
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Affiliation(s)
- Xiaohong Han
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingqing Weng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenchao Shi
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yingxin Wen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yirong Long
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinran Hu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoxi Ji
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuanye Wen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiping Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.W.); (W.S.); (Y.W.); (Y.L.); (X.H.); (G.J.); (Y.Z.); (X.W.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Almishri W, Altonsy MO, Swain MG. Cholestatic liver disease leads to significant adaptative changes in neural circuits regulating social behavior in mice to enhance sociability. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167100. [PMID: 38412926 DOI: 10.1016/j.bbadis.2024.167100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND & AIMS Cholestatic liver diseases (CLD) are commonly associated with behavioral changes, including social isolation, that negatively affects patient quality of life and remains unaltered by current therapies. It remains unclear whether CLD-associated social dysfunction stems from a direct effect on the brain, or from the psychological impact of CLD. The psychological component of disease is absent in animals, so we investigated the impact of CLD on social behavior and gene expression profiles in key social behavior-regulating brain regions in a mouse model. METHODS CLD due to bile duct ligation was used with the three-chamber sociability test for behavioral phenotyping. Differentially expressed gene (DEG) signatures were delineated in 3 key brain regions regulating social behavior using RNA-seq. Ingenuity Pathway Analysis (IPA®) was applied to streamline DEG data interpretation and integrate findings with social behavior-regulating pathways to identify important brain molecular networks and regulatory mechanisms disrupted in CLD. RESULTS CLD mice exhibited enhanced social interactive behavior and significantly altered gene expression in each of the three social behavior-regulating brain regions examined. DEG signatures in BDL mice were associated with key IPA®-identified social behavior-regulating pathways including Oxytocin in Brain Signaling, GABA Receptor Signaling, Dopamine Receptor Signaling, and Glutamate Receptor Signaling. CONCLUSIONS CLD causes complex alterations in gene expression profiles in key social behavior-regulating brain areas/pathways linked to enhanced social interactive behavior. These findings, if paralleled in CLD patients, suggest that CLD-associated reductions in social interactions predominantly relate to psychological impacts of disease and may inform new approaches to improve management.
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Affiliation(s)
- Wagdi Almishri
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Mohammed O Altonsy
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mark G Swain
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; University of Calgary Liver Unit, Division of Gastroenterology and Hepatology, Department of Medicine, University of Calgary, Calgary, AB, Canada.
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Rivedal M, Mikkelsen H, Marti HP, Liu L, Kiryluk K, Knoop T, Bjørneklett R, Haaskjold YL, Furriol J, Leh S, Paunas F, Bábíčková J, Scherer A, Serre C, Eikrem O, Strauss P. Glomerular transcriptomics predicts long term outcome and identifies therapeutic strategies for patients with assumed benign IgA nephropathy. Kidney Int 2024; 105:717-730. [PMID: 38154557 DOI: 10.1016/j.kint.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023]
Abstract
Some patients diagnosed with benign IgA nephropathy (IgAN) develop a progressive clinical course, not predictable by known clinical or histopathological parameters. To assess if gene expression can differentiate between progressors and non-progressors with assumed benign IgAN, we tested microdissected glomeruli from archival kidney biopsy sections from adult patients with stable clinical remission (21 non-progressors) or from 15 patients that had undergone clinical progression within a 25-year time frame. Based on 1 240 differentially expressed genes from patients with suitable sequencing results, we identified eight IgAN progressor and nine non-progressor genes using a two-component classifier. These genes, including APOL5 and ZXDC, predicted disease progression with 88% accuracy, 75% sensitivity and 100% specificity on average 21.6 years before progressive disease was clinically documented. APOL lipoproteins are associated with inflammation, autophagy and kidney disease while ZXDC is a zinc-finger transcription factor modulating adaptive immunity. Ten genes from our transcriptomics data overlapped with an external genome wide association study dataset, although the gene set enrichment test was not statistically significant. We also identified 45 drug targets in the DrugBank database, including angiotensinogen, a target of sparsentan (dual antagonist of the endothelin type A receptor and the angiotensin II type 1 receptor) currently investigated for IgAN treatment. Two validation cohorts were used for substantiating key results, one by immunohistochemistry and the other by nCounter technology. Thus, glomerular mRNA sequencing from diagnostic kidney biopsies from patients with assumed benign IgAN can differentiate between future progressors and non-progressors at the time of diagnosis.
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Affiliation(s)
- Mariell Rivedal
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Håvard Mikkelsen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Lili Liu
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Thomas Knoop
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rune Bjørneklett
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
| | - Yngvar Lunde Haaskjold
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jessica Furriol
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sabine Leh
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Flavia Paunas
- Department of Medicine, Haugesund Hospital, Haugesund, Norway
| | - Janka Bábíčková
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Andreas Scherer
- Spheromics, Kontiolahti, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Camille Serre
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Oystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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Chen Z, Zhao Q, Chen L, Gao S, Meng L, Liu Y, Wang Y, Li T, Xue J. MAGP2 promotes osteogenic differentiation during fracture healing through its crosstalk with the β-catenin pathway. J Cell Physiol 2024; 239:e31183. [PMID: 38348695 DOI: 10.1002/jcp.31183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 04/12/2024]
Abstract
Osteogenic differentiation is important for fracture healing. Microfibrial-associated glycoprotein 2 (MAGP2) is found to function as a proangiogenic regulator in bone formation; however, its role in osteogenic differentiation during bone repair is not clear. Here, a mouse model of critical-sized femur fracture was constructed, and the adenovirus expressing MAGP2 was delivered into the fracture site. Mice with MAGP2 overexpression exhibited increased bone mineral density and bone volume fraction (BV/TV) at Day 14 postfracture. Within 7 days postfracture, overexpression of MAGP2 increased collagen I and II expression at the fracture callus, with increasing chondrogenesis. MAGP2 inhibited collagen II level but elevated collagen I by 14 days following fracture, accompanied by increased endochondral bone formation. In mouse osteoblast precursor MC3T3-E1 cells, MAGP2 treatment elevated the expression of osteoblastic factors (osterix, BGLAP and collagen I) and enhanced ALP activity and mineralization through activating β-catenin signaling after osteogenic induction. Besides, MAGP2 could interact with lipoprotein receptor-related protein 5 (LRP5) and upregulated its expression. Promotion of osteogenic differentiation and β-catenin activation mediated by MAGP2 was partially reversed by LRP5 knockdown. Interestingly, β-catenin/transcription factor 4 (TCF4) increased MAGP2 expression probably by binding to MAGP2 promoter. These findings suggest that MAGP2 may interact with β-catenin/TCF4 to enhance β-catenin/TCF4's function and activate LRP5-activated β-catenin signaling pathway, thus promoting osteogenic differentiation for fracture repair. mRNA sequencing identified the potential targets of MAGP2, providing novel insights into MAGP2 function and the directions for future research.
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Affiliation(s)
- Zhiguang Chen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qi Zhao
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lianghong Chen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Songlan Gao
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lingshuai Meng
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yingjie Liu
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Wang
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tiegang Li
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jinqi Xue
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Yan X, Tong X, Jia Y, Zhao Y, Zhang Q, Hu M, Li X, Li B, Ming X, Xie Y, Wu X, Yu X, Qu L, Xiong L, Huang F, Nie J. Baiheqingjin formula reduces inflammation in mice with asthma by inhibiting the PI3K/AKT/NF-κb signaling pathway. J Ethnopharmacol 2024; 321:117565. [PMID: 38081397 DOI: 10.1016/j.jep.2023.117565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Baiheqingjin Decoction (BHQJ), which consists of 7 traditional Chinese herbs including Baibu (Stemona tuberosa Lour.), Hezi (Terminalia chebula Retz.), Mahuang (Ephedra sinica Stapf.), Ziwan (Aster tataricus L. f.), Dilong (Pheretima), Sangbaipi (Morus alba L.), and Xianhecao (Agrimonia pilosa Ledeb.). BHQJ is commonly used for treating cough asthma, and variant cough-variant asthma as it, is effective in improving asthma symptoms and reducing airway inflammation. AIM OF THE STUDY To investigate the mechanisms of BHQJ in treating allergic asthma. MATERIALS AND METHODS We collected information about the components and targets of 6 Chinese medicines (excluding Pheretima) from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Additionally, we obtained genes associated with asthma from six disease databases. To create a protein-protein interaction network, we conducted an intersection analysis using differentially expressed genes derived from RNA transcriptome data. Subsequently, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. To validate the findings from network pharmacology and transcriptomics, we established an allergic asthma mouse model induced by ovalbumin and conducted in vivo experiments. RESULTS Using network pharmacology and transcriptomics analyses, we identified the pathways including the PI3K/AKT signaling pathway, and NF-κB signaling pathway. Among these, the involvement of the PI3K/AKT/NF-κB signaling pathway in various pathological processes of asthma, such as airway inflammation, smooth muscle contraction, and excessive mucus production, are well-documented. Histopathological examinations indicated that BHQJ had the potential to mitigate inflammatory cell infiltration and the excessive growth of goblet cells in the airways of asthmatic mice, consequently reducing mucus secretion. Results from Western blot demonstrated that BHQJ could inhibit the activation of the PI3K/AKT/NF-κB pathway at the protein levels. Enzyme-linked immunosorbent assay findings revealed that BHQJ could reduce the production of typical "type 2 asthma" cytokines and immunoglobulin (Ig) E in the blood. These discoveries imply that BHQJ has the potential to reduce the release of inflammatory cytokines and suppress the overactivation of the PI3K/AKT/NF-κB signaling pathway, thus offering a therapeutic approach for asthma. CONCLUSION Our research offers initial insights into the fundamental mechanisms through which BHQJ treats asthma. This study reveals the potential mechanism of BHQJ in treating asthma, particularly its role in reducing inflammatory cytokines, mucus production, and cell infiltration, as well as inhibiting the expression of PI3K/AKT/P65 phosphorylated protein. These findings indicate the potential of BHQJ in treating asthma. In summary, our study provides preliminary insights into the asthma treatment mechanism of BHQJ and provides guidance for future research.
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Affiliation(s)
- Xiaodong Yan
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Xiaoyun Tong
- The First Affiliated Hospital of Yunnan University of Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yongrui Jia
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Yi Zhao
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Qiushi Zhang
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Min Hu
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Xiaohong Li
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Baojing Li
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Xi Ming
- The First Affiliated Hospital of Yunnan University of Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yuhuan Xie
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Xiangnong Wu
- The First Affiliated Hospital of Yunnan University of Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xiaoling Yu
- The Third Affiliated Hospital of Yunnan University of Chinese Medicine, Kunming, 650021, China
| | - Lu Qu
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China
| | - Lei Xiong
- The First Affiliated Hospital of Yunnan University of Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Feng Huang
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China.
| | - Jian Nie
- School of Chinese Materia Medical and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chines e Medicine, Kunming, 650500, China.
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Farhadi A, Xue L, Zhao Q, Han F, Xu C, Chen H, Li E. Identification of key genes and molecular pathways associated with claw regeneration in mud crab (Scylla paramamosain). Comp Biochem Physiol Part D Genomics Proteomics 2024; 49:101184. [PMID: 38154166 DOI: 10.1016/j.cbd.2023.101184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
The mud crab (Scylla paramamosain) possesses extensive regenerative abilities, enabling it to replace missing body parts, including claws, legs, and even eyes. Studying the genetic and molecular mechanisms underlying regenerative ability in diverse animal phyla has the potential to provide new insights into regenerative medicine in humans. In the present study, we performed mRNA sequencing to reveal the genetic mechanisms underlying the claw regeneration in mud crab. Several differentially expressed genes (DEGs) were expressed in biological pathways associated with cuticle synthase, collagen synthase, tissue regeneration, blastema formation, wound healing, cell cycle, cell division, and cell migration. The top GO enrichment terms were microtubule-based process, collagen trimer, cell cycle process, and extracellular matrix structural constituent. The most enriched KEGG pathways were ECM-receptor interaction and focal adhesion. The genes encoding key functional proteins, such as collagen alpha, cuticle protein, early cuticle protein, arthrodial cuticle protein, dentin sialophosphoprotein (DSPP), epidermal growth factor receptor (EGFR), kinesin family member C1 (KIFC1), and DNA replication licensing factor mcm2-like (MCM2) were the most significant and important DEGs suspected to participate in claw regeneration. The findings of this research offer a comprehensive and insightful understanding of the genetic and molecular mechanisms underlying claw regeneration in S. paramamosain. By elucidating the specific genes and molecular pathways implicated in this process, our study contributes significantly to the broader field of regenerative biology and offers potential avenues for further exploration in crustacean limb regeneration.
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Affiliation(s)
- Ardavan Farhadi
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China.
| | - Laizhong Xue
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China
| | - Qun Zhao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China
| | - Fenglu Han
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China
| | - Chang Xu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China
| | - Hu Chen
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan 570228, China.
| | - Erchao Li
- School of Life Sciences, East China Normal University, Shanghai 200241, China
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Zheng X, Guo C, Lv Z, Li J, Jiang H, Li S, Yu L, Zhang Z. Novel findings from arsenic‑lead combined exposure in mouse testicular TM4 Sertoli cells based on transcriptomics. Sci Total Environ 2024; 913:169611. [PMID: 38157908 DOI: 10.1016/j.scitotenv.2023.169611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Arsenic (As) and lead (Pb) exist widespread in daily life, and they are common harmful substances in the environment. As and Pb pollute the environment more often in combination than in isolation. The TM4 Sertoli cell line is one of the most common normal mouse testicular Sertoli cell lines. In vitro, we found that the type of combined action of As and Pb on TM4 Sertoli cells was additive action by using the isobologram analysis. To further investigate the combined toxicity of As and Pb, we performed mRNA and miRNA sequencing on TM4 Sertoli cells exposed to As alone (4 μM NaAsO2) and AsPb combined (4 μM NaAsO2 and 150 μM PbAc), respectively. Compared with the control group, 1391 differentially expressed genes (DEGs) and 6 differentially expressed miRNAs (DEMs) were identified in the As group. Compared with the control group, 2384 DEGs and 44 DEMs were identified in the AsPb group. Compared with the As group, 387 DEGs and 4 DEMs were identified in the AsPb group. Through data analysis, we discovered for the first time that As caused the dysfunction of cholesterol synthesis and energy metabolism, and disrupted cyclic adenosine monophosphate signaling pathway and wingless/integrated (Wnt) signaling pathway in TM4 Sertoli cells. In addition to affecting cholesterol synthesis and energy metabolism, AsPb combined exposure also up-regulated the antioxidant reaction level of TM4 Sertoli cells. Meanwhile, the Wnt signaling pathway of TM4 Sertoli cells was relatively normal when exposed to AsPb. In conclusion, at the transcription level, the combined action of AsPb is not merely additive effect, but involves synergistic and antagonistic effects. The new discovery of the joint toxic mechanism of As and Pb breaks the stereotype of the combined action and provides a good theoretical basis and research clue for future study of the combined-exposure of harmful materials.
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Affiliation(s)
- Xiaoyan Zheng
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Changming Guo
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhanjun Lv
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Jiayi Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Huijie Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Siyu Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Lu Yu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Zhigang Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
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9
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Zhang L, Peng J, Zhang A, Zhang S. Morphological change and genome-wide transcript analysis of Haloxylon ammodendron leaf development reveals morphological characteristics and genes associated with the different C3 and C4 photosynthetic metabolic pathways. Tree Physiol 2024; 44:tpae018. [PMID: 38284810 DOI: 10.1093/treephys/tpae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
C4 photosynthesis outperforms C3 photosynthesis in natural ecosystems by maintaining a high photosynthetic rate and affording higher water-use and nitrogen-use efficiencies. C4 plants can survive in environments with poor living conditions, such as high temperatures and arid regions, and will be crucial to ecological and agricultural security in the face of global climate change in the future. However, the genetic architecture of C4 photosynthesis remains largely unclear, especially the genetic regulation of C4 Kranz anatomy. Haloxylon ammodendron is an important afforestation tree species and a valuable C4 wood plant in the desert region. The unique characteristic of H. ammodendron is that, during the seedling stage, it utilizes C3 photosynthesis, while in mature assimilating shoots (maAS), it switches to the C4 pathway. This makes an exceptional opportunity for studying the development of the C4 Kranz anatomy and metabolic pathways within individual plants (identical genome). To provide broader insight into the regulation of Kranz anatomy and non-Kranz leaves of the C4 plant H. ammodendron, carbon isotope values, anatomical sections and transcriptome analyses were used to better understand the molecular and cellular processes related to the development of C4 Kranz anatomy. This study revealed that H. ammodendron conducts C3 in the cotyledon before it switches to C4 in AS. However, the switching requires a developmental process. Stable carbon isotope discrimination measurements on three different developmental stages showed that young AS have a C3-like δ13C even though C4 Kranz anatomy is found, which is inconsistent with the anatomical findings. A C4-like δ13C can be measured in AS until they are mature. The expression analysis of C4 key genes also showed that the maAS exhibited higher expression than the young AS. In addition, many genes that may be related to the development of Kranz anatomy were screened. Comparison of gene expression patterns with respect to anatomy during leaf ontogeny provided insight into the genetic features of Kranz anatomy. This study helps with our understanding of the development of Kranz anatomy and provides future directions for studies on key C4 regulatory genes.
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Affiliation(s)
- Lingling Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Jieying Peng
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Anna Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Sheng Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi 712100, China
- College of Life Science and Technology, Xinjiang University, 666 Shengli Road, Urumchi 830046, China
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10
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Chen R, Ai D, Wang G, Wang B. Comparative transcriptome analysis of the antenna and proboscis reveals feeding state-dependent chemosensory genes in Eupeodes corollae. Open Biol 2024; 14:230208. [PMID: 38195061 PMCID: PMC10776234 DOI: 10.1098/rsob.230208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
The physiological state of an insect can affect its olfactory system. However, the molecular mechanism underlying the effect of nutrition-dependent states on odour-guided behaviours in hoverflies remains unclear. In this study, comparative transcriptome analysis of the antenna and proboscis from Eupeodes corollae under different feeding states was conducted. Compared with the previously published antennal transcriptome, a total of 32 novel chemosensory genes were identified, including 4 ionotropic receptors, 17 gustatory receptors, 9 odorant binding proteins and 2 chemosensory proteins. Analysis of differences in gene expression between different feeding states in male and female antennae and proboscises revealed that the expression levels of chemosensory genes were impacted by feeding state. For instance, the expression levels of EcorOBP19 in female antennae, EcorOBP6 in female proboscis, and EcorOR6, EcorOR14, EcorIR5 and EcorIR84a in male antennae were significantly upregulated after feeding. On the other hand, the expression levels of EcorCSP7 in male proboscis and EcorOR40 in male antennae were significantly downregulated. These findings suggest that nutritional state plays a role in the adaptation of hoverflies' olfactory system to food availability. Overall, our study provides important insights into the plasticity and adaptation of chemosensory systems in hoverflies.
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Affiliation(s)
- Ruipeng Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Dong Ai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People’s Republic of China
| | - Bing Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
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Kim JS, Haimon Z, Boura-Halfon S, Jung S. Translatome Profiling of Tissue-Resident Macrophages Using the RiboTag Approach. Methods Mol Biol 2024; 2713:253-267. [PMID: 37639128 DOI: 10.1007/978-1-0716-3437-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Global gene expression profiling has provided valuable insights into the specific contributions of different cell types to various physiological processes. Notably though, both bulk and single-cell transcriptomics require the prior retrieval of the cells from their tissue context to be analyzed. Isolation protocols for tissue macrophages are, however, notoriously inefficient and, moreover, prone to introduce considerable bias and artifacts. Here, we will discuss a valuable alternative, originally introduced by Amieux and colleagues. This so-called RiboTag approach allows, in combination with respective macrophage-specific Cre transgenic lines, to retrieve macrophage translatomes from crude tissue extracts. We will review our experience with this ingenious method, focusing on the study of brain macrophages, including microglia and border-associated cells. We will elaborate on the advantages of the RiboTag approach that render it a valuable complement to standard cell sorting-based profiling strategies, especially for the investigation of tissue macrophages.
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Affiliation(s)
- Jung-Seok Kim
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Zhana Haimon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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Du G, Liu M, Qi Y, Lin M, Wu J, Xie W, Ren D, Du S, Jia T, Zhang F, Song W, Liu H. BMP4 up-regulated by 630 nm LED irradiation is associated with the amelioration of rheumatoid arthritis. J Photochem Photobiol B 2024; 250:112828. [PMID: 38101122 DOI: 10.1016/j.jphotobiol.2023.112828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Rheumatoid arthritis (RA) is caused by inflammatory response of joints with cartilage and damage of synovium and bone erosion. In our previous studies, it has showed that irradiation of 630 nm LED reduce inflammation of synovial fibroblasts and cartilage and bone destruction in RA. However, the key genes and mechanism in ameliorating RA by irradiation of 630 nm LED remains unknown. In this study, human fibroblast-like synoviocytes (FLS) cell line MH7A and primary human RA-FLSs were treated with TNF-α and 630 nm LED irradiation with the different energy density. The mRNA sequencing was performed to screen the differentially expressed genes (DEGs). In all datasets, 10 DEGs were identified through screening. The protein interaction network analysis showed that 8 out of the 10 DEGs interacted with each other including IL-6, CXCL2, CXCL3, MAF, PGF, IL-1RL1, RRAD and BMP4. This study focused on BMP4, which is identified as important morphogens in regulating the development and homeostasis. CCK-8 assay results showed that 630 nm LED irradiation did not affect the cell viability. The qPCR and ELISA results showed that TNF-α stimulation inhibited BMP4 mRNA and protein level and irradiation of 630 nm LED increased the BMP4 mRNA and protein level in MH7A cells. In CIA and transgenic hTNF-α mice models, H&E staining showed that irradiation of 630 nm LED decreased the histological scores assessed from inflammation and bone erosion, while BMP4 expression level was up-regulated after 630 nm LED irradiation. Pearson correlation analysis shown that BMP4 protein expression was negatively correlated with the histological score of CIA mice and transgenic hTNF-α mice. These results indicated that BMP4 increased by irradiation of 630 nm LED was associated with the amelioration of RA, which suggested that BMP4 may be a potential targeting gene for photobiomodulation.
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Affiliation(s)
- Guoming Du
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Mengyue Liu
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Yue Qi
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Monan Lin
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Jiaxin Wu
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Wenting Xie
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Dandan Ren
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Siqi Du
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Tong Jia
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Fengmin Zhang
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China
| | - Wuqi Song
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China.
| | - Hailiang Liu
- Wu Lien-Teh Institute, Heilongjiang Key Laboratory of Immunity and Infection, Department of Microbiology, Harbin Medical University, Harbin 150081, China.
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13
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Liu X, Ren J, Zhou R, Wen Z, Wen Z, Chen Z, He S, Zhang H. Construction of iron metabolism-related prognostic features of gastric cancer based on RNA sequencing and TCGA database. BMC Cancer 2023; 23:1106. [PMID: 37957566 PMCID: PMC10644585 DOI: 10.1186/s12885-023-11569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Researches have manifested that the disorder of iron metabolism is participated in Gastric cancer (GC), but whether iron metabolism-relevant genes (IMRGs) is related to the survival outcome of GC remain unknown. METHODS Eleven tumor as well as nine adjacent normal tissues from GC patients were underwent mRNA sequencing, and the The Cancer Genome Atlas Stomach Cancer (TCGA-STAD) datasets were acquired from the TCGA database. Cox analyses and least absolute shrinkage and selection operator (LASSO) regression were applied to build a IMRGs signature. The relationship between signature genes and the infiltration profiling of 24 immune cells were investigated using single-sample GSEA (ssGSEA). Meanwhile, the potential biological significance, genes that act synergistically with signature genes, and the upstream regulatory targets were predicted. Finally, the abundance of the signature genes were measured via the quantitative real-time PCR (qRT-PCR). RESULTS A IMRGs signature was constructed according to the expression and corresponding coefficient of DOHH, P4HA3 and MMP1 (The Schoenfeld individual test showed risk score was not significant with P values = 0.83). The prognostic outcome of patients in the high-risk group was terrible (p < 0.05). Receiver operating characteristic (ROC) curves confirmed that the IMRGs signature presented good efficiency for predicting GC prognosis (AUC > 0.6). The nomogram was performed well for clinical utilize (C-index = 0.60), and the MMP1 expression significantly increased in the cohorts at age > 60 and Stage II-IV (p < 0.05). The positive correlation of P4HA3 and MMP1 expression as well as the negative correlation of DOHH expression with risk score (p < 0.0001) and worse prognosis (p < 0.05) were detected as well. Furthermore, 11 differential immune cells were associated with these signature genes (most p < 0.01). Finally, qRT-PCR revealed that the abundance of DOHH, P4HA3 and MMP1 were high in tumor cases, indicating the complex mechanism between the high expression of DOHH as a protective factor and the high expression of P4HA3 and MMP1 as the risk factors in the development of GC. CONCLUSION An iron metabolism-related signature was constructed and has significant values for foretelling the OS of GC.
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Affiliation(s)
- Xihong Liu
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Junyu Ren
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Ruize Zhou
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zhengqi Wen
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zhengwei Wen
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zihao Chen
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Shanshan He
- Department of Oncology First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Hongbin Zhang
- Department of Pediatric Surgery First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, P. R. China.
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14
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Li JY, Wang TT, Ma L, Zheng LL. CARM1 deficiency inhibits osteoblastic differentiation of bone marrow mesenchymal stem cells and delays osteogenesis in mice. Biochim Biophys Acta Mol Cell Res 2023; 1870:119544. [PMID: 37468072 DOI: 10.1016/j.bbamcr.2023.119544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
Bone repair remains a clinical challenge due to low osteogenic capacity. Coactivator associated arginine methyltransferase 1 (CARM1) is a protein arginine methyltransferase that mediates arginine methylation and endochondral ossification. However, the roles of CARM1 in osteoblastic differentiation and bone remodeling have not been explored. In our study, heterozygous CARM1-knockout (KO) mice were generated using the CRISPR-Cas9 system and a model of femoral defect was created. At day 7 postsurgery, CARM1-KO mice exhibited obvious bone loss compared with wild type (WT) mice, as evidenced by reduced bone mineral density (BMD), bone volume/total volume (BV/TV), trabecular thickness (Tb.Th), and trabecular number (Tb.N), and increased trabecular separation (Tb.Sp). Deletion of CARM1 in mice lowered synthesis and accumulation of collagen at the injury sites. The alkaline phosphatase (ALP) activity and osteogenic-related gene expression were declined in CARM1-KO mice. To further understand the role of CARM1 in osteoblastic differentiation, bone marrow mesenchymal stem cells (BMSCs) were isolated from the tibia and femur of WT or CARM1-KO mice. CARM1 deletion decreased histone arginine methylation and inhibited osteoblastic differentiation and mineralization. The mRNA sequencing of CARM1-KO BMSCs revealed the possible regulatory molecules by CARM1, which could deepen our understanding of CARM1 regulatory mechanisms. These data could be of interest to basic researchers and provide the direction for future research into bone-related disorders.
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Affiliation(s)
- Jing-Yi Li
- Department of Medical Cosmetology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.
| | - Ting-Ting Wang
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Li Ma
- Department of Plastic Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Li-Li Zheng
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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15
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Tian X, Jia Y, Guo Y, Liu H, Cai X, Li Y, Tian Z, Sun C. Fibroblast growth factor 2 acts as an upstream regulator of inhibition of pulmonary fibroblast activation. FEBS Open Bio 2023; 13:1895-1909. [PMID: 37583315 PMCID: PMC10549223 DOI: 10.1002/2211-5463.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/06/2023] [Accepted: 08/11/2023] [Indexed: 08/17/2023] Open
Abstract
Fibroblast growth factor (FGF) signaling plays a crucial role in lung development and repair. Fibroblast growth factor 2 (FGF2) can inhibit fibrotic gene expression and suppress the differentiation of pulmonary fibroblasts (PFs) into myofibroblasts in vitro, suggesting that FGF2 is a potential target for inhibiting pulmonary fibrosis. To gain deeper insights into the molecular mechanism underlying FGF2-mediated regulation of PFs, we performed mRNA sequencing analysis to systematically and globally uncover the regulated genes and biological functions of FGF2 in PFs. Gene Ontology analysis revealed that the differentially expressed genes regulated by FGF2 were enriched in multiple cellular functions including extracellular matrix (ECM) organization, cytoskeleton formation, β-catenin-independent Wnt signaling pathway, supramolecular fiber organization, epithelial cell proliferation, and cell adhesion. Gene Set Enrichment Analysis and cellular experiments confirmed that FGF2 can suppress ECM and actin filament organization and increase PFs proliferation. Taken together, these findings indicate that FGF2 acts as an upstream regulator of the inhibition of PFs activation and may play a regulatory role in pulmonary fibrosis.
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Affiliation(s)
- Xiangqin Tian
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Yangyang Jia
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Yonglong Guo
- Department of Cardiology, The First Affiliated HospitalXinxiang Medical UniversityChina
| | - Hongyin Liu
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Xinhua Cai
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Yong Li
- Department of Biochemistry, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolUK
| | - Zhuangzhuang Tian
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Changye Sun
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
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Asbjornsdottir B, Sigurdsson S, Miranda-Ribera A, Fiorentino M, Konno T, Lan J, Gudmundsson LS, Gottfredsson M, Lauth B, Birgisdottir BE, Fasano A. Evaluating Prophylactic Effect of Bovine Colostrum on Intestinal Barrier Function in Zonulin Transgenic Mice: A Transcriptomic Study. Int J Mol Sci 2023; 24:14730. [PMID: 37834178 PMCID: PMC10572565 DOI: 10.3390/ijms241914730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The intestinal barrier comprises a single layer of epithelial cells tightly joined to form a physical barrier. Disruption or compromise of the intestinal barrier can lead to the inadvertent activation of immune cells, potentially causing an increased risk of chronic inflammation in various tissues. Recent research has suggested that specific dietary components may influence the function of the intestinal barrier, potentially offering a means to prevent or mitigate inflammatory disorders. However, the precise mechanism underlying these effects remains unclear. Bovine colostrum (BC), the first milk from cows after calving, is a natural source of nutrients with immunomodulatory, anti-inflammatory, and gut-barrier fortifying properties. This novel study sought to investigate the transcriptome in BC-treated Zonulin transgenic mice (Ztm), characterized by dysbiotic microbiota, intestinal hyperpermeability, and mild hyperactivity, applying RNA sequencing. Seventy-five tissue samples from the duodenum, colon, and brain of Ztm and wild-type (WT) mice were dissected, processed, and RNA sequenced. The expression profiles were analyzed and integrated to identify differentially expressed genes (DEGs) and differentially expressed transcripts (DETs). These were then further examined using bioinformatics tools. RNA-seq analysis identified 1298 DEGs and 20,952 DETs in the paired (Ztm treatment vs. Ztm control) and reference (WT controls) groups. Of these, 733 DEGs and 10,476 DETs were upregulated, while 565 DEGs and 6097 DETs were downregulated. BC-treated Ztm female mice showed significant upregulation of cingulin (Cgn) and claudin 12 (Cldn12) duodenum and protein interactions, as well as molecular pathways and interactions pertaining to tight junctions, while BC-treated Ztm males displayed an upregulation of transcripts like occludin (Ocln) and Rho/Rac guanine nucleotide exchange factor 2 (Arhgf2) and cellular structures and interfaces, protein-protein interactions, and organization and response mechanisms. This comprehensive analysis reveals the influence of BC treatment on tight junctions (TJs) and Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) signaling pathway gene expressions. The present study is the first to analyze intestinal and brain samples from BC-treated Ztm mice applying high-throughput RNA sequencing. This study revealed molecular interaction in intestinal barrier function and identified hub genes and their functional pathways and biological processes in response to BC treatment in Ztm mice. Further research is needed to validate these findings and explore their implications for dietary interventions aimed at improving intestinal barrier integrity and function. The MGH Institutional Animal Care and Use Committee authorized the animal study (2013N000013).
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Affiliation(s)
- Birna Asbjornsdottir
- Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; (B.A.); (M.F.); (T.K.); (J.L.)
- School of Health Sciences, Faculty of Medicine, University of Iceland, 102 Reykjavik, Iceland (M.G.)
- Unit for Nutrition Research, Landspitali University Hospital, Faculty of Food Science and Nutrition, University of Iceland, 102 Reykjavik, Iceland
| | - Snaevar Sigurdsson
- School of Health Sciences, Faculty of Medicine, University of Iceland, 102 Reykjavik, Iceland (M.G.)
- Biomedical Center, University of Iceland, 102 Reykjavik, Iceland
| | - Alba Miranda-Ribera
- Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; (B.A.); (M.F.); (T.K.); (J.L.)
| | - Maria Fiorentino
- Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; (B.A.); (M.F.); (T.K.); (J.L.)
| | - Takumi Konno
- Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; (B.A.); (M.F.); (T.K.); (J.L.)
- Department of Cell Science, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Jinggang Lan
- Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; (B.A.); (M.F.); (T.K.); (J.L.)
| | - Larus S. Gudmundsson
- School of Health Sciences, Faculty of Pharmaceutical Sciences, University of Iceland, 102 Reykjavik, Iceland
| | - Magnus Gottfredsson
- School of Health Sciences, Faculty of Medicine, University of Iceland, 102 Reykjavik, Iceland (M.G.)
- Department of Scientific Affairs, Landspitali University Hospital, 102 Reykjavik, Iceland
- Department of Infectious Diseases, Landspitali University Hospital, 102 Reykjavik, Iceland
| | - Bertrand Lauth
- School of Health Sciences, Faculty of Medicine, University of Iceland, 102 Reykjavik, Iceland (M.G.)
- Department of Child and Adolescent Psychiatry, Landspitali University Hospital, 102 Reykjavik, Iceland
| | - Bryndis Eva Birgisdottir
- Unit for Nutrition Research, Landspitali University Hospital, Faculty of Food Science and Nutrition, University of Iceland, 102 Reykjavik, Iceland
| | - Alessio Fasano
- Department of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; (B.A.); (M.F.); (T.K.); (J.L.)
- Department of Pediatrics, Harvard Medical School, Harvard University, Boston, MA 02138, USA
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Pandya Shesh B, Walter V, Palsa K, Slagle-Webb B, Neely E, Schell T, Connor JR. Sexually dimorphic effect of H-ferritin genetic manipulation on survival and tumor microenvironment in a mouse model of glioblastoma. J Neurooncol 2023; 164:569-586. [PMID: 37812288 DOI: 10.1007/s11060-023-04415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE Iron plays a crucial role in various biological mechanisms and has been found to promote tumor growth. Recent research has shown that the H-ferritin (FTH1) protein, traditionally recognized as an essential iron storage protein, can transport iron to GBM cancer stem cells, reducing their invasion activity. Moreover, the binding of extracellular FTH1 to human GBM tissues, and brain iron delivery in general, has been found to have a sex bias. These observations raise questions, addressed in this study, about whether H-ferritin levels extrinsic to the tumor can affect tumor cell pathways and if this impact is sex-specific. METHODS To interrogate the role of systemic H-ferritin in GBM we introduce a mouse model in which H-ferritin levels are genetically manipulated. Mice that were genetically manipulated to be heterozygous for H-ferritin (Fth1+/-) gene expression were orthotopically implanted with a mouse GBM cell line (GL261). Littermate Fth1 +/+ mice were used as controls. The animals were evaluated for survival and the tumors were subjected to RNA sequencing protocols. We analyzed the resulting data utilizing the murine Microenvironment Cell Population (mMCP) method for in silico immune deconvolution. mMCP analysis estimates the abundance of tissue infiltrating immune and stromal populations based on cell-specific gene expression signatures. RESULTS There was a clear sex bias in survival. Female Fth1+/- mice had significantly poorer survival than control females (Fth1+/+). The Fth1 genetic status did not affect survival in males. The mMCP analysis revealed a significant reduction in T cells and CD8 + T cell infiltration in the tumors of females with Fth1+/- background as compared to the Fth1+/+. Mast and fibroblast cell infiltration was increased in females and males with Fth1+/- background, respectively, compared to Fth1+/+ mice. CONCLUSION Genetic manipulation of Fth1 which leads to reduced systemic levels of FTH1 protein had a sexually dimorphic impact on survival. Fth1 heterozygosity significantly worsened survival in females but did not affect survival in male GBMs. Furthermore, the genetic manipulation of Fth1 significantly affected tumor infiltration of T-cells, CD8 + T cells, fibroblasts, and mast cells in a sexually dimorphic manner. These results demonstrate a role for FTH1 and presumably iron status in establishing the tumor cellular landscape that ultimately impacts survival and further reveals a sex bias that may inform the population studies showing a sex effect on the prevalence of brain tumors.
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Affiliation(s)
| | - Vonn Walter
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Kondaiah Palsa
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Becky Slagle-Webb
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Elizabeth Neely
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | - Todd Schell
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA, USA
| | - James R Connor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA.
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18
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Wang SS, Zhai GQ, Huang ZG, Luo JY, He J, Huang JZ, Yang L, Xiao CN, Li SL, Chen KR, Chen YY, Ji HC, Ding JP, Li SH, Cheng JW, Chen G. Nitidine chloride regulates cell function of bladder cancer in vitro through downregulating Lymphocyte antigen 75. Naunyn Schmiedebergs Arch Pharmacol 2023; 396:2071-2085. [PMID: 36914902 DOI: 10.1007/s00210-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023]
Abstract
Nitidine chloride (NC) is effective on cancer in many tumors, but its effect on bladder cancer (BC) is unknown. We conducted cell function experiments to verify the antineoplastic effect of NC on BC cell lines (5637, T24, and UM-UC-3) in vitro. Then, mRNAs of NC-treated and NC-untreated BC cells were extracted for mRNA sequencing. Differentially expressed genes (DEGs), expression analysis, and drug molecular docking were conducted to discover the target gene of NC. Finally, functional enrichment was analyzed to explore the underlying mechanisms. NC dramatically inhibited proliferation, migration, and invasion, and it induced apoptosis and arrested the S and G2/M phases of BC cell lines. Lymphocyte antigen 75 (LY75) appeared to be the target of NC. LY75 was highly expressed and had the ability to distinguish BC tissue from non-cancerous tissue. Then, drug molecular docking confirmed the targeting relationship between NC and LY75. Gene enrichment analysis showed that the downregulated genes, after being treated with NC, were mainly enriched in pathways relevant to cell pathophysiological processes. NC inhibits BC cell proliferation, migration, and invasion, induces apoptosis, and arrests cell cycles by downregulating the expression of LY75. This study provides molecular and theoretical bases for NC treatment of BC.
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Affiliation(s)
- Shi-Shuo Wang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Gao-Qiang Zhai
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Jia-Yuan Luo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Juan He
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Jie-Zhuang Huang
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ling Yang
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chu-Nan Xiao
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Su-Li Li
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Kai-Rong Chen
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yan-Yu Chen
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Han-Chu Ji
- Department of Urology, Eighth Affiliated Hospital of Guangxi Medical University (Guigang City People's Hospital), Guigang, 537100, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jun-Ping Ding
- Department of Urology, Liuzhou Municipal Liutie Central Hospital, Liuzhou, 545007, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Sheng-Hua Li
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ji-Wen Cheng
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China.
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Heo WY, Jang SY, Park TK, Ki C, Kim J, Kim D, Jang J. Identification of two novel COL3A1 variants in patients with vascular Ehlers-Danlos syndrome. Mol Genet Genomic Med 2023; 11:e2240. [PMID: 37461200 PMCID: PMC10496071 DOI: 10.1002/mgg3.2240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Vascular Ehlers-Danlos syndrome (vEDS) is an autosomal dominant disease caused by aberrations in COL3A1, which encodes type III collagen. Sanger sequencing has limitations for diagnosis since exon deletion/duplication and splicing alterations are not uncommon in COL3A1. We report 2 patients with vEDS who were not diagnosed by conventional Sanger sequencing. METHODS We performed either targeted panel or whole-genome sequencing. Complementary DNA (cDNA) sequencing was performed using cultured skin fibroblasts. Sanger sequencing of DNA was performed for the confirmation of breakpoints in the case of exon deletion. We also evaluated the sensitivity of the splicing prediction tool, SpliceAI. RESULTS An exon 27 deletion was suspected on targeted panel sequencing of 1 patient. The deletion was confirmed using cDNA sequencing (r.1870_1923del) and breakpoints were confirmed (c.1870-109_1923+10del). On targeted panel sequencing in the other patient, we found a novel intronic variant of c.1149+6T>C that leads to skipping of exon 16 (r.1051_1149del) by cDNA sequencing. SpliceAI showed 98.8% sensitivity for known splicing variants in COL3A1. CONCLUSION Our study highlights the necessity of a comprehensive approach to the genetic diagnosis of vEDS. In addition, cDNA sequencing was useful as an auxiliary method, especially considering the limited sensitivity of the splicing prediction tool.
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Affiliation(s)
- Won Young Heo
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulSouth Korea
| | - Shin Yi Jang
- Division of Cardiology, Department of Medicine, Samsung Medical CenterHeart Vascular Stroke Institute, Sungkyunkwan University School of MedicineSeoulSouth Korea
| | - Taek Kyu Park
- Division of Cardiology, Department of Medicine, Samsung Medical CenterHeart Vascular Stroke Institute, Sungkyunkwan University School of MedicineSeoulSouth Korea
| | | | - Jong‐Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulSouth Korea
- Department of Health Sciences and TechnologySamsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan UniversitySeoulSouth Korea
| | - Duk‐Kyung Kim
- Division of Cardiology, Department of Medicine, Samsung Medical CenterHeart Vascular Stroke Institute, Sungkyunkwan University School of MedicineSeoulSouth Korea
- Division of Cardiology, Department of MedicineSamsung Changwon Hospital, Sungkyunkwan University School of MedicineChangwon‐siSouth Korea
| | - Ja‐Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulSouth Korea
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20
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Sun C, Bai M, Jia Y, Tian X, Guo Y, Xu X, Guo Z. mRNA sequencing reveals the distinct gene expression and biological functions in cardiac fibroblasts regulated by recombinant fibroblast growth factor 2. PeerJ 2023; 11:e15736. [PMID: 37483983 PMCID: PMC10362857 DOI: 10.7717/peerj.15736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
After myocardial injury, cardiac fibroblasts (CFs) differentiate into myofibroblasts, which express and secrete extracellular matrix (ECM) components for myocardial repair, but also promote myocardial fibrosis. Recombinant fibroblast growth factor 2 (FGF2) protein drug with low molecular weight can promote cell survival and angiogenesis, and it was found that FGF2 could inhibit the activation of CFs, suggesting FGF2 has great potential in myocardial repair. However, the regulatory role of FGF2 on CFs has not been fully elucidated. Here, we found that recombinant FGF2 significantly suppressed the expression of alpha smooth muscle actin (α-SMA) in CFs. Through RNA sequencing, we analyzed mRNA expression in CFs and the differently expressed genes regulated by FGF2, including 430 up-regulated genes and 391 down-regulated genes. Gene ontology analysis revealed that the differentially expressed genes were strongly enriched in multiple biological functions, including ECM organization, cell adhesion, actin filament organization and axon guidance. The results of gene set enrichment analysis (GSEA) show that ECM organization and actin filament organization are down-regulated, while axon guidance is up-regulated. Further cellular experiments indicate that the regulatory functions of FGF2 are consistent with the findings of the gene enrichment analysis. This study provides valuable insights into the potential therapeutic role of FGF2 in treating cardiac fibrosis and establishes a foundation for further research to uncover the underlying mechanisms of CFs gene expression regulated by FGF2.
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Affiliation(s)
- Changye Sun
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Mengru Bai
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yangyang Jia
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiangqin Tian
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yonglong Guo
- Department of Cardiology, The First Affiliated Hospital, Xinxiang Medical University, Xinxiang, Henan, China
| | - Xinhui Xu
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhikun Guo
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China
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Zhou Y, Wang W, Todorov P, Pei C, Isachenko E, Rahimi G, Mallmann P, Nawroth F, Isachenko V. RNA Transcripts in Human Ovarian Cells: Two-Time Cryopreservation Does Not Affect Developmental Potential. Int J Mol Sci 2023; 24:ijms24086880. [PMID: 37108043 PMCID: PMC10139221 DOI: 10.3390/ijms24086880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/24/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Sometimes, for medical reasons, when a frozen tissue has already thawed, an operation by re-transplantation may be cancelled, and ovarian tissues should be re-frozen for transplantation next time. Research about the repeated cryopreservation of ovarian cells is rarely reported. It has been published that there is no difference in the follicle densities, proportions of proliferation of early preantral follicles, appearance of atretic follicles, or ultrastructural quality of frozen-thawed and re-frozen-rethawed tissue. However, the molecular mechanisms of a repeated cryopreservation effect on the developmental potential of ovarian cells are unknown. The aim of our experiments was to investigate the effect of re-freezing and re-thawing ovarian tissue on gene expression, gene function annotation, and protein-protein interactions. The morphological and biological activity of primordial, primary, and secondary follicles, aimed at using these follicles for the formation of artificial ovaries, was also detected. Second-generation mRNA sequencing technology with a high throughput and accuracy was adopted to determine the different transcriptome profiles in the cells of four groups: one-time cryopreserved (frozen and thawed) cells (Group 1), two-time cryopreserved (re-frozen and re-thawed after first cryopreservation) cells (Group 2), one-time cryopreserved (frozen and thawed) and in vitro cultured cells (Group 3), and two times cryopreserved (re-frozen and re-thawed after first cryopreservation) and in vitro cultured cells (Group 4). Some minor changes in the primordial, primary, and secondary follicles in terms of the morphology and biological activity were detected, and finally, the availability of these follicles for the formation of artificial ovaries was explored. It was established that during cryopreservation, the CEBPB/CYP19A1 pathway may be involved in regulating estrogen activity and CD44 is crucial for the development of ovarian cells. An analysis of gene expression in cryopreserved ovarian cells indicates that two-time (repeated) cryopreservation does not significantly affect the developmental potential of these cells. For medical reasons, when ovarian tissue is thawed but cannot be transplanted, it can be immediately re-frozen again.
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Affiliation(s)
- Yang Zhou
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
| | - Wanxue Wang
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
| | - Plamen Todorov
- Institute of Biology and Immunology of Reproduction of Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Cheng Pei
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
| | - Evgenia Isachenko
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
| | - Gohar Rahimi
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
| | - Peter Mallmann
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
| | - Frank Nawroth
- Center for Infertility, Prenatal Medicine, Endocrinology and Osteology, Amedes Medical Center MVZ Hamburg, 20095 Hamburg, Germany
| | - Volodimir Isachenko
- Department of Obstetrics and Gynecology, Medical Faculty, Cologne University, 50931 Cologne, Germany
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Wang P, Meng X, Xue J, Fan C, Wang J. Genome-wide analysis for nanofiber induced global gene expression profile: A study in MC3T3-E1 cells by RNA-Seq. Colloids Surf B Biointerfaces 2023; 223:113143. [PMID: 36682297 DOI: 10.1016/j.colsurfb.2023.113143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Nanofibers are one of the attractive biomaterials that can provide unique environments to direct cell behaviors. However, how nanofiber structure affects the global gene expression of laden cells remains unclear. Herein, high-throughput mRNA sequencing (RNA-seq) is applied to analyze the transcriptome of the MC3T3-E1 cells (a model osteoblast cell line) cultured on electrospun nanofibers. The cell-adhesive poly(L-lactide) nanofibers and membranes are developed by the mussel-inspired coating of gelatin-dopamine conjugate under H2O2-mediated oxidation. The MC3T3-E1 cells cultured on nanofibers exhibit elongated morphology and increased proliferation compared with those on membranes. The differences in global gene expression profiles are determined by RNA-seq, in which 905 differentially expressed genes (DEGs) are identified. Significantly, the DEGs related to cytoskeleton, promotion of cell cycle progression, cell adhesion, and cell proliferation, are higher expressed in the cells on nanofibers, while the DEGs involved in cell-cycle arrest and osteoblast mineralization are up-regulated in the cells on membranes. This study elucidates the roles of nanofiber structure in affecting gene expression of laden cells at the whole transcriptome level, and it will lay the foundation for understanding nanofiber-guided cell behaviors.
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Affiliation(s)
- Peiyan Wang
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, Shandong, PR China
| | - Xinyue Meng
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China
| | - Junqiang Xue
- Department of Rehabilitation Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266000, Shandong, PR China
| | - Changjiang Fan
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, Shandong, PR China.
| | - Jianxun Wang
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, Shandong, PR China.
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23
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Li Y, Li X, Cournoyer P, Choudhuri S, Yu X, Guo L, Chen S. Cannabidiol-induced transcriptomic changes and cellular senescence in human Sertoli cells. Toxicol Sci 2023; 191:227-238. [PMID: 36519830 PMCID: PMC10123764 DOI: 10.1093/toxsci/kfac131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cannabidiol (CBD), one of the major cannabinoids in the plant Cannabis sativa L., is the active ingredient in a drug approved for the treatment of seizures associated with certain childhood-onset epileptic disorders. CBD has been shown to induce male reproductive toxicity in multiple animal models. We previously reported that CBD inhibits cellular proliferation in the mouse Sertoli cell line TM4 and in primary human Sertoli cells. In this study, using a transcriptomic approach with mRNA-sequencing analysis, we identified molecular mechanisms underlying CBD-induced cytotoxicity in primary human Sertoli cells. Analysis of differentially expressed genes demonstrated that DNA replication, cell cycle, and DNA repair were the most significantly affected pathways. We confirmed the concentration-dependent changes in the expression of key genes in these pathways using real-time PCR. mRNA sequencing showed upregulation of a group of genes tightly associated with the senescence-associated secretory phenotype (SASP) and with the activation of the p53 signaling pathway, a key upstream event in cellular senescence. Prolonged treatment of 10 μM CBD-induced cellular senescence, as evidenced by the stable cessation of proliferation and the activation of senescence-associated β-galactosidase (SA-β-gal), 2 hallmarks of senescence. Additionally, using real-time PCR and Western blotting assays, we observed that CBD treatment increased the expression of p16, an important marker of cellular senescence. Taken together, our results show that CBD exposure disturbs various interrelated signaling pathways and induces cellular senescence in primary human Sertoli cells.
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Affiliation(s)
- Yuxi Li
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Xilin Li
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | | | - Supratim Choudhuri
- Office of Food Additive Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Xiaozhong Yu
- College of Nursing, University of New Mexico, Albuquerque, NM 87131, USA
| | - Lei Guo
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Si Chen
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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Yang Y, Fu Y, Sheng S, Ji C, Pu X, Xu G. Screening for diagnostic targets in tuberculosis and study on its pathogenic mechanism based on mRNA sequencing technology and miRNA-mRNA-pathway regulatory network. Front Immunol 2023; 14:1038647. [PMID: 36793717 PMCID: PMC9923233 DOI: 10.3389/fimmu.2023.1038647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023] Open
Abstract
Purpose Tuberculosis is common infectious diseases, characterized by infectivity, concealment and chronicity, and the early diagnosis is helpful to block the spread of tuberculosis and reduce the resistance of Mycobacterium tuberculosis to anti-tuberculosis drugs. At present, there are obvious limitations in the application of clinical detection methods used for the early diagnosis of tuberculosis. RNA sequencing (RNA-Seq) has become an economical and accurate gene sequencing method for quantifying transcripts and detecting unknown RNA species. Methods A peripheral blood mRNA sequencing was used to screen the differentially expressed genes between healthy people and tuberculosis patients. A protein-protein interaction (PPI) network of differentially expressed genes was constructed through Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. The potential diagnostic targets of tuberculosis were screened by the calculation of degree, betweenness and closeness in Cytoscape 3.9.1 software. Finally, the functional pathways and the molecular mechanism of tuberculosis were clarified in combination of the prediction results of key gene miRNAs, and by Gene Ontology (GO) enrichment analysis and the Kyoto Encyclopedia Genes and Genomes (KEGG) pathway annotation analysis. Results 556 Differential genes of tuberculosis were screened out by mRNA sequencing. Six key genes (AKT1, TP53, EGF, ARF1, CD274 and PRKCZ) were screened as the potential diagnostic targets for tuberculosis by analyzing the PPI regulatory network and using three algorithms. Three pathways related to the pathogenesis of tuberculosis were identified by KEGG pathway analysis, and two key miRNAs (has-miR-150-5p and has-miR-25-3p) that might participate in the pathogenesis of tuberculosis were screened out by constructing a miRNA-mRNA pathway regulatory network. Conclusion Six key genes and two important miRNAs that could regulate them were screened out by mRNA sequencing. The 6 key genes and 2 important miRNAs may participate in the pathogenesis of infection and invasion of Mycobacterium tuberculosis through herpes simplex virus 1 infection, endocytosis and B cell receptor signaling pathways.
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Mikołajczak K, Kuczyńska A, Krajewski P, Kempa M, Nuc M. Transcriptome profiling disclosed the effect of single and combined drought and heat stress on reprogramming of genes expression in barley flag leaf. Front Plant Sci 2023; 13:1096685. [PMID: 36726667 PMCID: PMC9885109 DOI: 10.3389/fpls.2022.1096685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Despite numerous studies aimed at unraveling the genetic background of barley's response to abiotic stress, the modulation of the transcriptome induced by combinatorial drought and increased temperature remains largely unrecognized. Very limited studies were done, especially on the flag leaf, which plays an important role in grain filling in cereals. In the present study, transcriptome profiles, along with chlorophyll fluorescence parameters and yield components, were compared between barley genotypes with different flag leaf sizes under single and combined drought and heat stress. High-throughput mRNA sequencing revealed 2,457 differentially expressed genes, which were functionally interpreted using Gene Ontology term enrichment analysis. The transcriptomic signature under double stress was more similar to effects caused by drought than by elevated temperature; it was also manifested at phenotypic and chlorophyll fluorescence levels. Both common and stress-specific changes in transcript abundance were identified. Genes regulated commonly across stress treatments, determining universal stress responses, were associated, among others, with responses to drought, heat, and oxidative stress. In addition, changes specific to the size of the flag leaf blade were found. Our study allowed us to identify sets of genes assigned to various processes underlying the response to drought and heat, including photosynthesis, the abscisic acid pathway, and lipid transport. Genes encoding LEA proteins, including dehydrins and heat shock proteins, were especially induced by stress treatments. Some association between genetic composition and flag leaf size was confirmed. However, there was no general coincidence between SNP polymorphism of genotypes and differential expression of genes induced by stress factors. This research provided novel insight into the molecular mechanisms of barley flag leaf that determine drought and heat response, as well as their co-occurrence.
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Shim JV, Xiong Y, Dhanan P, Dariolli R, Azeloglu EU, Hu B, Jayaraman G, Schaniel C, Birtwistle MR, Iyengar R, Dubois NC, Sobie EA. Predicting individual-specific cardiotoxicity responses induced by tyrosine kinase inhibitors. Front Pharmacol 2023; 14:1158222. [PMID: 37101545 PMCID: PMC10123273 DOI: 10.3389/fphar.2023.1158222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/28/2023] Open
Abstract
Introduction: Tyrosine kinase inhibitor drugs (TKIs) are highly effective cancer drugs, yet many TKIs are associated with various forms of cardiotoxicity. The mechanisms underlying these drug-induced adverse events remain poorly understood. We studied mechanisms of TKI-induced cardiotoxicity by integrating several complementary approaches, including comprehensive transcriptomics, mechanistic mathematical modeling, and physiological assays in cultured human cardiac myocytes. Methods: Induced pluripotent stem cells (iPSCs) from two healthy donors were differentiated into cardiac myocytes (iPSC-CMs), and cells were treated with a panel of 26 FDA-approved TKIs. Drug-induced changes in gene expression were quantified using mRNA-seq, changes in gene expression were integrated into a mechanistic mathematical model of electrophysiology and contraction, and simulation results were used to predict physiological outcomes. Results: Experimental recordings of action potentials, intracellular calcium, and contraction in iPSC-CMs demonstrated that modeling predictions were accurate, with 81% of modeling predictions across the two cell lines confirmed experimentally. Surprisingly, simulations of how TKI-treated iPSC-CMs would respond to an additional arrhythmogenic insult, namely, hypokalemia, predicted dramatic differences between cell lines in how drugs affected arrhythmia susceptibility, and these predictions were confirmed experimentally. Computational analysis revealed that differences between cell lines in the upregulation or downregulation of particular ion channels could explain how TKI-treated cells responded differently to hypokalemia. Discussion: Overall, the study identifies transcriptional mechanisms underlying cardiotoxicity caused by TKIs, and illustrates a novel approach for integrating transcriptomics with mechanistic mathematical models to generate experimentally testable, individual-specific predictions of adverse event risk.
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Affiliation(s)
- Jaehee V. Shim
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yuguang Xiong
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Priyanka Dhanan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Rafael Dariolli
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Evren U. Azeloglu
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bin Hu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gomathi Jayaraman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christoph Schaniel
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Ravi Iyengar, ; Eric A. Sobie,
| | - Nicole C. Dubois
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric A. Sobie
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- *Correspondence: Ravi Iyengar, ; Eric A. Sobie,
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Kuhns BD, Reuter JM, Hansen VL, Soles GL, Jonason JH, Ackert-Bicknell CL, Wu CL, Giordano BD. Whole-genome RNA sequencing identifies distinct transcriptomic profiles in impingement cartilage between patients with femoroacetabular impingement and hip osteoarthritis. J Orthop Res 2022. [PMID: 36463522 DOI: 10.1002/jor.25485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022]
Abstract
Femoroacetabular impingement (FAI) has a strong clinical association with the development of hip osteoarthritis (OA); however, the pathobiological mechanisms underlying the transition from focal impingement to global joint degeneration remain poorly understood. The purpose of this study is to use whole-genome RNA sequencing to identify and subsequently validate differentially expressed genes (DEGs) in femoral head articular cartilage samples from patients with FAI and hip OA secondary to FAI. Thirty-seven patients were included in the study with whole-genome RNA sequencing performed on 10 gender-matched patients in the FAI and OA cohorts and the remaining specimens were used for validation analyses. We identified a total of 3531 DEGs between the FAI and OA cohorts with multiple targets for genes implicated in canonical OA pathways. Quantitative reverse transcription-polymerase chain reaction validation confirmed increased expression of FGF18 and WNT16 in the FAI samples, while there was increased expression of MMP13 and ADAMTS4 in the OA samples. Expression levels of FGF18 and WNT16 were also higher in FAI samples with mild cartilage damage compared to FAI samples with severe cartilage damage or OA cartilage. Our study further expands the knowledge regarding distinct genetic reprogramming in the cartilage between FAI and hip OA patients. We independently validated the results of the sequencing analysis and found increased expression of anabolic markers in patients with FAI and minimal histologic cartilage damage, suggesting that anabolic signaling may be increased in early FAI with a transition to catabolic and inflammatory gene expression as FAI progresses towards more severe hip OA. Clinical significance:Cam-type FAI has a strong clinical association with hip OA; however, the cellular pathophysiology of disease progression remains poorly understood. Several previous studies have demonstrated increased expression of inflammatory markers in FAI cartilage samples, suggesting the involvement of these inflammatory pathways in the disease progression. Our study further expands the knowledge regarding distinct genetic reprogramming in the cartilage between FAI and hip OA patients. In addition to differences in inflammatory gene expression, we also identified differential expression in multiple pathways involved in hip OA progression.
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Affiliation(s)
- Benjamin D Kuhns
- Center for Regenerative and Personalized Medicine, Steadman-Philippon Research Institute, Vail, Colorado, USA
| | - John M Reuter
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Victoria L Hansen
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Gillian L Soles
- Department of Orthopedic Surgery, University of California Davis Health System, Sacramento, California, USA
| | - Jennifer H Jonason
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Cheryl L Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chia-Lung Wu
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Brian D Giordano
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
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Zhu B, Gao J, Zhang Y, Liao B, Zhu S, Li C, Liao J, Liu J, Jiang C, Zeng J. CircRNA/miRNA/mRNA axis participates in the progression of partial bladder outlet obstruction. BMC Urol 2022; 22:191. [PMID: 36434693 PMCID: PMC9700926 DOI: 10.1186/s12894-022-01132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND More and more evidence showed that circRNA/miRNA/mRNA axis played a vital role in the pathogenesis of some diseases. However, the role of circRNA/miRNA/mRNA axis in partial bladder outlet obstruction (pBOO) remains unknown. Our study aimed to explore the complex regulatory mechanism of circRNA/miRNA/mRNA axis in pBOO. METHODS The pBOO rat model was established, and the bladder tissues were collected for mRNA sequencing. The differentially expressed mRNAs were analyzed by high-throughput sequencing, and the GO and KEGG analysis of the differentially expressed mRNAs were performed. Competing endogenous RNAs (ceRNAs) analysis identified the potential regulation function of circRNA/miRNA/mRNA axis in pBOO. qRT-PCR detected the expression of circRNA/miRNA/mRNA. miRanda software was performed to predict the relationship between circRNA and miRNA, miRNA and mRNA. RESULTS Compared with the sham group, a total of 571 mRNAs were differentially expressed in the pBOO group, of which 286 were up-regulated and 285 were down-regulated. GO analysis showed that the mRNAs were mainly involved in cellular process, single-organism process, and cell, etc. KEGG analysis showed that the enriched signaling pathways were metabolic pathways, cell adhesion molecules (CAMs), and HTLV-I infection, etc. Based on the previous transcriptome data and differentially expressed circRNAs, we drew the ceRNA network regulation diagram. qRT-PCR results confirmed that chr3:113195876|113197193/rno-miR-30c-1-3p/Gata4, chr1:126188351|126195625/rno-miR-153-5p/Diaph3, and chr9:81258380|81275269/rno-miR-135b-5p/Pigr axis may have ceRNA function. miRanda confirmed there have the binding sites of circRNA/miRNA/mRNA axis. CONCLUSIONS CircRNA/miRNA/mRNA axis was involved in the progression of pBOO. Our research on the circRNA/miRNA/mRNA axis revealed new pathogenesis and treatment strategies for pBOO.
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Affiliation(s)
- Baoyi Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jun Gao
- grid.410737.60000 0000 8653 1072Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511518 Guangdong People’s Republic of China
| | - Yuying Zhang
- Department of Child Health Care, Shenzhen Longhua Maternity and Child Health Care Hospital, Shenzhen, 518000 Guangdong People’s Republic of China
| | - Baojian Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China ,grid.9227.e0000000119573309Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510700 Guangdong People’s Republic of China
| | - Sihua Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chunling Li
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Junhao Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianjia Liu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chonghe Jiang
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianwen Zeng
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
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Li Y, Su G, Huang F, Zhu Y, Luo X, Kijlstra A, Yang P. Identification of differently expressed mRNAs by peripheral blood mononuclear cells in Vogt-Koyanagi-Harada disease. Genes Dis 2022; 9:1378-1388. [PMID: 35873021 PMCID: PMC9293694 DOI: 10.1016/j.gendis.2021.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 11/29/2022] Open
Abstract
Vogt-Koyanagi-Harada disease (VKH) is a rare autoimmune disease characterized by diffuse and bilateral uveitis, alopecia, tinnitus, hearing loss, vitiligo and headache. The transcriptional expression pattern of peripheral blood mononuclear cells (PBMC) in VKH remains largely unknown. In this study, mRNA sequencing was conducted in PBMC from VKH patients with active uveitis before treatment (n = 7), the same patients after prednisone combined with cyclosporine treatment (n = 7) and healthy control subjects strictly matched with gender and age (n = 7). We found 118 differentially expressed genes (DEGs) between VKH patients and healthy control subjects, and 21 DEGs between VKH patients before and after treatment. TRIB1 was selected as a potential biomarker to monitor the development of VKH according to the mRNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to predict the possible biological functions and signaling pathways of DEGs. Neutrophil degranulation, peptidase regulator activity, secretory granule membrane, cellular response to peptide, growth factor binding and cell projection membrane were enriched as GO annotations of DEGs. Arachidonic acid metabolism and mitogen-activated protein kinase (MAPK) signaling pathway were potential signaling pathways involved in pathogenesis and drug response of VKH. A protein–protein interaction (PPI) network was constructed by STRING, and colony stimulating factor 1 receptor (CSF1R) was identified as the hubgene of all DEGs by Cytoscape. The cell type presumed to contribute to the aberrant expression of DEGs was analyzed with the use of publicly available single-cell sequencing data of PBMC from a healthy donor and single-cell sequencing dataset of monocytes from VKH patients. Our findings may help to decipher the underlying cellular and molecular pathogenesis of VKH and may lead novel therapeutic applications.
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Affiliation(s)
- Yujing Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing 400016, PR China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing 400016, PR China
| | - Fanfan Huang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing 400016, PR China
| | - Ying Zhu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing 400016, PR China
| | - Xiang Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing 400016, PR China
| | - Aize Kijlstra
- University Eye Clinic Maastricht, Maastricht 6211, the Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Lab of Ophthalmology, Chongqing Eye Institute, Chongqing 400016, PR China
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30
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Huang J, Lin S, Zhu F, Xu L. Exploring the underlying mechanism of oleanolic acid treating glioma by transcriptome and molecular docking. Biomed Pharmacother 2022; 154:113586. [PMID: 36007277 DOI: 10.1016/j.biopha.2022.113586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/02/2022] Open
Abstract
OBJECTIVE Oleanolic acid is a promising drug for treating gliomas, but its underlying mechanism is unclear. This study aimed to determine the potential effect of oleanolic acid on glioma and its mechanism. METHODS Firstly, the effects of oleanolic acid on the proliferation, invasion, and apoptosis of glioma U251 cells were detected by in vitro experiments such as MTT assay, cell cloning, and flow cytometry. The transcriptome data of U251 cells treated with oleanolic acid and untreated were sequenced by mRNA, and then the differentially expressed genes were analyzed by gene ontology (GO), genomic encyclopedia (KEGG) pathway enrichment analysis, and protein interaction topology analysis. The underlying mechanism of oleanolic acid was predicted, and the related protein interaction network was constructed. Finally, Western blotting and molecular docking techniques verified the mRNA sequencing results. RESULTS Oleanolic acid could effectively inhibit the proliferation, colony formation, and invasion of U251 cells and induce apoptosis. A total of 446 differentially expressed genes were detected by mRNA sequencing, of which 96 genes were up-regulated and 350 down-regulated. Oleanolic acid induces the TNF signal pathway and NOD-like receptor signal pathway at the intracellular level. In addition, OAS2, OASL, IFIT3, RSAD2, and IRF1 may be the core targets of oleanolic acid in treating glioma. CONCLUSION Transcriptome combined with molecular docking technique is used to predict the possible mechanism of oleanolic acid in the treatment of glioma, which provides new ideas and insights for developing and researching antitumor drugs.
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Affiliation(s)
- Jinxiang Huang
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.
| | - Shengnan Lin
- Department of Clinical Pharmacy, Sanming First Hospital, Affiliated Hospital of Fujian Medical University, Sanming City, Fujian Province, China.
| | - Feng Zhu
- Department of Neurosurgery, Sanming First Hospital, Affiliated Hospital of Fujian Medical University, Sanming City, Fujian Province, China.
| | - Luning Xu
- Department of Clinical Pharmacy, Sanming First Hospital, Affiliated Hospital of Fujian Medical University, Sanming City, Fujian Province, China.
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31
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Novosad VO, Polikanova IS, Tonevitsky EA, Maltseva DV. Expression of CD44 Isoforms in Tumor Samples and Cell Lines of Human Colorectal Cancer. Bull Exp Biol Med 2022; 173:155-159. [PMID: 35618971 DOI: 10.1007/s10517-022-05512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 10/18/2022]
Abstract
Detection of colorectal cancer biomarkers (CRC) remains an urgent task for the diagnosis and prediction of the disease course. A promising approach is the study of cancer stem cell markers. The cell surface glycoprotein CD44 is very important for CRC and its stem cells. Alternative splicing of 9 variable exons of CD44 mRNA leads to the formation of various isoforms of the protein with different roles in the progression of cancer. Studies of the functions of CD44 isoforms require adequate models considering the distribution of CD44 isoforms in real tumor samples. In the present study, the expression profile of CD44 isoforms in CRC was assessed based on the publicly available mRNA sequencing data of patient tumors from the TCGA-COAD database. It was shown that normal tissues predominantly expressed isoforms 3 and 4 at nearly equal levels, whereas tumors mainly expressed isoforms 2, 3, and 4; isoform 3 was expressed at the highest level. Further, the most relevant cell lines for studying the role of CD44 in CRC were identified based on the analysis of mRNA sequencing data of 55 CRC cell lines form CCLE database.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia.
| | - I S Polikanova
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
| | - E A Tonevitsky
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
| | - D V Maltseva
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
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32
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Haugen ØP, Khuu C, Weidemann HM, Utheim TP, Bergersen LH. Transcriptomic and functional studies reveal miR-431-5p as a tumour suppressor in pancreatic ductal adenocarcinoma cells. Gene 2022; 822:146346. [PMID: 35182679 DOI: 10.1016/j.gene.2022.146346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 01/16/2022] [Accepted: 02/15/2022] [Indexed: 12/24/2022]
Abstract
The lactate receptor HCAR1 (hydroxycarboxylic acid receptor 1) is highly expressed in pancreatic ductal adenocarcinoma (PDAC), where it regulates lactate transport between the cancer cells. Little is known about the underlying cause of high HCAR1 expression in PDAC, and in the present study, we investigated whether HCAR1 could be a target of miRNA regulation. By searching for predicted miRNA candidates in silico, we identified miR-431-5p as a possible regulator of HCAR1. We found miR-431-5p to repress HCAR1 expression through direct binding to the 3' UTR. The endogenous expression of miR-431-5p and HCAR1 was found to be negatively related in the PDAC cell lines BxPC-3, Capan-2, and PANC-1. Overexpression of miR-431-5p inhibited cell proliferation in all the cell lines, and a shift in cell cycle progression and induction of apoptosis were found in the BxPC-3 cells. Transcriptomic analysis of mRNA from BxPC-3 cells revealed numerous differentially expressed genes (DEGs), including HCAR1, in response to miR-431-5p overexpression. A significant proportion of these DEGs was enriched in cancer-related processes and signalling pathways. Among the most significantly repressed DEGs was ATP6V0E1, encoding the integral subunit e of vacuolar ATPase (V-ATPase), an enzyme that is important for cancer cell survival. Small interfering RNA (siRNA)-mediated knockdown of HCAR1 and ATP6V0E1 showed that only knockdown of ATP6V0E1 mimicked the effect of miR-431-5p overexpression on cell viability. Our findings indicate that miR-431-5p acts as a tumour suppressor in PDAC cells, with BxPC-3 cells being most responsive.
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Affiliation(s)
- Øyvind P Haugen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, P.O. Box 1052 Blindern, 0316 Oslo, Norway.
| | - Cuong Khuu
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, P.O. Box 1052 Blindern, 0316 Oslo, Norway
| | - Hanne M Weidemann
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, P.O. Box 1052 Blindern, 0316 Oslo, Norway
| | - Tor Paaske Utheim
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, P.O. Box 1052 Blindern, 0316 Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway
| | - Linda Hildegard Bergersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, P.O. Box 1052 Blindern, 0316 Oslo, Norway
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Li F, Wang Y, Wang X, Zhao Y, Xie F, Qian LJ. Dynamic effects of chronic unpredictable mild stress on the hippocampal transcriptome in rats. Mol Med Rep 2022; 25:110. [PMID: 35119083 PMCID: PMC8845063 DOI: 10.3892/mmr.2022.12626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/17/2022] [Indexed: 11/06/2022] Open
Abstract
Stress causes extensive changes in hippocampal genomic expression, leading to changes in hippocampal structure and function. The dynamic changes in hippocampal gene expression caused by stress of different durations are still unknown. mRNA sequencing was used to analyze the hippocampal transcriptome of rats subjected to chronic unpredictable mild stress (CUMS) of different durations. Compared with the control, 501, 442 and 235 differentially expressed genes (DEGs) were detected in the hippocampus of rats subjected to CUMS for 3 days and 2 and 6 weeks, respectively. Gene Ontology (GO) analysis was used to determine the potential mechanism underlying the dynamic harmful effects of stress on the hippocampus; Certain GO terms of the down‑regulated DEGs in CUMS (3 days) rats were also found in the up‑regulated DEGs in CUMS (6 weeks) rats. These results showed opposing regulation patterns of DEGs between CUMS at 3 days and 6 weeks, which suggested a functional change from adaptation to damage in during the early and late stages of chronic stress. GO analysis for upregulated genes in rats subjected to CUMS for 3 days and 2 weeks suggested significant changes in 'extracellular matrix' and 'wound healing'. Upregulated genes in rats subjected to CUMS for 2 weeks were involved in changes associated with visual function. GO analysis of DEGs in rats subjected to CUMS for 6 weeks revealed increased expression of genes associated with 'apoptotic process' and 'aging' and decreased expression of those associated with inhibition of cell proliferation and cell structure. These results suggest that the early and middle stages of chronic stress primarily promote adaptive regulation and damage repair in the organism, while the late stage of chronic stress leads to damage in the hippocampus.
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Affiliation(s)
- Feng Li
- Department of Military Cognitive and Stress Medicine, Beijing Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100039, P.R. China
| | - Ying Wang
- Department of Military Cognitive and Stress Medicine, Beijing Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100039, P.R. China
| | - Xue Wang
- Department of Military Cognitive and Stress Medicine, Beijing Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100039, P.R. China
| | - Yun Zhao
- Department of Military Cognitive and Stress Medicine, Beijing Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100039, P.R. China
| | - Fang Xie
- Department of Military Cognitive and Stress Medicine, Beijing Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100039, P.R. China
| | - Ling-Jia Qian
- Department of Military Cognitive and Stress Medicine, Beijing Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100039, P.R. China
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Tamai S, Fujita SI, Komine R, Kanki Y, Aoki K, Watanabe K, Takekoshi K, Sugasawa T. Acute cold stress induces transient MuRF1 upregulation in the skeletal muscle of zebrafish. Biochem Biophys Res Commun 2022; 608:59-65. [PMID: 35390673 DOI: 10.1016/j.bbrc.2022.03.093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 12/26/2022]
Abstract
Cryotherapy is one of the most common treatments for trauma or fatigue in the field of sports medicine. However, the molecular biological effects of acute cold exposure on skeletal muscle remain unclear. Therefore, we used zebrafish, which have recently been utilized as an animal model for skeletal muscle, to comprehensively investigate and selectively clarify the time-course changes induced by cryotherapy. Zebrafish were exposed intermittently to cold stimulation three times for 15 min each. Thereafter, skeletal muscle samples were collected after 15 min and 1, 2, 4, and 6 h. mRNA sequencing revealed the involvement of trim63a, fbxo32, fbxo30a, and klhl38b in "protein ubiquitination" from the top 10 most upregulated genes. Subsequently, we examined the time-course changes of the four genes by quantitative PCR, and their expression peaked 2 h after cryotherapy and returned to baseline after 6 h. Moreover, the proteins encoded by trim63a and fbxo32 (muscle-specific RING finger protein 1 [MuRF1] and muscle atrophy F-box, respectively), which are known to be major genes encoding E3 ubiquitin ligases, were examined by western blotting, and MuRF1 expression displayed similar temporal changes as trim63a expression. These findings suggest that acute cold exposure transiently upregulates E3 ubiquitin ligases, especially MuRF1; thus, cryotherapy may contribute to the treatment of trauma or fatigue by promoting protein processing.
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Affiliation(s)
- Shinsuke Tamai
- Doctoral Program in Sports Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shin-Ichiro Fujita
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ritsuko Komine
- Doctoral Program in Sports Medicine, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yasuharu Kanki
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kai Aoki
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Koichi Watanabe
- Faculty of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kazuhiro Takekoshi
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takehito Sugasawa
- Laboratory of Clinical Examination/Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Department of Sports Medicine Analysis, Open Facility Network Office, Research Facility Center for Science and Technology, University of Tsukuba, Japan.
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De Jong NP, Rudolph MC, Jackman MR, Sharp RR, Jones K, Houck J, Pan Z, Reusch JEB, MacLean PS, Bessesen DH, Bergouignan A. Short-Term Adaptations in Skeletal Muscle Mitochondrial Oxidative Capacity and Metabolic Pathways to Breaking up Sedentary Behaviors in Overweight or Obese Adults. Nutrients 2022; 14:nu14030454. [PMID: 35276813 PMCID: PMC8838620 DOI: 10.3390/nu14030454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/04/2022] Open
Abstract
Breaking up sedentary behavior with short-frequent bouts of physical activity (PA) differentially influences metabolic health compared with the performance of a single-continuous bout of PA matched for total active time. However, the underlying mechanisms are unknown. We compared skeletal muscle mitochondrial respiration (high-resolution respirometry) and molecular adaptations (RNA sequencing) following 4-day exposure to breaks vs. energy-matched single-continuous PA bout in inactive adults with overweight/obesity. Participants (9M/10F, 32.2 ± 6.4 years, 30.3 ± 3.0 kg/m2) completed three 4-day interventions of a randomized cross-over study: SED, sedentary control; MICRO, 5 min brisk walking each hour for 9 h; ONE: 45 min/d continuous brisk walking bout. Fasted muscle biopsies were collected on day 5. Mitochondrial coupling in the presence of lipid-associated substrates was higher after ONE (4.8 ± 2.5) compared to MICRO (3.1 ± 1.1, p = 0.02) and SED (2.3 ± 1.0, p = 0.001). Respiratory rates did not differ across groups with carbohydrate-associated substrates. In pathways associated with muscle contraction transcription signaling, ONE and MICRO similarly enhanced Oxidative Phosphorylation and Sirtuin Signaling expression (p < 0.0001, for both). However, ONE (p < 0.001, for all), but not MICRO, had greater pathway enrichment, including Ca++, mTOR, AMPK, and HIF1α signaling, than SED. Although breaking up sedentary behavior triggered skeletal muscle molecular adaptations favoring oxidative capacity, it did not improve mitochondrial function over the short term.
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Affiliation(s)
- Nathan P. De Jong
- Division of Endocrinology, Metabolism, Diabetes and Anschutz Health and Wellness Center, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.P.D.J.); (D.H.B.)
| | - Michael C. Rudolph
- Department of Physiology, Harold Hamm Diabetes Center, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA; (M.C.R.); (R.R.S.)
| | - Matthew R. Jackman
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (M.R.J.); (J.H.); (P.S.M.)
| | - Rachel R. Sharp
- Department of Physiology, Harold Hamm Diabetes Center, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA; (M.C.R.); (R.R.S.)
- Laboratory of Molecular Biology and Cytometric Research, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Ken Jones
- Laboratory of Molecular Biology and Cytometric Research, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Julie Houck
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (M.R.J.); (J.H.); (P.S.M.)
| | - Zhaoxing Pan
- Department of Biostatistics and Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA;
| | - Jane E. B. Reusch
- Center for Women’s Health Research, University of Colorado School of Medicine, Aurora, CO 80045, USA;
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO 80045, USA
| | - Paul S. MacLean
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (M.R.J.); (J.H.); (P.S.M.)
| | - Daniel H. Bessesen
- Division of Endocrinology, Metabolism, Diabetes and Anschutz Health and Wellness Center, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.P.D.J.); (D.H.B.)
- Denver Health Medical Center, Denver, CO 80204, USA
| | - Audrey Bergouignan
- Division of Endocrinology, Metabolism, Diabetes and Anschutz Health and Wellness Center, University of Colorado School of Medicine, Aurora, CO 80045, USA; (N.P.D.J.); (D.H.B.)
- Institut Pluridisciplinaire Hubert Curien, Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), UMR7178, 67037 Strasbourg, France
- Correspondence: or
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He QR, Cong M, Yu FH, Ji YH, Yu S, Shi HY, Ding F. Peripheral nerve fibroblasts secrete neurotrophic factors to promote axon growth of motoneurons. Neural Regen Res 2022; 17:1833-1840. [PMID: 35017446 PMCID: PMC8820717 DOI: 10.4103/1673-5374.332159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Peripheral nerve fibroblasts play a critical role in nerve development and regeneration. Our previous study found that peripheral nerve fibroblasts have different sensory and motor phenotypes. Fibroblasts of different phenotypes can guide the migration of Schwann cells to the same sensory or motor phenotype. In this study, we analyzed the different effects of peripheral nerve-derived fibroblasts and cardiac fibroblasts on motoneurons. Compared with cardiac fibroblasts, peripheral nerve fibroblasts greatly promoted motoneuron neurite outgrowth. Transcriptome analysis results identified 491 genes that were differentially expressed in peripheral nerve fibroblasts and cardiac fibroblasts. Among these, 130 were significantly upregulated in peripheral nerve fibroblasts compared with cardiac fibroblasts. These genes may be involved in axon guidance and neuron projection. Three days after sciatic nerve transection in rats, peripheral nerve fibroblasts accumulated in the proximal and distal nerve stumps, and most expressed brain-derived neurotrophic factor. In vitro, brain-derived neurotrophic factor secreted from peripheral nerve fibroblasts increased the expression of β-actin and F-actin through the extracellular regulated protein kinase and serine/threonine kinase pathways, and enhanced motoneuron neurite outgrowth. These findings suggest that peripheral nerve fibroblasts and cardiac fibroblasts exhibit different patterns of gene expression. Peripheral nerve fibroblasts can promote motoneuron neurite outgrowth.
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Affiliation(s)
- Qian-Ru He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Meng Cong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Fan-Hui Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Yu-Hua Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Shu Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Hai-Yan Shi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, Jiangsu Province, China
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Cheng B, Jia Y, Wen Y, Hou W, Xu K, Liang C, Cheng S, Liu L, Chu X, Ye J, Yao Y, Zhang F, Xu P. Integrative Analysis of MicroRNA and mRNA Sequencing Data Identifies Novel Candidate Genes and Pathways for Developmental Dysplasia of Hip. Cartilage 2021; 13:1618S-1626S. [PMID: 33522290 PMCID: PMC8804775 DOI: 10.1177/1947603521990859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Our aim is to explore the candidate pathogenesis genes and pathways of developmental dysplasia of hip (DDH). DESIGN Proliferating primary chondrocytes from hip cartilage were used for total RNA extraction including 5 DDH patients and 5 neck of femur fracture (NOF) subjects. Genome-wide mRNA and microRNA (miRNA) were then sequenced on the Illumina platform (HiSeq2500). Limma package was used for difference analysis of mRNA expression profiles. edgeR was used for difference analysis of miRNA expression profiles. miRanda was used to predict miRNA-target genes. The overlapped DDH associated genes identified by mRNA and miRNA integrative analysis were further compared with the differently expressed genes in hip osteoarthritis (OA) cartilage. RESULTS Differential expression analysis identified 1,833 differently expressed mRNA and 186 differently expressed miRNA for DDH. Integrative analysis of mRNA and miRNA expression profiles identified 175 overlapped candidate genes (differentially expressed genes, DEGs) for DDH, such as VWA1, TMEM119, and SCUBE3. Further gene ontology enrichment analysis detected 111 candidate terms for DDH, such as skeletal system morphogenesis (P = 4.92 × 10-5) and skeletal system development (P = 8.85 × 10-5). Pathway enrichment analysis identified 14 candidate pathways for DDH, such as Hedgehog signaling pathway (P = 4.29 × 10-5) and Wnt signaling pathway (P = 4.42 × 10-2). Among the identified DDH associated candidate genes, we also found some genes were detected in hip OA including EFNA1 and VWA1. CONCLUSIONS We identified multiple novel candidate genes and pathways for DDH, providing novel clues for understanding the molecular mechanism of DDH.
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Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China,Yumeng Jia, Key Laboratory of Trace Elements
and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and
Health Promotion for Silk Road Region, School of Public Health, Health Science
Center, Xi’an Jiaotong University, No. 76 Yan Ta West Road, Xi’an, 710061,
People’s Republic of China.
| | - Yan Wen
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Weikun Hou
- Department of Joint Surgery, Xi’an
Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, People’s
Republic of China
| | - Ke Xu
- Department of Joint Surgery, Xi’an
Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, People’s
Republic of China
| | - Chujun Liang
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Li Liu
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Jing Ye
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Yao Yao
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and
Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health
Promotion for Silk Road Region, School of Public Health, Health Science Center,
Xi’an Jiaotong University, Xi’an, People’s Republic of China,Feng Zhang, Key Laboratory of Trace Elements
and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and
Health Promotion for Silk Road Region, School of Public Health, Health Science
Center, Xi’an Jiaotong University, No. 76 Yan Ta West Road, Xi’an, 710061,
People’s Republic of China.
| | - Peng Xu
- Department of Joint Surgery, Xi’an
Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, People’s
Republic of China,Peng Xu, Department of Joint Surgery, Xi’an
Honghui Hospital, Xi’an Jiaotong University Health Science Center, No. 555 You
Yi East Road, Xi’an, 710000, People’s Repubic of China.
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Wei S, Zheng Q, Pan Y, Xu Y, Tang J, Cai X. Interplay between liver circadian rhythm and regeneration after PHx. Genomics 2021; 114:1-8. [PMID: 34822968 DOI: 10.1016/j.ygeno.2021.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Diurnal oscillations in gene expression are a hallmark of the liver internal clock and can be regulated by a variety of environmental stimuli. The circadian rhythm and liver regeneration (LR) are intimately linked. However, how they affect each other at the transcriptomic level is mainly unknown. Here, we revealed that partial hepatectomy (PHx)-induced LR led to reprogramming of rhythmic gene expression profiles as a consequence of disrupted BMAL1 occupation on the chromatin, while the rhythm of core clock genes remained robust. Furthermore, we demonstrated retarded LR when PHx was carried out in the evening, possibly due to the accumulation of DEC1. In summary, our data offer a broad perspective of the relationship between circadian rhythm and LR and suggest that the timing of PHx should be considered in the clinic application.
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Affiliation(s)
- Saisai Wei
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Qiang Zheng
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Yu Pan
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Yunwan Xu
- Shenzhen NeoCura Biotechnology corporation, Shenzhen 518055, China
| | - Jiacheng Tang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China
| | - Xiujun Cai
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, 310016 Hangzhou, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, 310016 Hangzhou, China; Zhejiang University Cancer Center, 310058 Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 311121 Hangzhou,China.
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Wang N, Bai D, Kristiansen E, Deng R, Zhang S. AKIP1 promotes tumor progression by cancer-related pathways and predicts prognosis in tongue squamous cell carcinoma. Am J Transl Res 2021; 13:12338-12351. [PMID: 34956456 PMCID: PMC8661143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/24/2021] [Indexed: 06/14/2023]
Abstract
The current study was designed to explore the effect of A-kinase-interacting protein 1 (AKIP1) on tongue squamous cell carcinoma (TSCC) viability and mobility and to investigate its molecular mechanism. Control overexpression (OE-NC group) and AKIP1 overexpression (OE-AKIP1 group) plasmids were transfected into CAL-27 cells; control knockdown (KD-NC group) and AKIP1 knockdown (KD-AKIP1 group) plasmids were transfected into SCC-9 cells. Cellular viability and mobility were determined, and mRNA sequencing was performed followed by RT-qPCR validation. Immunohistochemistry was utilized to detect AKIP1 expression in tumor and adjacent tissues from 90 TSCC patients. AKIP1 was more highly expressed in human TSCC cell lines compared to human normal lingual epithelial cells. Cell proliferation, migration, and invasion were increased in the OE-AKIP1 group compared to the OE-NC group but decreased in the KD-AKIP1 group compared to the KD-NC group. mRNA sequencing revealed 436 differentially expressed genes; most of the genes were mainly enriched in the mTOR, PI3K-Akt, MAPK, Hippo, and Wnt signaling pathways. These findings were subsequently confirmed by RT-qPCR quantification. In TSCC patients, AKIP1 expression was increased in tumor tissues and related to increased tumor size, lymph node metastasis and poor overall survival. AKIP1 is a therapeutic target that regulates multiple tumor-related pathways in TSCC.
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Affiliation(s)
- Ning Wang
- Department of Orthopaedics, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Dan Bai
- Department of Hematology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Einar Kristiansen
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University HospitalOslo 0424, Norway
| | - Ruoyu Deng
- Department of Biostatistics, Shanghai QeeJen InstitutionShanghai 200433, China
| | - Shijun Zhang
- Department of Orthopaedics, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
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Sunny S, Challa AK, Qiao A, Jyothidasan A, Krishnamurthy P, Ramamurthy MT, Crossman DK, Pogwizd S, Cinghu S, Rajasekaran NS. Transcriptional Regulation of Structural and Functional Adaptations in a Developing Adulthood Myocardium. ACTA ACUST UNITED AC 2021; 5:454-470. [PMID: 34497977 PMCID: PMC8423094 DOI: 10.26502/fccm.92920215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of the heart follows a synergic action of several signaling pathways during gestational, pre- & postnatal stages. The current study aimed to investigate whether the myocardium experiences transcriptional changes during the transition from post-natal to adult hood stages. Herein, we used C57/B16/J mice at 4 (28- days; post-natal/PN) and 20 weeks (adulthood/AH) of ages and employed the next generation RNAseq (NGS) to profile the transcriptome and echocardiography analysis to monitor the structural/functional changes in the heart. NGS-based RNA-seq revealed that 1215 genes were significantly upregulated and 2549 were down regulated in the AH versus PN hearts, indicating a significant transcriptional change during this transition. A synchronized cardiac transcriptional regulation through cell cycle, growth hormones, redox homeostasis and metabolic pathways was noticed in both PN and AH hearts. Echocardiography reveals significant structural and functional (i.e. systolic/diastolic) changes during the transition of PN to adult stage. Particularly, a progressive decline in ejection fraction and cardiac output was observed in AH hearts. These structural adaptations are in line with critical signaling pathways that drive the maturation of heart during AH. Overall, we have presented a comprehensive transcriptomic analysis along with structural-functional relationship during the myocardial development in adult mice.
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Affiliation(s)
- Sini Sunny
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Anil Kumar Challa
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Aijun Qiao
- Department of Biomedical Engineering, University of Alabama at Birmingham, AL, USA
| | - Arun Jyothidasan
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | | | | | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, AL, USA
| | - Steven Pogwizd
- Department of Medicine, University of Alabama at Birmingham, AL, USA
| | - Senthilkumar Cinghu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, USA
| | - Namakkal S Rajasekaran
- Department of Pathology, University of Alabama at Birmingham, AL, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Utah, UT, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, AL, USA
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Zhang L, Zhao X, Wang W. lncRNA and mRNA sequencing of the left testis in experimental varicocele rats treated with Morinda officinalis polysaccharide. Exp Ther Med 2021; 22:1136. [PMID: 34466146 PMCID: PMC8383328 DOI: 10.3892/etm.2021.10570] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/06/2021] [Indexed: 12/16/2022] Open
Abstract
Varicocele is a common disease of the male reproductive system. Morinda (M.) officinalis is a Chinese herbal medicine, whose main bioactive component M. officinalis polysaccharide (MOP) is believed to have a therapeutic effect on varicocele; however, the underlying molecular mechanisms of this effect are poorly understood. In the present study, 24 rats were randomly divided into three groups: i) Control group; ii) experimental varicocele group; and iii) 300 mg/kg MOP administration group. Analysis of mRNA and long non-coding RNA (lncRNA) expression in rat left testicular tissue was performed. The results suggested that a total of 144 mRNAs and 63 lncRNAs, 63 mRNAs and 148 lncRNAs, and 173 mRNAs and 54 lncRNAs were differentially expressed between the varicocele non-treatment and control groups, the varicocele treatment and varicocele non-treatment groups, and the varicocele treatment and control groups, respectively. Following validation by reverse transcription-quantitative PCR, the Yip1 domain family member 7 (YIPF7) gene was identified as a key mediator of varicocele pathogenesis and repair effect of MOP. Additionally, genes such as purinergic receptor P2X 4 (P2RX4), transmembrane protein 225B (TMEM255B) and Wnt family member 9B (WNT9B) were confirmed to be differentially expressed between the varicocele non-treatment and control groups. We hypothesize that TMEM255B could be a potential novel diagnostic biomarker for varicocele; WNT9B and P2RX4 likely play notable roles in the pathophysiology of the disease through the Wnt signaling pathway and regulation of transmembrane ion channels, respectively. In summary, the present study delineated the molecular mechanisms underlying varicocele pathogenesis and the therapeutic effect of MOP, identified a potential novel diagnostic marker and therapeutic target for varicocele, and provided feasible directions for further studies in the future.
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Affiliation(s)
- Lihong Zhang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.,Key Laboratory of Aging and Neurodegenerative Disease, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.,Laboratory of Clinical Applied Anatomy, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
| | - Xiaozhen Zhao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.,Key Laboratory of Aging and Neurodegenerative Disease, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.,Laboratory of Clinical Applied Anatomy, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
| | - Wei Wang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.,Key Laboratory of Aging and Neurodegenerative Disease, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China.,Laboratory of Clinical Applied Anatomy, Fujian Medical University, Fuzhou, Fujian 350108, P.R. China
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Sabella E, Luvisi A, Genga A, De Bellis L, Aprile A. Molecular Responses to Cadmium Exposure in Two Contrasting Durum Wheat Genotypes. Int J Mol Sci 2021; 22:7343. [PMID: 34298963 DOI: 10.3390/ijms22147343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 11/16/2022] Open
Abstract
Cadmium is a heavy metal that can be easily accumulated in durum wheat kernels and enter the human food chain. Two near-isogenic lines (NILs) with contrasting cadmium accumulation in grains, High-Cd or Low-Cd (H-Cd NIL and L-Cd NIL, respectively), were used to understand the Cd accumulation and transport mechanisms in durum wheat roots. Plants were cultivated in hydroponic solution, and cadmium concentrations in roots, shoots and grains were quantified. To evaluate the molecular mechanism activated in the two NILs, the transcriptomes of roots were analyzed. The observed response is complex and involves many genes and molecular mechanisms. We found that the gene sequences of two basic helix–loop–helix (bHLH) transcription factors (bHLH29 and bHLH38) differ between the two genotypes. In addition, the transporter Heavy Metal Tolerance 1 (HMT-1) is expressed only in the low-Cd genotype and many peroxidase genes are up-regulated only in the L-Cd NIL, suggesting ROS scavenging and root lignification as active responses to cadmium presence. Finally, we hypothesize that some aquaporins could enhance the Cd translocation from roots to shoots. The response to cadmium in durum wheat is therefore extremely complex and involves transcription factors, chelators, heavy metal transporters, peroxidases and aquaporins. All these new findings could help to elucidate the cadmium tolerance in wheat and address future breeding programs.
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Yin X, Wu Q, Song W, Yang Q, Wu Y, Fang M, Gong Z. Study on toxicological effect and the mechanism of cadmium in rice and inorganic cadmium on ICR mice. Toxicol Res (Camb) 2021; 10:639-650. [PMID: 34141178 PMCID: PMC8201557 DOI: 10.1093/toxres/tfab043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 11/15/2022] Open
Abstract
Cadmium (Cd) exposure may induce chronic intoxication, but the harm of cadmium in rice to human at chronic low-level Cd exposure remains unclear. This study employed a mouse model to investigate the toxicity and mechanism of cadmium in rice and CdCl2. After 8-week exposure to Cd (CdCl2 and Cd-contaminated rice), the biochemical indicators and oxidation indicators in the serum and liver of mice were determined, and used mRNA sequencing to investigate the mechanism of different forms of Cd. Results showed that the cadmium concentration of the liver in the CdCl2 + Rice-N group (CdCl2 mixed with feed and normal rice, 0.4mg/kg.bw) was higher than that in the Rice-H group (0.4mg/kg.bw). However, the cadmium concentration of the kidneys in the Rice-H group was higher than that in the CdCl2 + Rice-N group. Our study demonstrated that Cd-treated (Cd in rice and CdCl2) ICR mice generated obviously tissues injury, such as the increased biochemical studies, the activity of antioxidant enzymes debasement. Simultaneously, our data also indicated that there existed difference of the hepatic toxicity between Cd in rice and CdCl2. By means of transcriptomics, we discovered that CdCl2 and Cd in rice may affect different gene expression at the molecular level. We hope to provide some theoretical basis for the revision of food security standards.
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Affiliation(s)
- Xiaoyao Yin
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, 68 Xuefu South Road, Wuhan 430023, Hubei, China
| | - Qian Wu
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, 68 Xuefu South Road, Wuhan 430023, Hubei, China
| | - Wanying Song
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, 68 Xuefu South Road, Wuhan 430023, Hubei, China
| | - Qing Yang
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, 68 Xuefu South Road, Wuhan 430023, Hubei, China
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, 37 Guangqu Road, Chaoyang District, Beijing 100021, China
| | - Min Fang
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, 68 Xuefu South Road, Wuhan 430023, Hubei, China
| | - Zhiyong Gong
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, 68 Xuefu South Road, Wuhan 430023, Hubei, China
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Chakraborty S, Gourain V, Benz M, Scheiger JM, Levkin PA, Popova AA. Droplet microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape. Mater Today Bio 2021; 11:100112. [PMID: 34124640 DOI: 10.1016/j.mtbio.2021.100112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
The development of novel chemically developed and physically defined surfaces and environments for cell culture and screening is important for various biological applications. The Droplet microarray (DMA) platform based on hydrophilic-superhydrophobic patterning enables high-throughput cellular screening in nanoliter volumes and on various biocompatible surfaces. Here we performed phenotypic and transcriptomic analysis of HeLa-CCL2 cells cultured on DMA, with a goal to analyze cellular response on different surfaces and culture volumes down to 3 nL, compared with conventional cell culture platforms. Our results indicate that cells cultured on four tested substrates: nanostructured nonpolymer, rough and smooth variants of poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) polymer and poly(thioether) dendrimer are compatible with cells grown in Petri dish. Cells cultured on nanostructured nonpolymer coating exhibited the closet transcriptomic resemblance to that of cells grown in Petri dish. Analysis of cells cultured in 100, 9, and 3 nL media droplets on DMA indicated that all but cells grown in 3 nL volumes had unperturbed viability with minimal alterations in the transcriptome compared with 96-well plate. Our findings demonstrate the applicability of DMA for cell-based assays and highlight the possibility of establishing regular cell culture on various biomaterial-coated substrates and in nanoliter volumes, along with routinely used cell culture platforms.
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Liu S, Liu J, Wang Y, Deng L, Chen S, Wang X, Zuo T, Hu Q, Rao J, Wang Q, Dong Z. Differentially expressed genes induced by β-caryophyllene in a rat model of cerebral ischemia-reperfusion injury. Life Sci 2021; 273:119293. [PMID: 33705733 DOI: 10.1016/j.lfs.2021.119293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/10/2021] [Accepted: 02/20/2021] [Indexed: 10/22/2022]
Abstract
Experimental studies have shown that β-caryophyllene (BCP) improved neurological deficits of cerebral ischemia-reperfusion injury (CIRI) rats resulting from Middle Cerebral Artery Occlusion (MCAO). However, research on targets of BCP on CIRI has not been completed. In this study, the mRNA sequencing was used to distinguish various therapeutic multiple targets of BCP on CIRI. Differentially expressed genes (DEGs) were identified from RNA-seq analysis. CIRI induced up-regulated genes (CIRI vs. Sham) and BCP -induced down-regulated genes (BCP vs CIRI) were identified. Significant DEGs were identified only that expressed in each of all samples. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis of significant DEGs were determined by cluster Profiler. Protein interactive network (PPI) was analyzed using the String tool and Hub genes was identified by cytoHubba. Transcription factor (TF) regulatory network for the potential Hub genes was constructed. Western blot and ELISA were used to verified hub genes and relative inflammatory cytokines. After mRNA sequencing, a total of 411 DEGs were filtered based on the 2 series (CIRI vs. Sham and CIRI vs. BCP), with Pax1, Cxcl3 and Ccl20 are the most remarkable ones reversed by BCP. GO analysis was represented by DEGs involved in multiple biological process such as extra-cellular matrix organization, leukocyte migration, regulation of angiogenesis, reactive oxygen species metabolic process, etc. KEGG analysis showed that DEGs participated several signaling pathways including MAPK signaling pathway (rno04010), Cytokine-cytokine receptor interaction (rno04060), JAK-STAT signaling pathway (rno04630), and others. The protein-protein interaction (PPI) network consisted of 339 nodes and 1945 connections, and top ten Hub genes were identified by cytoHubba such as TIMP1, MMP-9, and STAT3. Subsequently, a TFs-miRNAs-targets regulatory network was established, involving 6 TFs, 5 miRNAs, and 10 hub genes, consisting of several regulated models such as Brd4 - rno-let-7e - Mmp9, Brd4 - rno-let-7i - Stat3, and Hnf4a- rno-let-7b -Timp1. Finally, western blot demonstrated that BCP could inhibit the increased TIMP1, MMP-9 and STAT3 expression in rat brains after I/R. ELISA represented that BCP could suppress inflammatory cytokines caused by CIRI and present anti-oxidative property. In conclusion, this study shows that the intervention of BCP can significantly reduce neurologic deficit, improve the cerebral ischemia, and a total of ten hub genes were found closely related to the treatment of BCP on CIRI. Prudent experimental validation suggests that the BCP might have the neuro-protective effects in CIRI by decreasing the expression of MMP-9 and TIMP-1, STAT3. In a sense, this study reveals that the MMP-9/TIMP-1 signaling pathway may be involved in the injury after CIRI and thus provides a new treatment strategy as well as a researching method for stroke.
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Affiliation(s)
- Shengwei Liu
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China; Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
| | - Jingdong Liu
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yuchun Wang
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Ling Deng
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Sha Chen
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Xuan Wang
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Tianrui Zuo
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Qingwen Hu
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Jiangyan Rao
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Qian Wang
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Zhi Dong
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
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Ptáková N, Martínek P, Holubec L, Janovský V, Vančurová J, Grossmann P, Navarro PA, Rodriguez Moreno JF, Alaghehbandan R, Hes O, Májek O, Pešek M, Michal M, Ondič O. Identification of tumors with NRG1 rearrangement, including a novel putative pathogenic UNC5D-NRG1 gene fusion in prostate cancer by data-drilling a de-identified tumor database. Genes Chromosomes Cancer 2021; 60:474-481. [PMID: 33583086 DOI: 10.1002/gcc.22942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion genes containing neuregulin-1 (NRG1) are newly described potentially actionable oncogenic drivers. Initial clinical trials have shown a positive response to targeted treatment in some cases of NRG1 rearranged lung adenocarcinoma, cholangiocarcinoma, and pancreatic carcinoma. The cost-effective large scale identification of NRG1 rearranged tumors is an open question. We have tested a data-drilling approach by performing a retrospective assessment of a de-identified molecular profiling database of 3263 tumors submitted for fusion testing. Gene fusion detection was performed by RNA-based targeted next-generation sequencing using the Archer Fusion Plex kits for Illumina (ArcherDX Inc., Boulder, CO). Novel fusion transcripts were confirmed by a custom-designed RT-PCR. Also, the aberrant expression of CK20 was studied immunohistochemically. The frequency of NRG1 rearranged tumors was 0.2% (7/3263). The most common histologic type was lung adenocarcinoma (n = 5). Also, renal carcinoma (n = 1) and prostatic adenocarcinoma (n = 1) were found. Identified fusion partners were of a wide range (CD74, SDC4, TNC, VAMP2, UNC5D), with CD74, SDC4 being found twice. The UNC5D is a novel fusion partner identified in prostate adenocarcinoma. There was no co-occurrence with the other tested fusions nor KRAS, BRAF, and the other gene mutations specified in the applied gene panels. Immunohistochemically, the focal expression of CK20 was present in 2 lung adenocarcinomas. We believe it should be considered as an incidental finding. In conclusion, the overall frequency of tumors with NRG1 fusion was 0.2%. All tumors were carcinomas. We confirm (invasive mucinous) lung adenocarcinoma as being the most frequent tumor presenting NRG1 fusion. Herein novel putative pathogenic gene fusion UNC5D-NRG1 is described. The potential role of immunohistochemistry in tumor identification should be further addressed.
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Affiliation(s)
- Nikola Ptáková
- Molecular Genetics Department, Bioptická Laboratoř s.r.o., Pilsen, Czech Republic.,Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Martínek
- Molecular Genetics Department, Bioptická Laboratoř s.r.o., Pilsen, Czech Republic
| | - Luboš Holubec
- Department of Clinical Oncology, Na Homolce Hospital, Prague, Czech Republic.,Second Department of Internal Medicine, Medical Faculty in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Václav Janovský
- Department of Oncology, Hospital České Budějovice, České Budějovice, Czech Republic
| | - Jana Vančurová
- Department of Oncology, Hospital České Budějovice, České Budějovice, Czech Republic
| | - Petr Grossmann
- Molecular Genetics Department, Bioptická Laboratoř s.r.o., Pilsen, Czech Republic
| | - Paloma Alcaraz Navarro
- Department of Pathology, FiHM-Centro Integral Oncológico Hospital de Madrid Clara Campal, Madrid, Spain
| | - Juan F Rodriguez Moreno
- Department of Pathology, FiHM-Centro Integral Oncológico Hospital de Madrid Clara Campal, Madrid, Spain
| | - Reza Alaghehbandan
- Department of Pathology, University of British Columbia, Royal Columbian Hospital, Vancouver, British Columbia, Canada
| | - Ondřej Hes
- Department of Pathology, Medical Faculty in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Ondřej Májek
- Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Miloš Pešek
- Department of Pneumology and Phthisiology, Medical Faculty in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Michal Michal
- Department of Pathology, Medical Faculty in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Ondrej Ondič
- Molecular Genetics Department, Bioptická Laboratoř s.r.o., Pilsen, Czech Republic.,Department of Pathology, Medical Faculty in Pilsen, Charles University Prague, Pilsen, Czech Republic
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Giovannozzi S, Demeulemeester J, Schrijvers R, Gijsbers R. Transcriptional Profiling of STAT1 Gain-of-Function Reveals Common and Mutation-Specific Fingerprints. Front Immunol 2021; 12:632997. [PMID: 33679782 PMCID: PMC7925617 DOI: 10.3389/fimmu.2021.632997] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
STAT1 gain-of-function (GOF) is a primary immunodeficiency typically characterized by chronic mucocutaneous candidiasis (CMC), recurrent respiratory infections, and autoimmunity. Less commonly, also immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX)-like syndromes with CMC, and combined immunodeficiency without CMC have been described. Recently, our group and others have shown that different mutation-specific mechanisms underlie STAT1 GOF in vitro, including faster nuclear accumulation (R274W), and reduced mobility (R321, N574I) to near immobility in the nucleus (T419R) upon IFNγ stimulation. In this work, we evaluated the transcriptomic fingerprint of the aforementioned STAT1 GOF mutants (R274W, R321S, T419R, and N574I) relative to STAT1 wild-type upon IFNγ stimulation in an otherwise isogenic cell model. The majority of genes up-regulated in wild-type STAT1 cells were significantly more up-regulated in cells expressing GOF mutants, except for T419R. In addition to the common interferon regulated genes (IRG), STAT1 GOF mutants up-regulated an additional set of genes, that were in part shared with other GOF mutants or mutation-specific. Overall, R274W and R321S transcriptomes clustered with STAT1 WT, while T419R and N574I had a more distinct fingerprint. We observed reduced frequency of canonical IFNγ activation site (GAS) sequences in promoters of genes up-regulated by all the STAT1 GOF mutants, suggesting loss of DNA binding specificity for the canonical GAS consensus. Interestingly, the T419R mutation, expected to directly increase the affinity for DNA, showed the most pronounced effects on the transcriptome. T419R STAT1 dysregulated more non-IRG than the other GOF mutants and fewer GAS or degenerate GAS promotor sequences could be found in the promoter regions of these genes. In conclusion, our work confirms hyperactivation of common sets of IFNγ-induced genes in STAT1 GOF with additional dysregulation of mutation-specific genes, in line with the earlier observed mutation-specific mechanisms. Binding to more degenerate GAS sequences is proposed as a mechanism toward transcriptional dysregulation in R274W, R321S, and N574I. For T419R, an increased interaction with the DNA is suggested to result in a broader and less GAS-specific response. Our work indicates that multiple routes leading to STAT1 GOF are associated with common and private transcriptomic fingerprints, which may contribute to the phenotypic variation observed in vivo.
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Affiliation(s)
- Simone Giovannozzi
- Allergy and Clinical Immunology Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jonas Demeulemeester
- Laboratories for Computational Biology and Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Rik Schrijvers
- Allergy and Clinical Immunology Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.,Leuven Viral Vector Core, KU Leuven, Leuven, Belgium
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Nesterenko PA, McLaughlin J, Cheng D, Bangayan NJ, Burton Sojo G, Seet CS, Qin Y, Mao Z, Obusan MB, Phillips JW, Witte ON. Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning. Proc Natl Acad Sci U S A 2021; 118:e2021190118. [PMID: 33431692 DOI: 10.1073/pnas.2021190118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
T cell receptors (TCRs) surveil cellular environment by recognizing peptides presented by the major histocompatibility complex. TCR sequencing allows for understanding the scope of T cell reactivity in health and disease. Specific TCR clones can be used as therapeutics in cancer and autoimmune disease. We present a technique that allows for TCR sequencing based on intracellular signaling molecules, such as cytokines and transcription factors. The core concept is highly generalizable and should be applicable to global gene expression analysis where intracellular marker-based cell isolation is required. T cell receptors (TCRs) are generated by somatic recombination of V/D/J segments to produce up to 1015 unique sequences. Highly sensitive and specific techniques are required to isolate and identify the rare TCR sequences that respond to antigens of interest. Here, we describe the use of mRNA sequencing via cross-linker regulated intracellular phenotype (CLInt-Seq) for efficient recovery of antigen-specific TCRs in cells stained for combinations of intracellular proteins such as cytokines or transcription factors. This method enables high-throughput identification and isolation of low-frequency TCRs specific for any antigen. As a proof of principle, intracellular staining for TNFα and IFNγ identified cytomegalovirus (CMV)- and Epstein-Barr virus (EBV)-reactive TCRs with efficiencies similar to state-of-the-art peptide-MHC multimer methodology. In a separate experiment, regulatory T cells were profiled based on intracellular FOXP3 staining, demonstrating the ability to examine phenotypes based on transcription factors. We further optimized the intracellular staining conditions to use a chemically cleavable primary amine cross-linker compatible with current single-cell sequencing technology. CLInt-Seq for TNFα and IFNγ performed similarly to isolation with multimer staining for EBV-reactive TCRs. We anticipate CLInt-Seq will enable droplet-based single-cell mRNA analysis from any tissue where minor populations need to be isolated by intracellular markers.
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Barreiro K, Dwivedi OP, Leparc G, Rolser M, Delic D, Forsblom C, Groop P, Groop L, Huber TB, Puhka M, Holthofer H. Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease. J Extracell Vesicles 2020; 10:e12038. [PMID: 33437407 PMCID: PMC7789228 DOI: 10.1002/jev2.12038] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
Urinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of kidney damage, holding potential to replace the conventional invasive techniques including kidney biopsy. However, comprehensive studies characterizing uEV isolation methods with patient samples are rare. Here we compared performance of three established uEV isolation workflows for their subsequent use in transcriptomics analysis for biomarker discovery in diabetic kidney disease. We collected urine samples from individuals with type 1 diabetes with macroalbuminuria and healthy controls. We isolated uEV by Hydrostatic Filtration Dialysis (HFD), ultracentrifugation (UC), and a commercial kit- based isolation method (NG), each with different established urine clearing steps. Purified EVs were analysed by electron microscopy, nanoparticle tracking analysis, and Western blotting. Isolated RNAs were subjected to miRNA and RNA sequencing. HFD and UC samples showed close similarities based on mRNA sequencing data. NG samples had a lower number of reads and different mRNA content compared to HFD or UC. For miRNA sequencing data, satisfactory miRNA counts were obtained by all methods, but miRNA contents differed slightly. This suggests that the isolation workflows enrich specific subpopulations of miRNA-rich uEV preparation components. Our data shows that HFD,UC and the kit-based method are suitable methods to isolate uEV for miRNA-seq. However, only HFD and UC were suitable for mRNA-seq in our settings.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - German Leparc
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Marcel Rolser
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre MannheimUniversity of HeidelbergHeidelbergGermany
| | - Carol Forsblom
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Abdominal Center, NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Per‐Henrik Groop
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Abdominal Center, NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Diabetes, Central Clinical SchoolMonash UniversityMelbourneVICAustralia
| | - Leif Groop
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Tobias B. Huber
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Harry Holthofer
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
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Hao Y, Hu P, Zhang J. Genomic analysis of the prognostic effect of tumor-associated neutrophil-related genes across 15 solid cancer types: an immune perspective. Ann Transl Med 2020; 8:1507. [PMID: 33313252 PMCID: PMC7729319 DOI: 10.21037/atm-20-6629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Tumor-associated neutrophils (TANs) have been a research hotspot in recent years. However, the role and relevant mechanisms of TANs in the tumor microenvironment (TME) have not yet been elucidated. Method The ribonucleic acid (RNA) expression levels of fucosyltransferase 4 (FUT4) and elastase, neutrophil expressed (ELANE) in samples from The Cancer Genome Atlas (TCGA) (n=4,538) were analyzed. Receiver operating characteristic (ROC) curves were used to calculate the critical cutoff values, and different data were defined as high and low expression. The tumor microenvironment immune type (TMIT) was defined according to the activation state of TAN, and the samples were classified into three TMITs based on their cut-off values. Mutational datasets and overall survival were compared according to the TMITs. Results The prognostic significance of FUT4, ELANE, and myeloperoxidase (MPO) was different among the 15 cancers, and the prognostic significance of different TMITs varied across the different tumors. Compared with the other groups, TMIT 3 had a favorable prognostic effect, which was most prominent in lung adenocarcinoma (LUAD) [hazard ratio (HR) =0.292, 95% confidence interval (CI): 0.185–0.459, P<0.001]. Conclusions Our study demonstrated that highly-activated TANs predicted a favorable prognosis in humans using genomic analyses for the first time. This provides a realistic basis for further exploring the role of TANs in the immune microenvironment and provides real world data for tumor immunotherapy.
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Affiliation(s)
- Yuying Hao
- Department of Radiation Oncology, the First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China.,Department of Radiation Oncology, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pingping Hu
- Department of Radiation Oncology, the First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Jiandong Zhang
- Department of Radiation Oncology, the First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
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