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Wu JD, Xu L, Chen W, Zhou Y, Zheng G, Gu W. LncRNA PCAT6 mediates UBFD1 expression via sponging miR-545-3p in breast cancer cells. Noncoding RNA Res 2024; 9:421-428. [PMID: 38511057 PMCID: PMC10950603 DOI: 10.1016/j.ncrna.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/22/2024] Open
Abstract
Background LncRNA PCAT6 has been shown to involve in carcinogenesis of different tumors. In this study, we investigated underline mechanism by which PCAT6 promoted breast cancer cell progression. Methods RIP was used to identify lncRNAs associated with IMP1. Bioinformatics assays were used to predict potential miRNAs that interact with PCAT6 and mRNAs that are targeted by miR-545-3p. RNA-seq and RT-qPCR were used to analyze differential expression of lncRNAs and miRNA-targeted genes. Luciferase reporter and RNA pull-down assays were performed to identify the molecular interactions between PCAT6 and individual miRNAs. The role of PCAT6-mediated cell proliferation and invasion were tested by CCK-8 and transwell assays following loss-of-function and gain-of-function effects. Results We identified that PCAT6 is one of the lncRNAs that associated with IMP1. PCAT6 not only binds to IMP1, but also acts as a ceRNA to interact with multiple miRNAs, including miR-545-3p. Binding of IMP1 destabilized PCAT6, while competitive interaction with miR-545-3p allowed PCAT6 to positively regulate UBFD1 expression. Silencing UBFD1 mRNA could effectively rescue PCAT6-induced cell proliferation and invasive abilities. Conclusions Our study provided evidence that PCAT6 activates UBFD1 expression via sponging miR-545-3p to increase carcinogenesis of breast cancer cells. Based on the nature of UBFD1 as a polyubiquitin binding protein, our study suggested that ubiquitin pathway might contribute to breast cancer progression.
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Affiliation(s)
- Jun-Dong Wu
- Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Liqun Xu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Weibin Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Yanchun Zhou
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Guiyu Zheng
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Wei Gu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
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Liu X, Xie X, Sui C, Liu X, Song M, Luo Q, Zhan P, Feng J, Liu J. Unraveling the cross-talk between N6-methyladenosine modification and non-coding RNAs in breast cancer: Mechanisms and clinical implications. Int J Cancer 2024; 154:1877-1889. [PMID: 38429857 DOI: 10.1002/ijc.34900] [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: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
In recent years, breast cancer (BC) has surpassed lung cancer as the most common malignant tumor worldwide and remains the leading cause of cancer death in women. The etiology of BC usually involves dysregulation of epigenetic mechanisms and aberrant expression of certain non-coding RNAs (ncRNAs). N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, widely exists in ncRNAs to affect its biosynthesis and function, and is an important regulator of tumor-related signaling pathways. Interestingly, ncRNAs can also regulate or target m6A modification, playing a key role in cancer progression. However, the m6A-ncRNAs regulatory network in BC has not been fully elucidated, especially the regulation of m6A modification by ncRNAs. Therefore, in this review, we comprehensively summarize the interaction mechanisms and biological significance of m6A modifications and ncRNAs in BC. Meanwhile, we also focused on the clinical application value of m6A modification in BC diagnosis and prognosis, intending to explore new biomarkers and potential therapeutic targets.
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Affiliation(s)
- Xuan Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Xuelong Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Chentao Sui
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Miao Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Qing Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Ping Zhan
- Department of Obstetrics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
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Hwang SP, Denicourt C. The impact of ribosome biogenesis in cancer: from proliferation to metastasis. NAR Cancer 2024; 6:zcae017. [PMID: 38633862 PMCID: PMC11023387 DOI: 10.1093/narcan/zcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The dysregulation of ribosome biogenesis is a hallmark of cancer, facilitating the adaptation to altered translational demands essential for various aspects of tumor progression. This review explores the intricate interplay between ribosome biogenesis and cancer development, highlighting dynamic regulation orchestrated by key oncogenic signaling pathways. Recent studies reveal the multifaceted roles of ribosomes, extending beyond protein factories to include regulatory functions in mRNA translation. Dysregulated ribosome biogenesis not only hampers precise control of global protein production and proliferation but also influences processes such as the maintenance of stem cell-like properties and epithelial-mesenchymal transition, contributing to cancer progression. Interference with ribosome biogenesis, notably through RNA Pol I inhibition, elicits a stress response marked by nucleolar integrity loss, and subsequent G1-cell cycle arrest or cell death. These findings suggest that cancer cells may rely on heightened RNA Pol I transcription, rendering ribosomal RNA synthesis a potential therapeutic vulnerability. The review further explores targeting ribosome biogenesis vulnerabilities as a promising strategy to disrupt global ribosome production, presenting therapeutic opportunities for cancer treatment.
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Affiliation(s)
- Sseu-Pei Hwang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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104
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Stover L, Bahramimoghaddam H, Wang L, Schrecke S, Yadav GP, Zhou M, Laganowsky A. Grafting the ALFA tag for structural studies of aquaporin Z. J Struct Biol X 2024; 9:100097. [PMID: 38361954 PMCID: PMC10867769 DOI: 10.1016/j.yjsbx.2024.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Aquaporin Z (AqpZ), a bacterial water channel, forms a tetrameric complex and, like many other membrane proteins, activity is regulated by lipids. Various methods have been developed to facilitate structure determination of membrane proteins, such as the use of antibodies. Here, we graft onto AqpZ the ALFA tag (AqpZ-ALFA), an alpha helical epitope, to make use of the high-affinity anti-ALFA nanobody (nB). Native mass spectrometry reveals the AqpZ-ALFA fusion forms a stable, 1:1 complex with nB. Single-particle cryogenic electron microscopy studies reveal the octameric (AqpZ-ALFA)4(nB)4 complex forms a dimeric assembly and the structure was determined to 1.9 Å resolution. Dimerization of the octamer is mediated through stacking of the symmetrically bound nBs. Tube-like density is also observed, revealing a potential cardiolipin binding site. Grafting of the ALFA tag, or other epitope, along with binding and association of nBs to promote larger complexes will have applications in structural studies and protein engineering.
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Affiliation(s)
- Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | | | - Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Gaya P. Yadav
- Laboratory for Biomolecular Structure and Dynamics (LBSD), Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
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105
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Wang W, Bu Y, Li W, Zhu W, Li J, Li X. Effects of nano freezing-thawing on myofibrillar protein of Atlantic salmon fillets: Protein structure and label-free proteomics. Food Chem 2024; 442:138369. [PMID: 38232615 DOI: 10.1016/j.foodchem.2024.138369] [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: 09/07/2023] [Revised: 12/24/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
This study investigated the impact of magnetic nanoparticles (MNPs) -assisted cryogenic freezing integrated with MNPs combined microwave thawing (NNMT) on the structural integrity of myofibrillar proteins and alterations in protein profiles in salmon fillets. The NNMT showed the lowest myofibrillar fragmentation index (MFI) value (2.73 ± 0.31) among the four freezing-thawing groups. The myofibrillar structure exhibited the highest level of integrity, while the myofibrillar proteins demonstrated minimal aggregation and displayed the most stable secondary and tertiary structures in response to NNMT treatment. Compared with the other three treatments, NNMT exhibited a high abundance of ionic and hydrogen bonds, resulting in stronger interactions between the proteins and water molecules. The label-free proteomics analysis revealed that different freezing-thawing methods primarily affected the cytoskeletal proteins, with collagen and myosin being down-regulated due to degradation caused by cold stress and recrystallization. Additionally, NNMT demonstrated a superior capability in stabilizing salmon cytoskeletal proteins.
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Affiliation(s)
- Wenxuan Wang
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China; The Fresh Food Storage and Processing Technology Research Institute of Liaoning Provincial Universities, Jinzhou, Liaoning 121013, China
| | - Ying Bu
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China; The Fresh Food Storage and Processing Technology Research Institute of Liaoning Provincial Universities, Jinzhou, Liaoning 121013, China
| | - Wenzheng Li
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China; The Fresh Food Storage and Processing Technology Research Institute of Liaoning Provincial Universities, Jinzhou, Liaoning 121013, China
| | - Wenhui Zhu
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China; The Fresh Food Storage and Processing Technology Research Institute of Liaoning Provincial Universities, Jinzhou, Liaoning 121013, China.
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China; The Fresh Food Storage and Processing Technology Research Institute of Liaoning Provincial Universities, Jinzhou, Liaoning 121013, China
| | - Xuepeng Li
- College of Food Science and Engineering, Bohai University, Jinzhou, Liaoning 121013, China; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, Liaoning 121013, China; The Fresh Food Storage and Processing Technology Research Institute of Liaoning Provincial Universities, Jinzhou, Liaoning 121013, China.
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Yuan Q, Liang R, Lv K, Shi X, Leng J, Liu Y, Xiao J, Zhang L, Zhao L. Structural characterization of a Chlorella heteropolysaccharide by analyzing its depolymerized product and finding an inducer of human dendritic cell maturation. Carbohydr Polym 2024; 333:122000. [PMID: 38494209 DOI: 10.1016/j.carbpol.2024.122000] [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: 09/12/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
Chlorella polysaccharides have been gaining increasing attention because of their high yield from dried Chlorella powder and their remarkable immunomodulatory activity. In this study, the major polysaccharide fraction, CPP-3a, in Chlorella pyrenoidosa, was isolated, and its detailed structure was investigated by analyzing the low-molecular-weight product prepared via free radical depolymerization. The results indicated that CPP-3a with a molecular weight of 195.2 kDa was formed by →2)-α-L-Araf-(1→, →2)-α-D-Rhap-(1→, →5)-α-L-Araf-(1→, →3)-β-D-Glcp-(1→, →4)-α-D-Glcp-(1→, →4)-α-D-GlcpA-(1→, →2,3)-α-D-Manp-(1→, →3,4)-α-D-Manp-(1→, →3,4)-β-D-Galp-(1→, →3,6)-β-D-Galp-(1→, and →2,3,6)-α-D-Galp-(1→ residues, branched at C2, C3, C4, or C6 of α/β-D-Galp and α-D-Manp, and terminated by α/β-L-Araf, α-L-Arap, α-D-Galp, and β-D-Glcp. Biological assays showed that CPP-3a significantly altered the dendritic morphology of immature dendritic cells (DCs). Enhanced CD80, CD86, and MHC I expression on the cell surface and decreased phagocytic ability indicated that CPP-3a could induce the maturation of DCs. Furthermore, CPP-3a-stimulated DCs not only stimulated the proliferation of allogeneic naïve CD4+ T cells and the secretion of IFN-γ, but also directly stimulated the activation and proliferation of CD8+ T cells through cross-antigen presentation. These findings indicate that CPP-3a can promote human DC maturation and T-cell stimulation and may be a novel DC maturation inducer with potential developmental value in DC immunotherapy.
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Affiliation(s)
- Qingxia Yuan
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China; Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Rongyi Liang
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Kunling Lv
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Xiaohuo Shi
- Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Jing Leng
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China; Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Jian Xiao
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China.
| | - Lifeng Zhang
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China.
| | - Longyan Zhao
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China; Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China.
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107
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Chauhan R, Nate Z, Ike B, Kwabena Adu D, Alake J, Gill AAS, Miya L, Bachheti Thapliyal N, Karpoormath R. One pot fabrication of diamino naphthalene -AuNPs decorated graphene nanoplatform for the MRSA detection in the biological sample. Bioelectrochemistry 2024; 157:108674. [PMID: 38460467 DOI: 10.1016/j.bioelechem.2024.108674] [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: 10/23/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/11/2024]
Abstract
Early monitoring of MRSA can effectively mitigate the disease risk by using Penicillin-binding protein 2a (PbP2a) biomarker. Diamino naphthalene-AuNPs decorated graphene (AuNPsGO-DN) nanocomposite was synthesized for a rapid and sensitive immunosensor detecting PbP2a. The synthesized AuNPsGO-DN nanocomposites were characterized by field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (SEM-EDX), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, and X-ray diffraction spectroscopy (XRD). Electrochemical characterization done with cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrical impedance spectroscopy (EIS) techniques. Anti-PbP2a monoclonal antibodies immobilized at AuNPsGO-DN/GCE via covalent bonding. AuNPs enhanced the electrode surface area and the antibodies' loading. Mercaptopropionic acid (MPA) was a linker between the AuNPs and antibodies, orientated the antibodies as opposite to the PbP2a antigen, and improved the sensitivity and specificity. The antiPbP2a/MPA/AuNPsGO-DN/GCE electrode displayed sensitive and selective detection towards the PbP2a antigen in phosphate buffer saline (PBS pH 7.4). The broad linear range from 0.01 to 8000 pg/mL was obtained with LOD of 0.154 pg/mL and 0.0239 pg/mL, respectively. A label-free, simple, and sensitive immunosensor was developed with a 98-106 % recovery rate in spiked biological samples. It shows the potential applicability of the developed immunoelectrode.
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Affiliation(s)
- Ruchika Chauhan
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Zondi Nate
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Blessing Ike
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Darko Kwabena Adu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - John Alake
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Atal A S Gill
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Lungelo Miya
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Neeta Bachheti Thapliyal
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa.
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Zhang Z, Yu C, Wu Y, Wang Z, Xu H, Yan Y, Zhan Z, Yin S. Semiconducting polymer dots for multifunctional integrated nanomedicine carriers. Mater Today Bio 2024; 26:101028. [PMID: 38590985 PMCID: PMC11000120 DOI: 10.1016/j.mtbio.2024.101028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
The expansion applications of semiconducting polymer dots (Pdots) among optical nanomaterial field have long posed a challenge for researchers, promoting their intelligent application in multifunctional nano-imaging systems and integrated nanomedicine carriers for diagnosis and treatment. Despite notable progress, several inadequacies still persist in the field of Pdots, including the development of simplified near-infrared (NIR) optical nanoprobes, elucidation of their inherent biological behavior, and integration of information processing and nanotechnology into biomedical applications. This review aims to comprehensively elucidate the current status of Pdots as a classical nanophotonic material by discussing its advantages and limitations in terms of biocompatibility, adaptability to microenvironments in vivo, etc. Multifunctional integration and surface chemistry play crucial roles in realizing the intelligent application of Pdots. Information visualization based on their optical and physicochemical properties is pivotal for achieving detection, sensing, and labeling probes. Therefore, we have refined the underlying mechanisms and constructed multiple comprehensive original mechanism summaries to establish a benchmark. Additionally, we have explored the cross-linking interactions between Pdots and nanomedicine, potential yet complete biological metabolic pathways, future research directions, and innovative solutions for integrating diagnosis and treatment strategies. This review presents the possible expectations and valuable insights for advancing Pdots, specifically from chemical, medical, and photophysical practitioners' standpoints.
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Affiliation(s)
- Ze Zhang
- Department of Hepatobiliary and Pancreatic Surgery II, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin 130012, PR China
| | - Chenhao Yu
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No.2699 Qianjin Street, Changchun, Jilin 130012, PR China
| | - Yuyang Wu
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No.2699 Qianjin Street, Changchun, Jilin 130012, PR China
| | - Zhe Wang
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No.2699 Qianjin Street, Changchun, Jilin 130012, PR China
| | - Haotian Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Third Bethune Hospital of Jilin University, Changchun, Jilin 130000, PR China
| | - Yining Yan
- Department of Radiology, The Third Bethune Hospital of Jilin University, Changchun, Jilin 130000, PR China
| | - Zhixin Zhan
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin 130012, PR China
| | - Shengyan Yin
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No.2699 Qianjin Street, Changchun, Jilin 130012, PR China
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109
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Padhy I, Dwibedy SK, Mohapatra SS. A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development. Microbiol Res 2024; 283:127679. [PMID: 38508087 DOI: 10.1016/j.micres.2024.127679] [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: 07/31/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
With the rising incidences of antimicrobial resistance (AMR) and the diminishing options of novel antimicrobial agents, it is paramount to decipher the molecular mechanisms of action and the emergence of resistance to the existing drugs. Polymyxin, a cationic antimicrobial lipopeptide, is used to treat infections by Gram-negative bacterial pathogens as a last option. Though polymyxins were identified almost seventy years back, their use has been restricted owing to toxicity issues in humans. However, their clinical use has been increasing in recent times resulting in the rise of polymyxin resistance. Moreover, the detection of "mobile colistin resistance (mcr)" genes in the environment and their spread across the globe have complicated the scenario. The mechanism of polymyxin action and the development of resistance is not thoroughly understood. Specifically, the polymyxin-bacterial lipopolysaccharide (LPS) interaction is a challenging area of investigation. The use of advanced biophysical techniques and improvement in molecular dynamics simulation approaches have furthered our understanding of this interaction, which will help develop polymyxin analogs with better bactericidal effects and lesser toxicity in the future. In this review, we have delved deeper into the mechanisms of polymyxin-LPS interactions, highlighting several models proposed, and the mechanisms of polymyxin resistance development in some of the most critical Gram-negative pathogens.
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Affiliation(s)
- Indira Padhy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India
| | - Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Biotechnology, Berhampur University, Bhanja Bihar, Berhampur 760007, Odisha, India.
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110
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Zhou Y, Chen SJ. Advances in machine-learning approaches to RNA-targeted drug design. Artif Intell Chem 2024; 2:100053. [PMID: 38434217 PMCID: PMC10904028 DOI: 10.1016/j.aichem.2024.100053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
RNA molecules play multifaceted functional and regulatory roles within cells and have garnered significant attention in recent years as promising therapeutic targets. With remarkable successes achieved by artificial intelligence (AI) in different fields such as computer vision and natural language processing, there is a growing imperative to harness AI's potential in computer-aided drug design (CADD) to discover novel drug compounds that target RNA. Although machine-learning (ML) approaches have been widely adopted in the discovery of small molecules targeting proteins, the application of ML approaches to model interactions between RNA and small molecule is still in its infancy. Compared to protein-targeted drug discovery, the major challenges in ML-based RNA-targeted drug discovery stem from the scarcity of available data resources. With the growing interest and the development of curated databases focusing on interactions between RNA and small molecule, the field anticipates a rapid growth and the opening of a new avenue for disease treatment. In this review, we aim to provide an overview of recent advancements in computationally modeling RNA-small molecule interactions within the context of RNA-targeted drug discovery, with a particular emphasis on methodologies employing ML techniques.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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111
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Liang Q, Liu Z, Liang Z, Zhu C, Li D, Kong Q, Mou H. Development strategies and application of antimicrobial peptides as future alternatives to in-feed antibiotics. Sci Total Environ 2024; 927:172150. [PMID: 38580107 DOI: 10.1016/j.scitotenv.2024.172150] [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: 01/12/2024] [Revised: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
The use of in-feed antibiotics has been widely restricted due to the significant environmental pollution and food safety concerns they have caused. Antimicrobial peptides (AMPs) have attracted widespread attention as potential future alternatives to in-feed antibiotics owing to their demonstrated antimicrobial activity and environment friendly characteristics. However, the challenges of weak bioactivity, immature stability, and low production yields of natural AMPs impede practical application in the feed industry. To address these problems, efforts have been made to develop strategies for approaching the AMPs with enhanced properties. Herein, we summarize approaches to improving the properties of AMPs as potential alternatives to in-feed antibiotics, mainly including optimization of structural parameters, sequence modification, selection of microbial hosts, fusion expression, and industrially fermentation control. Additionally, the potential for application of AMPs in animal husbandry is discussed. This comprehensive review lays a strong theoretical foundation for the development of in-feed AMPs to achieve the public health globally.
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Affiliation(s)
- Qingping Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Zhemin Liu
- Fundamental Science R&D Center of Vazyme Biotech Co. Ltd., Nanjing 210000, China
| | - Ziyu Liang
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Changliang Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Dongyu Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Qing Kong
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China.
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112
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Chen J, Jiao Z, Liu Y, Zhang M, Wang D. USP7 interacts with and destabilizes oncoprotein SET. Biochem Biophys Res Commun 2024; 709:149818. [PMID: 38555840 DOI: 10.1016/j.bbrc.2024.149818] [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: 02/28/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
Oncoprotein SE translocation (SET) is frequently overexpressed in different types of tumors and correlated with poor prognosis of cancer patients. Targeting SET has been considered a promising strategy for cancer intervention. However, the mechanisms by which SET is regulated under cellular conditions are largely unknown. Here, by performing a tandem affinity purification-mass spectrometry (TAP-MS), we identify that the ubiquitin-specific protease 7 (USP7) forms a stable protein complex with SET in cancer cells. Further analyses reveal that the acidic domain of SET directly binds USP7 while both catalytic domain and ubiquitin-like (UBL) domains of USP7 are required for SET binding. Knockdown of USP7 has no effect on the mRNA level of SET. However, we surprisingly find that USP7 depletion leads to a dramatic elevation of SET protein levels, suggesting that USP7 plays a key role in destabilizing oncoprotein SET, possibly through an indirect mechanism. To our knowledge, our data report the first deubiquitinase (DUB) that physically associates with oncoprotein SET and imply an unexpected regulatory effect of USP7 on SET stability.
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Affiliation(s)
- Jianyuan Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zishan Jiao
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yajing Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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Choi BH, Lee CJ, Kim TH, Kim DNJ, Park YS, Choi JM, Park JS. pH Dependence of HSF1 trimerization is shaped by intramolecular interactions. Biochem Biophys Res Commun 2024; 709:149824. [PMID: 38537598 DOI: 10.1016/j.bbrc.2024.149824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
Heat shock factor 1 (HSF1) primarily regulates various cellular stress responses. Previous studies have shown that low pH within the physiological range directly activates HSF1 function in vitro. However, the detailed molecular mechanisms remain unclear. This study proposes a molecular mechanism based on the trimerization behavior of HSF1 at different pH values. Extensive mutagenesis of human and goldfish HSF1 revealed that the optimal pH for trimerization depended on the identity of residue 103. In particular, when residue 103 was occupied by tyrosine, a significant increase in the optimal pH was observed, regardless of the rest of the sequence. This behavior can be explained by the protonation state of the neighboring histidine residues, His101 and His110. Residue 103 plays a key role in trimerization by forming disulfide or non-covalent bonds with Cys36. If tyrosine resides at residue 103 in an acidic environment, its electrostatic interactions with positively charged histidine residues prevent effective trimerization. His101 and His110 are neutralized at a higher pH, which releases Tyr103 to interact with Cys36 and drives the effective trimerization of HSF1. This study showed that the protonation state of a histidine residue can regulate the intramolecular interactions, which consequently leads to a drastic change in the oligomerization behavior of the entire protein.
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Affiliation(s)
- Bo-Hee Choi
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - Chang-Ju Lee
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - Tae Hwan Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - David Nahm-Joon Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea; Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Young-Shang Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea.
| | - Jang-Su Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735, South Korea.
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Li L, Xie G, Dong P, Tang H, Wu L, Zhang L. Anticyanobacterial effect of p-coumaric acid on Limnothrix sp. determined by proteomic and metabolomic analysis. Sci Total Environ 2024; 926:171632. [PMID: 38471589 DOI: 10.1016/j.scitotenv.2024.171632] [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: 11/01/2023] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Regulating photosynthetic machinery is a powerful but challenging strategy for selectively inhibiting bloom-forming cyanobacteria, in which photosynthesis mainly occurs in thylakoids. P-coumaric acid (p-CA) has several biological properties, including free radical scavenging and antibacterial effects, and studies have shown that it can damage bacterial cell membranes, reduce chlorophyll a in cyanobacteria, and effectively inhibit algal growth at concentrations exceeding 0.127 g/L. Allelochemicals typically inhibit cyanobacteria by inhibiting photosynthesis; however, research on inhibiting harmful algae using phenolic acids has focused mainly on their inhibitory and toxic effects and metabolite levels, and the molecular mechanism by which p-CA inhibits photosynthesis remains unclear. Thus, we examined the effect of p-CA on the photosynthesis of Limnothrix sp. in detail. We found that p-CA inhibits algal growth and damages photosynthesis-related proteins in Limnothrix sp., reduces carotenoid and allophycocyanin levels, and diminishes the actual quantum yield of Photosystem II (PSII). Moreover, p-CA significantly altered algal cell membrane protein systems, and PSII loss resulting from p-CA exposure promoted reactive oxygen species production. It significantly altered algae cell membrane protein systems. Finally, p-CA was found to be environmentally nontoxic; 80 % of 48-h-old Daphnia magna larvae survived when exposed to 0.15 g/L p-CA. These findings provide insight into the mechanism of cyanobacterial inhibition by p-CA, providing a more practical approach to controlling harmful algal blooms.
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Affiliation(s)
- Lingzhi Li
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Gengxin Xie
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
| | - Pan Dong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Hui Tang
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Liping Wu
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Liang Zhang
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
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115
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Dai S, Wang Z, Cai M, Guo T, Mao S, Yang Y. A multi-omics investigation of the lung injury induced by PM 2.5 at environmental levels via the lung-gut axis. Sci Total Environ 2024; 926:172027. [PMID: 38552982 DOI: 10.1016/j.scitotenv.2024.172027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/25/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Long-term exposure to fine particulate matter (PM2.5) posed injury for gastrointestinal and respiratory systems, ascribing with the lung-gut axis. However, the cross-talk mechanisms remain unclear. Here, we attempted to establish the response networks of lung-gut axis in mice exposed to PM2.5 at environmental levels. Male Balb/c mice were exposed to PM2.5 (dose of 0.1, 0.5, and 1.0 mg/kg) collected from Chengdu, China for 10 weeks, through intratracheally instillation, and examined the effect of PM2.5 on lung functions of mice. The changes of lung and gut microbiota and metabolic profiles of mice in different groups were determined. Furthermore, the results of multi-omics were conjointly analyzed to elucidate the primary microbes and the associated metabolites in lung and gut responsible for PM2.5 exposure. Accordingly, the cross-talk network and key pathways between lung-gut axis were established. The results indicated that exposed to PM2.5 0.1 mg/kg induced obvious inflammations in mice lung, while emphysema was observed at 1.0 mg/kg. The levels of metabolites guanosine, hypoxanthine, and hepoxilin B3 increased in the lung might contribute to lung inflammations in exposure groups. For microbiotas in lung, PM2.5 exposure significantly declined the proportions of Halomonas and Lactobacillus. Meanwhile, the metabolites in gut including L-tryptophan, serotonin, and spermidine were up-regulated in exposure groups, which were linked to the decreasing of Oscillospira and Helicobacter in gut. Via lung-gut axis, the activations of pathways including Tryptophan metabolism, ABC transporters, Serotonergic synapse, and Linoleic acid metabolism contributed to the cross-talk between lung and gut tissues of mice mediated by PM2.5. In summary, the microbes including Lactobacillus, Oscillospira, and Parabacteroides, and metabolites including hepoxilin B3, guanosine, hypoxanthine, L-tryptophan, and spermidine were the main drivers. In this lung-gut axis study, we elucidated some pro- and pre-biotics in lung and gut microenvironments contributed to the adverse effects on lung functions induced by PM2.5 exposure.
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Affiliation(s)
- Shuiping Dai
- National Center for Geriatrics Clinical Medicine Research, Department of Geriatrics and Gerontology, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Zhenglu Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Min Cai
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai 201403, PR China
| | - Tingting Guo
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Shengqiang Mao
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Ying Yang
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, PR China
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116
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Paul S, Arias MA, Wen L, Liao SE, Zhang J, Wang X, Regev O, Fei J. RNA molecules display distinctive organization at nuclear speckles. iScience 2024; 27:109603. [PMID: 38638569 PMCID: PMC11024929 DOI: 10.1016/j.isci.2024.109603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/05/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and nuclear speckles as a model system, we demonstrate that different sequence domains of RNA transcripts exhibit differential spatial distributions within speckles. Specifically, we image transcripts containing a region enriched in binding motifs of serine/arginine-rich (SR) proteins and another region enriched in binding motifs of heterogeneous nuclear ribonucleoproteins (hnRNPs). We show that these transcripts localize to the outer shell of speckles, with the SR motif-rich region localizing closer to the speckle center relative to the hnRNP motif-rich region. Further, we identify that this intra-speckle RNA organization is driven by the strength of RNA-protein interactions inside and outside speckles. Our results hint at novel functional roles of nuclear speckles and likely other membraneless organelles in organizing RNA substrates for biochemical reactions.
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Affiliation(s)
- Sneha Paul
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Mauricio A. Arias
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- Institute for System Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Li Wen
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Susan E. Liao
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Jiacheng Zhang
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoshu Wang
- The College, The University of Chicago, Chicago, IL 60637, USA
| | - Oded Regev
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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117
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Jacob-Dolan C, Lifton M, Powers OC, Miller J, Hachmann NP, Vu M, Surve N, Mazurek CR, Fisher JL, Rodrigues S, Patio RC, Anand T, Le Gars M, Sadoff J, Schmidt AG, Barouch DH. B cell somatic hypermutation following COVID-19 vaccination with Ad26.COV2.S. iScience 2024; 27:109716. [PMID: 38655202 PMCID: PMC11035370 DOI: 10.1016/j.isci.2024.109716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/02/2024] [Accepted: 04/07/2024] [Indexed: 04/26/2024] Open
Abstract
The viral vector-based COVID-19 vaccine Ad26.COV2.S has been recommended by the WHO since 2021 and has been administered to over 200 million people. Prior studies have shown that Ad26.COV2.S induces durable neutralizing antibodies (NAbs) that increase in coverage of variants over time, even in the absence of boosting or infection. Here, we studied humoral responses following Ad26.COV2.S vaccination in individuals enrolled in the initial Phase 1/2a trial of Ad26.COV2.S in 2020. Through 8 months post vaccination, serum NAb responses increased to variants, including B.1.351 (Beta) and B.1.617.2 (Delta), without additional boosting or infection. The level of somatic hypermutation, measured by nucleotide changes in the VDJ region of the heavy and light antibody chains, increased in Spike-specific B cells. Highly mutated mAbs from these sequences neutralized more SARS-CoV-2 variants than less mutated comparators. These findings suggest that the increase in NAb breadth over time following Ad26.COV2.S vaccination is mediated by affinity maturation.
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Affiliation(s)
- Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
| | - Michelle Lifton
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivia C. Powers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Nicole P. Hachmann
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mya Vu
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Nehalee Surve
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Camille R. Mazurek
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jana L. Fisher
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Stefanie Rodrigues
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert C. Patio
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Trisha Anand
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mathieu Le Gars
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Jerald Sadoff
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Aaron G. Schmidt
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Microbiology, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Department of Immunology, Boston, MA, USA
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118
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Lin CT, Ting RT, Ou YH, Shao TL, Lee MC. Protein degradation of Lsd1 is mediated by Bre1 yet opposed by Lsd1-interacting lncRNAs during fly follicle development. iScience 2024; 27:109683. [PMID: 38655201 PMCID: PMC11035368 DOI: 10.1016/j.isci.2024.109683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/13/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Tissue development, homeostasis, and repair all require efficient progenitor expansion. Lysine-specific demethylase 1 (Lsd1) maintains plastic epigenetic states to promote progenitor proliferation while overexpressed Lsd1 protein causes oncogenic gene expression in cancer cells. However, the precise regulation of Lsd1 protein expression at the molecular level to drive progenitor differentiation remains unclear. Here, using Drosophila melanogaster oogenesis as our experimental system, we discovered molecular machineries that modify Lsd1 protein stability in vivo. Through genetic and biochemical analyses, an E3 ubiquitin ligase, Bre1, was identified as required for follicle progenitor differentiation, likely by mediating Lsd1 protein degradation. Interestingly, specific Lsd1-interacting long non-coding RNAs (LINRs) were found to antagonize Bre1-mediated Lsd1 protein degradation. The intricate interplay discovered among the Lsd1 complex, LINRs and Bre1 provides insight into how Lsd1 protein stability is fine-tuned to underlie progenitor differentiation in vivo.
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Affiliation(s)
- Chun Ting Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Ruei-Teng Ting
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Yang-Hsuan Ou
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Tzu-Ling Shao
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Ming-Chia Lee
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
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119
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Zhu G, Jiang L, Tan K, Li Y, Hu M, Zhang S, Liu Z, Li L. MSCs-derived exosomes containing miR-486-5p attenuate cerebral ischemia and reperfusion (I/R) injury. Gene 2024; 906:148262. [PMID: 38346456 DOI: 10.1016/j.gene.2024.148262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
OBJECTIVES This study aims to investigate the impact of mesenchymal stem cell (MSC)-derived exosomes (Exo) on cerebral ischemia and reperfusion (I/R) injury, along with the underlying mechanism. METHODS An animal model of cerebral ischemia was induced using middle cerebral artery occlusion (MCAO), and a cell model utilizing Neuro-2a cells was established through oxygen-glucose deprivation/reoxygenation (OGD/R). Exosomes isolated from mouse MSCs were administered to mice or used to stimulate Neuro-2a cells. Exosomes from MSCs transfected with miR-NC, miR-486-5p mimics, miR-486-5p inhibitor, or phosphatase and tensin homolog (PTEN) short hairpin RNAs (sh-PTEN) were employed to stimulate Neuro-2a cells. The regulatory axis of miR-486-5p and PTEN was confirmed through rescue experiments. RESULTS Exo-miR-486-5p mimics alleviated cerebral I/R injury, improving neurological deficits and reducing the infarct ratio. Furthermore, Exo-miR-486-5p mimics attenuated OGD/R-induced defects in cell viability and inhibited apoptosis in Neuro-2a cells. These mimics also reduced levels of lactate dehydrogenase (LDH) and malondialdehyde (MDA) while enhancing superoxide dismutase (SOD) activity, both in brain tissue homogenates of mice and cell supernatants. Mechanistically, PTEN was identified as a target of miR-486-5p, and the downregulation of PTEN notably elevated Exo-miR-486-inhibitor-induced reductions in cell viability while mitigating cell apoptosis. CONCLUSION The results of this study demonstrate the potential of exosomes derived from MSCs to protect against cerebral I/R injury via the miR-486-5p and PTEN axis.
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Affiliation(s)
- Genbao Zhu
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - La Jiang
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - Kemeng Tan
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - Yafen Li
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - Mengxue Hu
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - Shengnan Zhang
- The Department of Neurosurgery, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - Zhenlin Liu
- The Department of Neurosurgery, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China
| | - Lili Li
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China.
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120
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Cardoso JCR, Mc Shane JC, Li Z, Peng M, Power DM. Revisiting the evolution of Family B1 GPCRs and ligands: Insights from mollusca. Mol Cell Endocrinol 2024; 586:112192. [PMID: 38408601 DOI: 10.1016/j.mce.2024.112192] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Family B1 G protein-coupled receptors (GPCRs) are one of the most well studied neuropeptide receptor families since they play a central role in many biological processes including endocrine, gastrointestinal, cardiovascular and reproduction in animals. The genes for these receptors emerged from a common ancestral gene in bilaterian genomes and evolved via gene/genome duplications and deletions in vertebrate and invertebrate genomes. Their existence and function have mostly been characterized in vertebrates and few studies exist in invertebrate species. Recently, an increased interest in molluscs, means a series of genomes have become available, and since they are less modified than insect and nematode genomes, they are ideal to explore the origin and evolution of neuropeptide gene families. This review provides an overview of Family B1 GPCRs and their peptide ligands and incorporates new data obtained from Mollusca genomes and taking a comparative approach challenges existing models on their origin and evolution.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Jennifer C Mc Shane
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Zhi Li
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Maoxiao Peng
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
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Yuan H, Liu RD, Gao ZY, Zhong LT, Zhou YC, Tan JH, Huang ZS, Li Z, Chen SB. Targeting ATP-binding site of WRN Helicase: Identification of novel inhibitors through pocket analysis and Molecular Dynamics-Enhanced virtual screening. Bioorg Med Chem Lett 2024; 104:129711. [PMID: 38521175 DOI: 10.1016/j.bmcl.2024.129711] [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: 08/16/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
WRN helicase is a critical protein involved in maintaining genomic stability, utilizing ATP hydrolysis to dissolve DNA secondary structures. It has been identified as a promising synthetic lethal target for microsatellite instable (MSI) cancers. However, few WRN helicase inhibitors have been discovered, and their potential binding sites remain unexplored. In this study, we analyzed potential binding sites for WRN inhibitors and focused on the ATP-binding site for screening new inhibitors. Through molecular dynamics-enhanced virtual screening, we identified two compounds, h6 and h15, which effectively inhibited WRN's helicase and ATPase activity in vitro. Importantly, these compounds selectively targeted WRN's ATPase activity, setting them apart from other non-homologous proteins with ATPase activity. In comparison to the homologous protein BLM, h6 exhibits some degree of selectivity towards WRN. We also investigated the binding mode of these compounds to WRN's ATP-binding sites. These findings offer a promising strategy for discovering new WRN inhibitors and present two novel scaffolds, which might be potential for the development of MSI cancer treatment.
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Affiliation(s)
- Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Run-Duo Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuo-Yu Gao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Li-Ting Zhong
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Ying-Chen Zhou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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122
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Yao Q, Gao Y, Zheng N, Delcenserie V, Wang J. Unlocking the mysteries of milk oligosaccharides: Structure, metabolism, and function. Carbohydr Polym 2024; 332:121911. [PMID: 38431414 DOI: 10.1016/j.carbpol.2024.121911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/18/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024]
Abstract
Milk oligosaccharides (MOs), complex carbohydrates prevalent in human breast milk, play a vital role in infant nutrition. Serving as prebiotics, they inhibit pathogen adherence, modulate the immune system, and support newborn brain development. Notably, MOs demonstrate significant variations in concentration and composition, both across different species and within the same species. These characteristics of MOs lead to several compelling questions: (i) What distinct beneficial functions do MOs offer and how do the functions vary along with their structural differences? (ii) In what ways do MOs in human milk differ from those in other mammals, and what factors drive these unique profiles? (iii) What are the emerging applications of MOs, particularly in the context of their incorporation into infant formula? This review delves into the structural characteristics, quantification methods, and species-specific concentration differences of MOs. It highlights the critical role of human MOs in infant growth and their potential applications, providing substantial evidence to enhance infant health and development.
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Affiliation(s)
- Qianqian Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Department of Food Science, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Yanan Gao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Veronique Delcenserie
- Department of Food Science, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Sánchez-Marañón M, Ortega R, Pulido-Fernández M, Barrena-González J, Lavado-Contador F, Miralles I, García-Salcedo JA, Soriano M. Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing. Sci Total Environ 2024; 925:171811. [PMID: 38508263 DOI: 10.1016/j.scitotenv.2024.171811] [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: 11/28/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.
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Affiliation(s)
- Manuel Sánchez-Marañón
- Department of Soil Science and Agricultural Chemistry, Science Faculty, University of Granada, E-18071 Granada, Spain
| | - Raúl Ortega
- Research Center for Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almería, Ctra. Sacramento s/n, E-04120 Almería, Spain
| | - Manuel Pulido-Fernández
- Grupo de Investigación GeoAmbiental, Universidad de Extremadura, Avenida de la Universidad s/n, E-10071 Cáceres, Spain
| | - Jesús Barrena-González
- Grupo de Investigación GeoAmbiental, Universidad de Extremadura, Avenida de la Universidad s/n, E-10071 Cáceres, Spain
| | - Francisco Lavado-Contador
- Grupo de Investigación GeoAmbiental, Universidad de Extremadura, Avenida de la Universidad s/n, E-10071 Cáceres, Spain
| | - Isabel Miralles
- Research Center for Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almería, Ctra. Sacramento s/n, E-04120 Almería, Spain
| | - José A García-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114 - E-18016 Granada, Spain; Microbiology Unit, University Hospital Virgen de las Nieves, E-18014 Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Miguel Soriano
- Research Center for Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almería, Ctra. Sacramento s/n, E-04120 Almería, Spain; GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114 - E-18016 Granada, Spain
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124
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Lienhart PH, Rohra V, Clement C, Toppen LC, DeCola AC, Rizzo DM, Scarborough MJ. Landfill intermediate cover soil microbiomes and their potential for mitigating greenhouse gas emissions revealed through metagenomics. Sci Total Environ 2024; 925:171697. [PMID: 38492594 DOI: 10.1016/j.scitotenv.2024.171697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Landfills are a major source of anthropogenic methane emissions and have been found to produce nitrous oxide, an even more potent greenhouse gas than methane. Intermediate cover soil (ICS) plays a key role in reducing methane emissions but may also result in nitrous oxide production. To assess the potential for microbial methane oxidation and nitrous oxide production, long sequencing reads were generated from ICS microbiome DNA and reads were functionally annotated for 24 samples across ICS at a large landfill in New York. Further, incubation experiments were performed to assess methane consumption and nitrous oxide production with varying amounts of ammonia supplemented. Methane was readily consumed by microbes in the composite ICS and all incubations with methane produced small amounts of nitrous oxide even when ammonia was not supplemented. Incubations without methane produced significantly less nitrous oxide than those incubated with methane. In incubations with methane added, the observed specific rate of methane consumption was 0.776 +/- 0.055 μg CH4 g dry weight (DW) soil-1 h-1 and the specific rate of nitrous oxide production was 3.64 × 10-5 +/- 1.30 × 10-5 μg N2O g DW soil-1 h-1. The methanotrophs Methylobacter and an unclassified genus within the family Methlyococcaceae were present in the original ICS samples and the incubation samples, and their abundance increased during incubations with methane. Genes encoding particulate methane monooxygenase/ ammonia monooxygenase (pMMO) were much more abundant than genes encoding soluble methane monooxygenase (sMMO) across the landfill ICS. Genes encoding proteins that convert hydroxylamine to nitrous oxide were not highly abundant in the ICS or incubation metagenomes. In total, these results suggest that although ammonia oxidation via methanotrophs may result in low levels of nitrous oxide production, ICS microbial communities have the potential to greatly reduce the overall global warming potential of landfill emissions.
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Affiliation(s)
- Peyton H Lienhart
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Venus Rohra
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Courtney Clement
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Lucinda C Toppen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States.
| | - Amy C DeCola
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Donna M Rizzo
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
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125
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Tripathy RK, Pande AH. Molecular and functional insight into anti-EGFR nanobody: Theranostic implications for malignancies. Life Sci 2024; 345:122593. [PMID: 38554946 DOI: 10.1016/j.lfs.2024.122593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Targeted therapy and imaging are the most popular techniques for the intervention and diagnosis of cancer. A potential therapeutic target for the treatment of cancer is the epidermal growth factor receptor (EGFR), primarily for glioblastoma, lung, and breast cancer. Over-production of ligand, transcriptional up-regulation due to autocrine/paracrine signalling, or point mutations at the genomic locus may contribute to the malfunction of EGFR in malignancies. This exploit makes use of EGFR, an established biomarker for cancer diagnostics and treatment. Despite considerable development in the last several decades in making EGFR inhibitors, they are still not free from limitations like toxicity and a short serum half-life. Nanobodies and antibodies share similar binding properties, but nanobodies have the additional advantage that they can bind to antigenic epitopes deep inside the target that conventional antibodies are unable to access. For targeted therapy, anti-EGFR nanobodies can be conjugated to various molecules such as drugs, peptides, toxins and photosensitizers. These nanobodies can be designed as novel immunoconjugates using the universal modular antibody-based platform technology (UniCAR). Furthermore, Anti-EGFR nanobodies can be expressed in neural stem cells and visualised by effective fluorescent and radioisotope labelling.
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Affiliation(s)
- Rajan K Tripathy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, (Mohali) 160062, Punjab, India
| | - Abhay H Pande
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, (Mohali) 160062, Punjab, India.
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126
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Qin J, Qi X, Li Y, Tang Z, Zhang X, Ru S, Xiong JQ. Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation. J Hazard Mater 2024; 470:134149. [PMID: 38554512 DOI: 10.1016/j.jhazmat.2024.134149] [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: 02/03/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.
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Affiliation(s)
- Jingyu Qin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xin Qi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yuejiao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhuyun Tang
- School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xiaona Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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127
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Shi YB, Fu L, Tanizaki Y. Intestinal remodeling during Xenopus metamorphosis as a model for studying thyroid hormone signaling and adult organogenesis. Mol Cell Endocrinol 2024; 586:112193. [PMID: 38401883 PMCID: PMC10999354 DOI: 10.1016/j.mce.2024.112193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
Intestinal development takes places in two phases, the initial formation of neonatal (mammals)/larval (anurans) intestine and its subsequent maturation into the adult form. This maturation occurs during postembryonic development when plasma thyroid hormone (T3) level peaks. In anurans such as the highly related Xenopus laevis and Xenopus tropicalis, the larval/tadpole intestine is drastically remodeled from a simple tubular structure to a complex, multi-folded adult organ during T3-dependent metamorphosis. This involved complete degeneration of larval epithelium via programmed cell death and de novo formation of adult epithelium, with concurrent maturation of the muscles and connective tissue. Here, we will summarize our current understanding of the underlying molecular mechanisms, with a focus on more recent genetic and genome-wide studies.
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Affiliation(s)
- Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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128
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Zahra N, Rafique S, Naveed Z, Nadeem J, Waqas M, Ali A, Shah M, Idrees M. Regulatory pathways and therapeutic potential of PDE4 in liver pathophysiology. Life Sci 2024; 345:122565. [PMID: 38521388 DOI: 10.1016/j.lfs.2024.122565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/25/2024]
Abstract
Phosphodiesterase 4 (PDE4), crucial in regulating the cyclic adenosine monophosphate (cAMP) signaling pathway, significantly impacts liver pathophysiology. This article highlights the comprehensive effects of PDE4 on liver health and disease, and its potential as a therapeutic agent. PDE4's role in degrading cAMP disrupts intracellular signaling, increasing pro-inflammatory cytokines like tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6). This contributes to liver inflammation in conditions such as hepatitis and non-alcoholic steatohepatitis (NASH). Additionally, PDE4 is a key factor in liver fibrosis, characterized by excessive extracellular matrix deposition. Inhibiting PDE4 shows promise in reducing liver fibrosis by decreasing the activation of hepatic stellate cells, which is pivotal in fibrogenesis. PDE4 also influences hepatocyte apoptosis a common feature of liver diseases. PDE4 inhibitors protect against hepatocyte apoptosis by raising intracellular cAMP levels, thus activating anti-apoptotic pathways. This suggests potential in targeting PDE4 to prevent hepatocyte loss. Moreover, PDE4 regulates hepatic glucose production and lipid metabolism, essential for liver function. Altering cAMP levels through PDE4 affects enzymes in these metabolic pathways, making PDE4 a target for metabolic disorders like type 2 diabetes and non-alcoholic fatty liver disease (NAFLD). Since PDE4 plays a multifaceted role in liver pathophysiology, influencing PDE4's mechanisms in liver diseases could lead to novel therapeutic strategies. Still, extensive research is required to explore the molecular mechanisms and clinical potential of targeting PDE4 in liver pathologies.
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Affiliation(s)
- Noureen Zahra
- National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.
| | - Zoya Naveed
- National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Jannat Nadeem
- National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Pakistan
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Pakistan
| | - Masaud Shah
- Department of Physiology Ajou University, South Korea
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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129
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Kong H, Luo K, Yong Z. Methacrylic acid in situ modified steel converter slag/natural rubber composites: Resourceful utilization of steelmaking solid wastes. Waste Manag 2024; 180:36-46. [PMID: 38503032 DOI: 10.1016/j.wasman.2024.03.024] [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: 09/18/2023] [Revised: 03/04/2024] [Accepted: 03/16/2024] [Indexed: 03/21/2024]
Abstract
As a by-product of the steelmaking industry, the large-volume production and accumulation of steel converter slag cause environmental issues such as land occupation and dust pollution. Since metal salts of unsaturated carboxylic acid can be used to reinforce rubber, this study explores the innovative application of in-situ modified steel slag, mainly comprising metal oxides, with methacrylic acid (MAA) as a rubber filler partially replacing carbon black. By etching the surface of steel slag particles with MAA, their surface roughness was increased, and the chemical bonding of metal methacrylate salt was introduced to enhance their interaction with the molecular chain of natural rubber (NR). The results showed that using the steel slag filler effectively shortened the vulcanization molding cycle of NR composites. The MAA in-situ modification effectively improved the interaction between steel slag and NR molecular chains. Meanwhile, the physical and mechanical properties, fatigue properties, and dynamic mechanical properties of the experimental group with MAA in-situ modified steel slag (MAA-in-situ-m-SS) were significantly enhanced compared with those of NR composites partially filled with unmodified slag. With the dosage of 7.5 phr or 10 phr, the above properties matched or even exceeded those of NR composites purely filled with carbon black. More importantly, partially replacing carbon black with modified steel slag reduced fossil fuel consumption and greenhouse gas emission from carbon black production. This study pioneered an effective path for the resourceful utilization of steel slag and the green development of the steelmaking and rubber industries.
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Affiliation(s)
- Hao Kong
- Ministry of Education/Shandong Provincial Key Laboratory of Rubber-plastics, School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Kangyu Luo
- Ministry of Education/Shandong Provincial Key Laboratory of Rubber-plastics, School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Zhanfu Yong
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China; Qingdao Automotive Research Institute, JiLin University, Qingdao 266042, PR China.
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130
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Rao C, Chu F, Fang F, Xiang D, Xian B, Liu X, Bao S, Fang T. Toxic effects and comparison of common amino antioxidants (AAOs) in the environment on zebrafish: A comprehensive analysis based on cells, embryos, and adult fish. Sci Total Environ 2024; 924:171678. [PMID: 38485016 DOI: 10.1016/j.scitotenv.2024.171678] [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: 11/28/2023] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
The ubiquity of amino antioxidants (AAOs) in the environment has attracted increasing attention, given their potential toxicity. This investigation represents a pioneering effort, systematically scrutinizing the toxicological effects of four distinct AAOs across the developmental spectrum of zebrafish, encompassing embryonic, larvae, and adult stages. The results indicate that four types of AAO exhibit varying degrees of cell proliferation toxicity. Although environmentally relevant concentrations of AAOs exhibit a comparatively circumscribed impact on zebrafish embryo development, heightened concentrations (300 μg/L) of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) and N-isopropyl-N'-phenyl-p-phenylenediamine (IPPD) distinctly evoke developmental toxicity. Behavioral analysis results indicate that at concentrations of 20 and 300 μg/L, the majority of AAOs significantly reduced the swimming speed and activity of larvae. Moreover, each AAO triggers the generation of reactive oxygen species (ROS) in larvae, instigating diverse levels of oxidative stress. The study delineates parallel toxicological patterns in zebrafish exposed to 300 μg/L of 6PPD and IPPD, thereby establishing a comparable toxicity profile. The comprehensive toxicity effects among the four AAOs is as follows: IPPD >6PPD > N-Phenyl-1-naphthylamine (PANA) > diphenylamine (DPA). These findings not only enrich our comprehension of the potential hazards associated with AAOs but also provide data support for structure-based toxicity prediction models.
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Affiliation(s)
- Chenyang Rao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fuhao Chu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fang Fang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Dongfang Xiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bo Xian
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaying Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Shaopan Bao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Tao Fang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Jia L, Gong Y, Jiang X, Fan X, Ji Z, Ma T, Li R, Liu F. Ginkgolide C inhibits ROS-mediated activation of NLRP3 inflammasome in chondrocytes to ameliorate osteoarthritis. J Ethnopharmacol 2024; 325:117887. [PMID: 38346525 DOI: 10.1016/j.jep.2024.117887] [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: 11/24/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ginkgo biloba, as the most widely available medicinal plant worldwide, has been frequently utilized for treat cardiovascular, cerebrovascular, diabetic and other diseases. Due to its distinct pharmacological effects, it has been broadly applications in pharmaceuticals, health products, dietary supplements, and so on. Ginkgolide C (GC), a prominent extract of Ginkgo biloba, possesses potential in anti-inflammatory and anti-oxidant efficacy. AIMS OF THE STUDY To determine whether GC mitigated the progressive degeneration of articular cartilage in a Monosodium Iodoacetate (MIA)-induced osteoarthritis (OA) rat model by inhibiting the activation of the NLRP3 inflammasome, and the specific underlying mechanisms. MATERIALS AND METHODS In vivo, an OA rat model was established by intra-articular injection of MIA. The protective effect of GC (10 mg/kg) on articular cartilage was evaluated. Application of ATDC5 cells to elucidate the mechanism of the protective effect of GC on articular cartilage. Specifically, the expression levels of molecules associated with cartilage ECM degrading enzymes, OS, ERS, and NLRP3 inflammasome activation were analyzed. RESULTS In vivo, GC ameliorated MIA-induced OA rat joint pain, and exhibited remarkable anti-inflammatory and anti- ECM degradation effects via inhibition of the activation of NLRP3 inflammasome, the release of inflammatory factors, and the expression of matrix-degrading enzymes in cartilage. Mechanically, GC inhibited the activation of NLRP3 inflammasome by restraining ROS-mediated p-IRE1α and activating Nrf2/NQO1 signal path, thereby alleviating OA. The ROS scavenger NAC was as effective as GC in reducing ROS production and inhibiting the activation of NLRP3 inflammasome. CONCLUSIONS GC have exerted chondroprotective effects by inhibiting the activation of NLRP3 inflammasome.
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Affiliation(s)
- Lina Jia
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Yingchao Gong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Xinru Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Xianan Fan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Zhenghua Ji
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Tianwen Ma
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Rui Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China
| | - Fangping Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, 150030, PR China.
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132
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Liu CC, Capart MMM, Lin JJ. Mismatch repair enzymes regulate telomere recombination in Saccharomycescerevisiae. Biochem Biophys Res Commun 2024; 707:149768. [PMID: 38489874 DOI: 10.1016/j.bbrc.2024.149768] [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: 02/20/2024] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
DNA mismatch repair (MMR) is a crucial mechanism that ensures chromosome stability and prevents the development of various human cancers. Apart from its role in correcting mismatches during DNA replication, MMR also plays a significant role in regulating recombination between non-identical sequences, a process known as homeologous recombination. Telomeres, the protective ends of eukaryotic chromosomes, possess sequences that are not perfectly homologous. While telomerase primarily maintains telomere length in the yeast Saccharomyces cerevisiae, recombination between telomeres becomes a major pathway for length maintenance in cells lacking telomerase. This study investigates the participation of MMR in telomere recombination. Our findings reveal that mutations in MMR genes activate type I recombination. Notably, among the MMR proteins, MutSα (Msh2 and Msh6) and MutLα (Mlh1 and Pms1) exerted the most pronounced effects on telomere recombination. We also found that yeast cells containing simple human telomeric TTAGGG DNA sequences preferentially utilize type II recombination to maintain their telomeres, highlighting the influence of the heterogeneous nature of yeast telomeric sequences on type II recombination. Furthermore, our observations indicate that MMR activity is indispensable for its impact on telomere recombination. Collectively, these results contribute to a more comprehensive understanding of the role of MMR in telomere recombination.
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Affiliation(s)
- Chia-Chun Liu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mathilde M M Capart
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jing-Jer Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan.
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Sun C, Li R, Weng S, Zhu C, Chen L, Jiang S, Li L, Xiao X, Liu C, Chen L, Deng T, Wang X, Fan X. Reduction-Tolerance Electrolyte Design for High-Energy Lithium Batteries. Angew Chem Int Ed Engl 2024; 63:e202400761. [PMID: 38497902 DOI: 10.1002/anie.202400761] [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: 01/11/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/19/2024]
Abstract
Lithium batteries employing Li or silicon (Si) anodes hold promise for the next-generation energy storage systems. However, their cycling behavior encounters rapid capacity degradation due to the vulnerability of solid electrolyte interphases (SEIs). Though anion-derived SEIs mitigate this degradation, the unavoidable reduction of solvents introduces heterogeneity to SEIs, leading to fractures during cycling. Here, we elucidate how the reductive stability of solvents, dominated by the electrophilicity (EPT) and coordination ability (CDA), delineates the SEI formed on Li or Si anodes. Solvents exhibiting lower EPT and CDA demonstrate enhanced tolerance to reduction, resulting in inorganic-rich SEIs with homogeneity. Guided by these criteria, we synthesized three promising solvents tailored for Li or Si anodes. The decomposition of these solvents is dictated by their EPTs under similar solvation structures, imparting distinct characteristics to SEIs and impacting battery performance. The optimized electrolyte, 1 M lithium bis(fluorosulfonyl)imide (LiFSI) in N-Pyrrolidine-trifluoromethanesulfonamide (TFSPY), achieves 600 cycles of Si anodes with a capacity retention of 81 % (1910 mAh g-1). In anode-free Cu||LiNi0.5Co0.2Mn0.3O2 (NCM523) pouch cells, this electrolyte sustains over 100 cycles with an 82 % capacity retention. These findings illustrate that reducing solvent decomposition benefits SEI formation, offering valuable insights for the designing electrolytes in high-energy lithium batteries.
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Affiliation(s)
- Chuangchao Sun
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ruhong Li
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Suting Weng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Chunnan Zhu
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Long Chen
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- Polytechnic Institute, Zhejiang University, Hangzhou, 310027, China
| | - Sen Jiang
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Long Li
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xuezhang Xiao
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Chengwu Liu
- Department of Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lixin Chen
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- Key Laboratory of Advanced Materials and Applications for Batteries of Zhejiang Province, Hangzhou, 310013, China
| | - Tao Deng
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 201306, China
| | - Xuefeng Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiulin Fan
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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135
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Jiang Z, Zhang C, Sun Q, Wang X, Chen Y, He W, Guo Z, Liu Z. A NIR-II Photoacoustic Probe for High Spatial Quantitative Imaging of Tumor Nitric Oxide in Vivo. Angew Chem Int Ed Engl 2024; 63:e202320072. [PMID: 38466238 DOI: 10.1002/anie.202320072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/12/2024]
Abstract
Nitric oxide (NO) exhibits both pro- and anti-tumor effects. Therefore, real-time in vivo imaging and quantification of tumor NO dynamics are essential for understanding the conflicting roles of NO played in pathophysiology. The current molecular probes, however, cannot provide high-resolution imaging in deep tissues, making them unsuitable for these purposes. Herein, we designed a photoacoustic probe with an absorption maximum beyond 1000 nm for high spatial quantitative imaging of in vivo tumor NO dynamics. The probe exhibits remarkable sensitivity, selective ratiometric response behavior, and good tumor-targeting abilities, facilitating ratiometric imaging of tumor NO throughout tumor progression in a micron-resolution level. Using the probe as the imaging agent, we successfully quantified NO dynamics in tumor, liver and kidney. We have pinpointed an essential concentration threshold of around 80 nmol/cm3 for NO, which plays a crucial role in the "double-edged-sword" function of NO in tumors. Furthermore, we revealed a reciprocal relationship between the NO concentration in tumors and that in the liver, providing initial insights into the possible NO-mediated communication between tumor and the liver. We believe that the probe will help resolve conflicting aspects of NO biology and guide the design of imaging agents for tumor diagnosis and anti-cancer drug screening.
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Affiliation(s)
- Zhiyong Jiang
- College of Materials Science and Engineering, Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Changli Zhang
- School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, China
| | - Qian Sun
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Xiaoqing Wang
- College of Materials Science and Engineering, Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
- College of Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuncong Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Weijiang He
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Zhipeng Liu
- College of Materials Science and Engineering, Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
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Chen Y, Liu J, Song T, Zou X, Li L, Nie Q, Zhang P. Gaps in forensic toxicological analysis: The veiled abrin. Toxicon 2024; 242:107684. [PMID: 38513827 DOI: 10.1016/j.toxicon.2024.107684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Abrus precatorius is an herbaceous, flowering plant that is widely distributed in tropical and subtropical regions. Its toxic component, known as abrin, is classified as one of the potentially significant biological warfare agents and bioterrorism tools due to its high toxicity. Abrin poisoning can be utilized to cause accidents, suicides, and homicides, which necessitates attention from clinicians and forensic scientists. Although a few studies have recently identified the toxicological and pharmacological mechanisms of abrin, the exact mechanism remains unclear. Furthermore, the clinical symptoms and pathological changes induced by abrin poisoning have not been fully characterized, and there is a lack of standardized methods for identifying biological samples of the toxin. Therefore, there is an urgent need for further toxicopathologic studies and the development of detection methods for abrin in the field of forensic medicine. This review provides an overview of the clinical symptoms, pathological changes, metabolic changes, toxicologic mechanisms, and detection methods of abrin poisoning from the perspective of forensic toxicology. Additionally, the evidence on abrin in the field of forensic toxicology and forensic pathology is discussed. Overall, this review serves as a reference for understanding the toxicological mechanism of abrin, highlighting the clinical applications of the toxin, and aiding in the diagnosis and forensic identification of toxin poisoning.
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Affiliation(s)
- Yinyu Chen
- Department of Forensic Medicine, Hainan Provincial Academician Workstation (tropical forensic medicine), Hainan Provincial Tropical Forensic Engineering Research Center, Hainan Medical University, Haikou, 571199, China
| | - Jiaqi Liu
- Department of Neurology, the First Affiliated Hospital, International School of Public Health and One Health, Hainan Medical University, Haikou, 570102, China
| | - Tao Song
- Department of Forensic Medicine, Hainan Provincial Academician Workstation (tropical forensic medicine), Hainan Provincial Tropical Forensic Engineering Research Center, Hainan Medical University, Haikou, 571199, China
| | - Xing Zou
- Department of Forensic Medicine, Hainan Provincial Academician Workstation (tropical forensic medicine), Hainan Provincial Tropical Forensic Engineering Research Center, Hainan Medical University, Haikou, 571199, China
| | - Leilei Li
- Department of Forensic Medicine, Hainan Provincial Academician Workstation (tropical forensic medicine), Hainan Provincial Tropical Forensic Engineering Research Center, Hainan Medical University, Haikou, 571199, China
| | - Qianyun Nie
- Department of Pathology, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China; Department of Pathology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, China.
| | - Peng Zhang
- Department of Forensic Medicine, Hainan Provincial Academician Workstation (tropical forensic medicine), Hainan Provincial Tropical Forensic Engineering Research Center, Hainan Medical University, Haikou, 571199, China.
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137
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Xiao T, English AM, Wilson ZN, Maschek J, Cox JE, Hughes AL. The phospholipids cardiolipin and phosphatidylethanolamine differentially regulate MDC biogenesis. J Cell Biol 2024; 223:e202302069. [PMID: 38497895 PMCID: PMC10949074 DOI: 10.1083/jcb.202302069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Cells utilize multiple mechanisms to maintain mitochondrial homeostasis. We recently characterized a pathway that remodels mitochondria in response to metabolic alterations and protein overload stress. This remodeling occurs via the formation of large membranous structures from the mitochondrial outer membrane called mitochondrial-derived compartments (MDCs), which are eventually released from mitochondria and degraded. Here, we conducted a microscopy-based screen in budding yeast to identify factors that regulate MDC formation. We found that two phospholipids, cardiolipin (CL) and phosphatidylethanolamine (PE), differentially regulate MDC biogenesis. CL depletion impairs MDC biogenesis, whereas blocking mitochondrial PE production leads to constitutive MDC formation. Additionally, in response to metabolic MDC activators, cellular and mitochondrial PE declines, and overexpressing mitochondrial PE synthesis enzymes suppress MDC biogenesis. Altogether, our data indicate a requirement for CL in MDC biogenesis and suggest that PE depletion may stimulate MDC formation downstream of MDC-inducing metabolic stress.
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Affiliation(s)
- Tianyao Xiao
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alyssa M. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Zachary N. Wilson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - J.Alan. Maschek
- Metabolomics Core Research Facility, University of Utah, Salt Lake City, UT, USA
- Department of Nutrition and Integration. Physiology, University of Utah College of Health, Salt Lake City, UT, USA
| | - James E. Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Metabolomics Core Research Facility, University of Utah, Salt Lake City, UT, USA
| | - Adam L. Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
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Li H, Han X, Song L, Li X, Zhang L, Jin Z, Zhang Y, Wang T, Huang Z, Jia Z, Yang J. LINC00645 inhibits renal cell carcinoma progression by interacting with HNRNPA2B1 to regulate the ROCK1 mRNA stability. Gene 2024; 905:148232. [PMID: 38309317 DOI: 10.1016/j.gene.2024.148232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
The lncRNA plays an important role in tumorigenesis and the progression of renal cell carcinoma (RCC). LINC00645 is one of the most different expressed lncRNA between RCC and normal renal tissue. However, the regulatory mechanism of LINC00645 in RCC remains unknown. Our results indicated that LINC00645 inhibited RCC proliferation, migration, and invasion. Mechanistically, HNRNPA2B1 directly bound to ROCK1 mRNA and strengthened its stability. LINC00645 competitively bound to the RRM1 domain, which is responsible for interacting with ROCK1 mRNA, reducing ROCK1 mRNA level by affecting posttranscriptional destabilization. The expression of LINC00645 was significantly reduced in RCC cells, significantly upregulating ROCK1 by abolishing the interaction with HNRNPA2B1, finally promoting RCC proliferation, migration, and invasion. Moreover, RCC cells with lower LINC00645 expression were more sensitive to the ROCK1 inhibitor Y-27632. Our study indicates that decreased expression of LINC00645 promotes the RCC progression via HNRNPA2B1/ROCK1 axis, providing a promising treatment strategy for RCC patients with decreased LINC00645 expression.
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Affiliation(s)
- Hao Li
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Xu Han
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Liang Song
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Xiang Li
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Liwei Zhang
- Department of Vascular and Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Zhibo Jin
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Yu Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Tao Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Zhenlin Huang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.
| | - Zhankui Jia
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.
| | - Jinjian Yang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.
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Yadav A, Dabur R. Skeletal muscle atrophy after sciatic nerve damage: Mechanistic insights. Eur J Pharmacol 2024; 970:176506. [PMID: 38492879 DOI: 10.1016/j.ejphar.2024.176506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024]
Abstract
Sciatic nerve injury leads to molecular events that cause muscular dysfunction advancement in atrophic conditions. Nerve damage renders muscles permanently relaxed which elevates intracellular resting Ca2+ levels. Increased Ca2+ levels are associated with several cellular signaling pathways including AMPK, cGMP, PLC-β, CERB, and calcineurin. Also, multiple enzymes involved in the tricarboxylic acid cycle and oxidative phosphorylation are activated by Ca2+ influx into mitochondria during muscle contraction, to meet increased ATP demand. Nerve damage induces mitophagy and skeletal muscle atrophy through increased sensitivity to Ca2+-induced opening of the permeability transition pore (PTP) in mitochondria attributed to Ca2+, ROS, and AMPK overload in muscle. Activated AMPK interacts negatively with Akt/mTOR is a highly prevalent and well-described central pathway for anabolic processes. Over the decade several reports indicate abnormal behavior of signaling machinery involved in denervation-induced muscle loss but end up with some controversial outcomes. Therefore, understanding how the synthesis and inhibitory stimuli interact with cellular signaling to control muscle mass and morphology may lead to new pharmacological insights toward understanding the underlying mechanism of muscle loss after sciatic nerve damage. Hence, the present review summarizes the existing literature on denervation-induced muscle atrophy to evaluate the regulation and expression of differential regulators during sciatic damage.
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Affiliation(s)
- Aarti Yadav
- Clinical Biochemistry Laboratory, Department of Biochemistry, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Rajesh Dabur
- Clinical Biochemistry Laboratory, Department of Biochemistry, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
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Hussain S, Mursal M, Verma G, Hasan SM, Khan MF. Targeting oncogenic kinases: Insights on FDA approved tyrosine kinase inhibitors. Eur J Pharmacol 2024; 970:176484. [PMID: 38467235 DOI: 10.1016/j.ejphar.2024.176484] [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: 09/24/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
Protein kinases play pivotal roles in various biological functions, influencing cell differentiation, promoting survival, and regulating the cell cycle. The disruption of protein kinase activity is intricately linked to pathways in tumor development. This manuscript explores the transformative impact of protein kinase inhibitors on cancer therapy, particularly their efficacy in cases driven by targeted mutations. Focusing on key tyrosine kinase inhibitors (TKIs) like Bcr-Abl, Epidermal Growth Factor Receptor (EGFR), and Vascular Endothelial Growth Factor Receptor (VEGFR), it targets critical kinase families in cancer progression. Clinical trial details of these TKIs offer insights into their therapeutic potentials. Learning from FDA-approved kinase inhibitors, the review dissects trends in kinase drug development since imatinib's paradigm-shifting approval in 2001. TKIs have evolved into pivotal drugs, extending beyond oncology. Ongoing clinical trials explore novel kinase targets, revealing the vast potential within the human kinome. The manuscript provides a detailed analysis of advancements until 2022, discussing the roles of specific oncogenic protein kinases in cancer development and carcinogenesis. Our exploration on PubMed for relevant and significant TKIs undergoing pre-FDA approval phase III clinical trials enriches the discussion with valuable findings. While kinase inhibitors exhibit lower toxicity than traditional chemotherapy in cancer treatment, challenges like resistance and side effects emphasize the necessity of understanding resistance mechanisms, prompting the development of novel inhibitors like osimertinib targeting specific mutant proteins. The review advocates thorough research on effective combination therapies, highlighting the future development of more selective RTKIs to optimize patient-specific cancer treatment and reduce adverse events.
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Affiliation(s)
- Sahil Hussain
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India
| | - Mohd Mursal
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India
| | - Garima Verma
- RWE Specialist, HealthPlix Technologies, Bengaluru, Karnataka 560103, India
| | - Syed Misbahul Hasan
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India
| | - Mohemmed Faraz Khan
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India.
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141
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Panda SP, Kesharwani A, Datta S, Prasanth DSNBK, Panda SK, Guru A. JAK2/STAT3 as a new potential target to manage neurodegenerative diseases: An interactive review. Eur J Pharmacol 2024; 970:176490. [PMID: 38492876 DOI: 10.1016/j.ejphar.2024.176490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Neurodegenerative diseases (NDDs) are a collection of incapacitating disorders in which neuroinflammation and neuronal apoptosis are major pathological consequences due to oxidative stress. Neuroinflammation manifests in the impacted cerebral areas as a result of pro-inflammatory cytokines stimulating the Janus Kinase2 (JAK2)/Signal Transducers and Activators of Transcription3 (STAT3) pathway via neuronal cells. The pro-inflammatory cytokines bind to their respective receptor in the neuronal cells and allow activation of JAK2. Activated JAK2 phosphorylates tyrosines on the intracellular domains of the receptor which recruit the STAT3 transcription factor. The neuroinflammation issues are exacerbated by the active JAK2/STAT3 signaling pathway in conjunction with additional transcription factors like nuclear factor kappa B (NF-κB), and the mammalian target of rapamycin (mTOR). Neuronal apoptosis is a natural process made worse by persistent neuroinflammation and immunological responses via caspase-3 activation. The dysregulation of micro-RNA (miR) expression has been observed in the consequences of neuroinflammation and neuronal apoptosis. Neuroinflammation and neuronal apoptosis-associated gene amplification may be caused by dysregulated miR-mediated aberrant phosphorylation of JAK2/STAT3 signaling pathway components. Therefore, JAK2/STAT3 is an attractive therapeutic target for NDDs. Numerous synthetic and natural small molecules as JAK2/STAT3 inhibitors have therapeutic advances against a wide range of diseases, and many are now in human clinical studies. This review explored the interactive role of the JAK2/STAT3 signaling system with key pathological factors during the reinforcement of NDDs. Also, the clinical trial data provides reasoning evidence about the possible use of JAK2/STAT3 inhibitors to abate neuroinflammation and neuronal apoptosis in NDDs.
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Affiliation(s)
- Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India.
| | - Adarsh Kesharwani
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Samaresh Datta
- Department of Pharmaceutical Chemistry, Birbhum Pharmacy School, Sadaipur, Birbhum, West Bengal, India
| | - D S N B K Prasanth
- School of Pharmacy and Technology Management, SVKM's Narsee Monjee Institute of Management Studies (NMIMS), Polepally SEZ, TSIIC, Jadcherla, Mahbubnagar, Hyderabad, 509301, India
| | | | - Ajay Guru
- Department of Cariology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
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142
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Ru YX, Dong SX, Liu J, Liu JH, Zhou Y, Eyden B. Malformation of the endoplasmic reticulum system evolving into giant inclusions and Auer bodies in acute promyelocytic leukemia: an ultrastructural study of 6 cases. Ultrastruct Pathol 2024; 48:221-233. [PMID: 38619116 DOI: 10.1080/01913123.2024.2340965] [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: 02/10/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
The endoplasmic reticulum(ER)is the largest membranous network serving as a region for protein, lipid and steroid synthesis, transport and storage. Detailed information about ER-cisternae, ER-tubules and rough endoplasmic reticulum (rER) is scarce in human blood cells. This study describes a series of giant inclusions and Auer bodies in promyeloblasts in six patients with acute promyelocytic leukemia (APL), by light microscopy, transmission electron microscopy (TEM) and cytochemical stains. TEM revealed that giant inclusions and pro-Auer bodies were associated with rER and surrounded by tubular structures composed of degenerated or redundant membrane in promyeloblasts, which corresponded with elements of the ER system. This paper reveals that in the promyeloblasts of APL, ER is the source of and transforms progressively into giant inclusions and Auer bodies.
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Affiliation(s)
- Yong-Xin Ru
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Shu-Xu Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jing Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jin-Hua Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yuan Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of the Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Brian Eyden
- Department of Histopathology, Christie NHS Foundation Trust, Manchester, UK
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143
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Wei L, Dankwa S, Vijayan K, Smith JD, Kaushansky A. Interrogating endothelial barrier regulation by temporally resolved kinase network generation. Life Sci Alliance 2024; 7:e202302522. [PMID: 38467420 PMCID: PMC10927359 DOI: 10.26508/lsa.202302522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Kinases are key players in endothelial barrier regulation, yet their temporal function and regulatory phosphosignaling networks are incompletely understood. We developed a novel methodology, Temporally REsolved KInase Network Generation (TREKING), which combines a 28-kinase inhibitor screen with machine learning and network reconstruction to build time-resolved, functional phosphosignaling networks. We demonstrated the utility of TREKING for identifying pathways mediating barrier integrity after activation by thrombin with or without TNF preconditioning in brain endothelial cells. TREKING predicted over 100 kinases involved in barrier regulation and discerned complex condition-specific pathways. For instance, the MAPK-activated protein kinase 2 (MAPKAPK2/MK2) had early barrier-weakening activity in both inflammatory conditions but late barrier-strengthening activity exclusively with thrombin alone. Using temporal Western blotting, we confirmed that MAPKAPK2/MK2 was differentially phosphorylated under the two inflammatory conditions. We further showed with lentivirus-mediated knockdown of MAPK14/p38α and drug targeting the MAPK14/p38α-MAPKAPK2/MK2 complex that a MAP3K20/ZAK-MAPK14/p38α axis controlled the late activation of MAPKAPK2/MK2 in the thrombin-alone condition. Beyond the MAPKAPK2/MK2 switch, TREKING predicts extensive interconnected networks that control endothelial barrier dynamics.
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Affiliation(s)
- Ling Wei
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Selasi Dankwa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kamalakannan Vijayan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Joseph D Smith
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
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144
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Langeland J, Lindkvist TT, Kjær C, Nielsen SB. Gas-phase Förster resonance energy transfer in mass-selected and trapped ions. Mass Spectrometry Reviews 2024; 43:477-499. [PMID: 36514825 DOI: 10.1002/mas.21828] [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] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Förster Resonance Energy transfer (FRET) is a nonradiative process that may occur from an electronically excited donor to an acceptor when the emission spectrum of the donor overlaps with the absorption spectrum of the acceptor. FRET experiments have been done in the gas phase based on specially designed mass-spectroscopy setups with the goal to obtain structural information on biomolecular ions labeled with a FRET pair (i.e., donor and acceptor dyes) and to shed light on the energy-transfer process itself. Ions are accumulated in a radio-frequency ion trap or a Penning trap where mass selection of those of interest takes place, followed by photoexcitation. Gas-phase FRET is identified from detection of emitted light either from the donor, the acceptor, or both, or from a fragmentation channel that is specific to the acceptor when electronically excited. The challenge associated with the first approach is the collection and detection of photons emitted from a thin ion cloud that is not easily accessible while the second approach relies both on the photophysical and chemical behavior of the acceptor. In this review, we present the different instrumentation used for gas-phase FRET, including a discussion of advantages and disadvantages, and examples on how the technique has provided important structural information that is not easily obtainable otherwise. Furthermore, we describe how the spectroscopic properties of the dyes are affected by nearby electric fields, which is readily discernable from experiments on simple model systems with alkyl or π-conjugated bridges. Such spectral changes can have a significant effect on the FRET efficiency. Ideas for new directions are presented at the end with special focus on cold-ion spectroscopy.
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Affiliation(s)
- Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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145
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Ringo JM, Segal D. Altered Grooming Cycles in Transgenic Drosophila. Behav Genet 2024; 54:290-301. [PMID: 38536593 DOI: 10.1007/s10519-024-10180-3] [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: 09/27/2023] [Accepted: 03/14/2024] [Indexed: 04/21/2024]
Abstract
Head grooming in Drosophila consists of repeated sweeps of the legs across the head, comprising regular cycles. We used the GAL4-UAS system to study the effects of overexpressing shibirets1 and of Adar knockdown via RNA interference, on the period of head-grooming cycles in Drosophila. Overexpressing shibirets1 interferes with synaptic vesicle recycling and thus with cell communication, while Adar knockdown reduces RNA editing of neuronal transcripts for a large number of genes. All transgenic flies and their controls were tested at 22° to avoid temperature effects; in wild type, cycle frequency varied with temperature with a Q10 of 1.3. Two experiments were performed with transgenic shibirets1: (1) each fly was heat-shocked for 10 min at 30° immediately before testing at 22° and (2) flies were not heat shocked. In both experiments, cycle period was increased when shibirets1 was overexpressed in all neurons, but was not increased when shibirets1 was overexpressed in motoneurons alone. We hypothesize that grooming cycles in flies overexpressing shibirets1 are lengthened because of synaptic impairment in neural circuits that control head-grooming cycles. In flies with constitutive, pan-neuronal Adar knockdown, cycle period was more variable within individuals, but mean cycle period was not significantly altered. We conclude that RNA editing is essential for the maintenance of within-individual stereotypy of head-grooming cycles.
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Affiliation(s)
- John M Ringo
- School of Biology and Ecology, University of Maine, Orono, ME, 04473, USA.
| | - Daniel Segal
- Shmunis School of Biomedicine and Cancer Research, Sagol School of Neuroscience, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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146
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Madrazo N, Khattar Z, Powers ET, Rosarda JD, Wiseman RL. Mapping stress-responsive signaling pathways induced by mitochondrial proteostasis perturbations. Mol Biol Cell 2024; 35:ar74. [PMID: 38536439 DOI: 10.1091/mbc.e24-01-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
Imbalances in mitochondrial proteostasis are associated with pathologic mitochondrial dysfunction implicated in etiologically diverse diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria in response to mitochondrial stress. Numerous stress-responsive signaling pathways have been suggested to regulate mitochondria in response to proteotoxic stress. These include the integrated stress response (ISR), the heat shock response (HSR), and the oxidative stress response (OSR). Here, we define the stress signaling pathways activated in response to chronic mitochondrial proteostasis perturbations by monitoring the expression of sets of genes regulated downstream of each of these signaling pathways in published Perturb-seq datasets from K562 cells CRISPRi-depleted of mitochondrial proteostasis factors. Interestingly, we find that the ISR is preferentially activated in response to chronic, genetically-induced mitochondrial proteostasis stress, with no other pathway showing significant activation. Further, we demonstrate that CRISPRi depletion of other mitochondria-localized proteins similarly shows preferential activation of the ISR relative to other stress-responsive signaling pathways. These results both establish our gene set profiling approach as a viable strategy to probe stress responsive signaling pathways induced by perturbations to specific organelles and identify the ISR as the predominant stress-responsive signaling pathway activated in response to chronic disruption of mitochondrial proteostasis.
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Affiliation(s)
- Nicole Madrazo
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
| | - Zinia Khattar
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
- Del Norte High School, San Diego, CA 92127
| | - Evan T Powers
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
| | - Jessica D Rosarda
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - R Luke Wiseman
- Department of Molecular and Cellular Biology, Scripps Research, La Jolla, CA 92037
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147
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Maharjan S, Ma C, Singh B, Kang H, Orive G, Yao J, Shrike Zhang Y. Advanced 3D imaging and organoid bioprinting for biomedical research and therapeutic applications. Adv Drug Deliv Rev 2024; 208:115237. [PMID: 38447931 PMCID: PMC11031334 DOI: 10.1016/j.addr.2024.115237] [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: 11/08/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Organoid cultures offer a valuable platform for studying organ-level biology, allowing for a closer mimicry of human physiology compared to traditional two-dimensional cell culture systems or non-primate animal models. While many organoid cultures use cell aggregates or decellularized extracellular matrices as scaffolds, they often lack precise biochemical and biophysical microenvironments. In contrast, three-dimensional (3D) bioprinting allows precise placement of organoids or spheroids, providing enhanced spatial control and facilitating the direct fusion for the formation of large-scale functional tissues in vitro. In addition, 3D bioprinting enables fine tuning of biochemical and biophysical cues to support organoid development and maturation. With advances in the organoid technology and its potential applications across diverse research fields such as cell biology, developmental biology, disease pathology, precision medicine, drug toxicology, and tissue engineering, organoid imaging has become a crucial aspect of physiological and pathological studies. This review highlights the recent advancements in imaging technologies that have significantly contributed to organoid research. Additionally, we discuss various bioprinting techniques, emphasizing their applications in organoid bioprinting. Integrating 3D imaging tools into a bioprinting platform allows real-time visualization while facilitating quality control, optimization, and comprehensive bioprinting assessment. Similarly, combining imaging technologies with organoid bioprinting can provide valuable insights into tissue formation, maturation, functions, and therapeutic responses. This approach not only improves the reproducibility of physiologically relevant tissues but also enhances understanding of complex biological processes. Thus, careful selection of bioprinting modalities, coupled with appropriate imaging techniques, holds the potential to create a versatile platform capable of addressing existing challenges and harnessing opportunities in these rapidly evolving fields.
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Affiliation(s)
- Sushila Maharjan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Bibhor Singh
- Winthrop L. Chenery Upper Elementary School, Belmont, MA 02478, USA
| | - Heemin Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea; College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gorka Orive
- NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN). Vitoria-Gasteiz, Spain; University Institute for Regenerative Medicine and Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, 01007, Spain; Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
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148
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Pawlak P, Lipinska P, Sell-Kubiak E, Kajdasz A, Derebecka N, Warzych E. Energy metabolism disorders during in vitro maturation of bovine cumulus-oocyte complexes interfere with blastocyst quality and metabolism. Dev Biol 2024; 509:51-58. [PMID: 38342400 DOI: 10.1016/j.ydbio.2024.02.004] [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: 09/18/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 02/13/2024]
Abstract
Glucose and fatty acids (FA) metabolism disturbances during oocyte in vitro maturation (IVM) affect their metabolism and surrounding cumulus cells, but only inhibition of glucose metabolism decreases embryo culture efficiency. Therefore, the present experiment aimed to reveal if glucose or FA metabolism inhibition leads to the disruption of embryo developmental potential, and to characterize the metabolic landscape of embryos reaching the blastocyst stage. Inhibitors of glucose (IO + DHEA) or FA (ETOMOXIR) metabolism were applied during IVM, and the control group was matured under standard conditions. Blastocysts obtained from experimental and control groups were analyzed with regard to lipidome and metabolome (mass spectrometry), transcriptome (RNA-Seq) and fluorescence lipid droplets staining (BODIPY). We showed that inhibition of glucose and fatty acid metabolism leads to cellular stress response compromising the quality of preimplantation embryos. The inhibition of energy metabolism affects membrane fluidity as well as downregulates fatty acids biosynthesis and gene expression of trophectoderm cell line markers. Therefore, we conclude that oocyte maturation environment exerts a substantial effect on preimplantation development programming at cellular and molecular levels.
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Affiliation(s)
- Piotr Pawlak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Paulina Lipinska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Ewa Sell-Kubiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Arkadiusz Kajdasz
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Ewelina Warzych
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
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149
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Umegawa Y, Kato S, Seo S, Shinoda W, Kawatake S, Matsuoka S, Murata M. Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Biophys Chem 2024; 308:107204. [PMID: 38412762 DOI: 10.1016/j.bpc.2024.107204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.
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Affiliation(s)
- Yuichi Umegawa
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Sho Kato
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Division of Supercomputing, Korea Institute of Science and Technology Information, 245 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1, Tsushima-naka, Okayama 700-8530, Japan
| | - Satoshi Kawatake
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST-ERATO, Lipid Active Structure Project, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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150
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Cui H, Li J, Li X, Su T, Wen P, Wang C, Deng X, Fu Y, Zhao W, Li C, Hua P, Zhu Y, Wan W. TNF-α promotes osteocyte necroptosis by upregulating TLR4 in postmenopausal osteoporosis. Bone 2024; 182:117050. [PMID: 38367924 DOI: 10.1016/j.bone.2024.117050] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Postmenopausal osteoporosis (PMOP) is a common kind of osteoporosis that is associated with excessive osteocyte death and bone loss. Previous studies have shown that TNF-α-induced osteocyte necroptosis might exert a stronger effect on PMOP than apoptosis, and TLR4 can also induce cell necroptosis, as confirmed by recent studies. However, little is known about the relationship between TNF-α-induced osteocyte necroptosis and TLR4. In the present study, we showed that TNF-α increased the expression of TLR4, which promoted osteocyte necroptosis in PMOP. In patients with PMOP, TLR4 was highly expressed at skeletal sites where exists osteocyte necroptosis, and high TLR4 expression is correlated with enhanced TNF-α expression. Osteocytes exhibited robust TLR4 expression upon exposure to necroptotic osteocytes in vivo and in vitro. Western blotting and immunofluorescence analyses demonstrated that TNF-α upregulated TLR4 expression in vitro, which might further promote osteocyte necroptosis. Furthermore, inhibition of TLR4 by TAK-242 in vitro effectively blocked osteocyte necroptosis induced by TNF-α. Collectively, these results suggest a novel TLR4-mediated process of osteocyte necroptosis, which might increase osteocyte death and bone loss in the process of PMOP.
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Affiliation(s)
- Hongwang Cui
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China.
| | - Ji Li
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Xiangtao Li
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Tian Su
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Peng Wen
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Chuanling Wang
- Department of Nephrology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Xiaozhong Deng
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Yonghua Fu
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Weijie Zhao
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Changjia Li
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Pengbing Hua
- Department of Emergency Surgery Trauma Medicine Center, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
| | - Yongjun Zhu
- Department of Nephrology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, China.
| | - Wei Wan
- Department of Orthorpedic Oncology, The Second Affiliated Hospital of Naval Medical University, 415 Fengyang Road, Shanghai 200003, China.
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