151
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Shukla K, Idanwekhai K, Naradikian M, Ting S, Schoenberger SP, Brunk E. Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation. J Chem Inf Model 2024. [PMID: 38635316 DOI: 10.1021/acs.jcim.3c01967] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Research in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants of unknown significance (VUS). Bioinformatic analyses can successfully reveal rare variants and variants with clear associations with disease-related phenotypes. These studies have had a significant impact on how clinical genetic screens are interpreted and how patients are stratified for treatment. There are few, if any, computational methods for variants comparable to biological activity predictions. To address this gap, we developed a machine learning method that uses protein three-dimensional structures from AlphaFold to predict how a variant will influence changes to a gene's downstream biological pathways. We trained state-of-the-art machine learning classifiers to predict which protein regions will most likely impact transcriptional activities of two proto-oncogenes, nuclear factor erythroid 2 (NFE2L2)-related factor 2 (NRF2) and c-Myc. We have identified classifiers that attain accuracies higher than 80%, which have allowed us to identify a set of key protein regions that lead to significant perturbations in c-Myc or NRF2 transcriptional pathway activities.
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Affiliation(s)
- Kriti Shukla
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
| | - Kelvin Idanwekhai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
| | - Martin Naradikian
- La Jolla Institute for Immunology, San Diego, California 92093, United States
| | - Stephanie Ting
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
| | | | - Elizabeth Brunk
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Integrative Program for Biological and Genome Sciences (IBGS), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516, United States
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152
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Matveyenka M, Zhaliazka K, Kurouski D. Macrophages and Natural Killers Degrade α-Synuclein Aggregates. Mol Pharm 2024. [PMID: 38635186 DOI: 10.1021/acs.molpharmaceut.4c00160] [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] [Indexed: 04/19/2024]
Abstract
Amyloid oligomers and fibrils are protein aggregates that exert a high cell toxicity. Efficient degradation of these protein aggregates can minimize the spread and progression of neurodegeneration. In this study, we investigate the properties of natural killer (NK) cells and macrophages in the degradation of α-synuclein (α-Syn) aggregates grown in a lipid-free environment and in the presence of phosphatidylserine and cholesterol (PS/Cho), which are lipids that are directly associated with the onset and progression of Parkinson's disease. We found that both types of α-Syn aggregates were endocytosed by neurons, which caused strong damage to cell endosomes. Our results also indicated that PS/Cho vesicles drastically increased the toxicity of α-Syn fibrils formed in their presence compared to the toxicity of α-Syn aggregates grown in a lipid-free environment. Both NK cells and macrophages were able to degrade α-Syn and α-Syn/Cho monomers, oligomers, and fibrils. Quantitative analysis of protein degradation showed that macrophages demonstrated substantially more efficient internalization and degradation of amyloid aggregates in comparison to NK cells. We also found that amyloid aggregates induced the proliferation of macrophages and NK cells and significantly changed the expression of their cytokines and chemokines.
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Affiliation(s)
- Mikhail Matveyenka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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153
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Quiniou G, Andromaque L, Duclaux-Loras R, Dinet O, Cervantes O, Verdet M, Meunier C, Boschetti G, Viret C, Nancey S, Faure M, Rozières A. Impaired reprogramming of the autophagy flux in maturing dendritic cells from crohn disease patients with core autophagy gene-related polymorphisms. Autophagy 2024:1-17. [PMID: 38615686 DOI: 10.1080/15548627.2024.2338574] [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: 03/02/2023] [Accepted: 03/29/2024] [Indexed: 04/16/2024] Open
Abstract
Crohn disease (CD) is an inflammatory bowel disease whose pathogenesis involves inappropriate immune responses toward gut microbiota on genetically predisposed backgrounds. Notably, CD is associated with single-nucleotide polymorphisms affecting several genes involved in macroautophagy/autophagy, the catabolic process that ensures the degradation and recycling of cytosolic components and microorganisms. In a clinical translation perspective, monitoring the autophagic activity of CD patients will require some knowledge on the intrinsic functional status of autophagy. Here, we focused on monocyte-derived dendritic cells (DCs) to characterize the intrinsic quantitative features of the autophagy flux. Starting with DCs from healthy donors, we documented a reprogramming of the steady state flux during the transition from the immature to mature status: both the autophagosome pool size and the flux were diminished at the mature stage while the autophagosome turnover remained stable. At the cohort level, DCs from CD patients were comparable to control in term of autophagy flux reprogramming capacity. However, the homozygous presence of ATG16L1 rs2241880 A>G (T300A) and ULK1 rs12303764 (G/T) polymorphisms abolished the capacity of CD patient DCs to reprogram their autophagy flux during maturation. This effect was not seen in the case of CD patients heterozygous for these polymorphisms, revealing a gene dose dependency effect. In contrast, the NOD2 rs2066844 c.2104C>T (R702W) polymorphism did not alter the flux reprogramming capacity of DCs. The data, opening new clinical translation perspectives, indicate that polymorphisms affecting autophagy-related genes can differentially influence the capacity of DCs to reprogram their steady state autophagy flux when exposed to proinflammatory challenges.Abbreviation: BAFA1: bafilomycin A1, CD: Crohn disease; DC: dendritic cells; HD: healthy donor; iDCs: immature DCs; IL: interleukin; J: autophagosome flux; LPS: lipopolysaccharide; MHC: major histocompatibility complex; nA: autophagosome pool size; SNPs: single-nucleotide polymorphisms; PCA: principal component analysis; TLR: toll like receptor; τ: transition time; TNF: tumor necrosis factor.
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Affiliation(s)
- Gaëlle Quiniou
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Leslie Andromaque
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Rémi Duclaux-Loras
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Pediatric Hepatology, Gastroenterology and Nutrition, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Bron, France
| | - Océane Dinet
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Ornella Cervantes
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Mallorie Verdet
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Camille Meunier
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Lyon, France
| | - Gilles Boschetti
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Lyon, France
| | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Stéphane Nancey
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Lyon, France
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
- Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM, France
| | - Aurore Rozières
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
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154
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Quapp W, Bofill JM. Theory and Examples of Catch Bonds. J Phys Chem B 2024. [PMID: 38634732 DOI: 10.1021/acs.jpcb.4c00468] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
We discuss slip bonds, catch bonds, and the tug-of-war mechanism using mathematical arguments. The aim is to explain the theoretical tool of molecular potential energy surfaces (PESs). For this, we propose simple 2-dimensional surface models to demonstrate how a molecule under an external force behaves. Examples are selectins. Catch bonds, in particular, are explained in more detail, and they are contrasted to slip bonds. We can support special two-dimensional molecular PESs for E- and L-selectin which allow the catch bond property. We demonstrate that Newton trajectories (NT) are powerful tools to describe these phenomena. NTs form the theoretical background of mechanochemistry.
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Affiliation(s)
- Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig, PF 100920, Leipzig D-04009, Germany
| | - Josep Maria Bofill
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
- Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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155
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Ma T, Tan JR, Lu JY, Li S, Zhang Y. S-acylation of YKT61 modulates its unconventional participation in the formation of SNARE complexes in Arabidopsis. J Genet Genomics 2024:S1673-8527(24)00077-8. [PMID: 38642801 DOI: 10.1016/j.jgg.2024.04.007] [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: 02/02/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/22/2024]
Abstract
Hetero-tetrameric soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) complexes are critical for vesicle-target membrane fusion within the endomembrane system of eukaryotic cells. SNARE assembly involves four different SNARE motifs, Qa, Qb, Qc, and R, provided by three or four SNARE proteins. YKT6 is an atypical R-SNARE that lacks a transmembrane domain and is involved in multiple vesicle-target membrane fusions. Although YKT6 is evolutionarily conserved and essential, its function and regulation in different phyla seem distinct. Arabidopsis YKT61, the yeast and metazoan YKT6 homolog, is essential for gametophytic development, plays a critical role in sporophytic cells, and mediates multiple vesicle-target membrane fusion. However, its molecular regulation is unclear. We report here that YKT61 is S-acylated. Abolishing its S-acylation by a C195S mutation dissociates YKT61 from endomembrane structures and causes its functional loss. Although interacting with various SNARE proteins, YKT61 functions not as a canonical R-SNARE but coordinates with other R-SNAREs to participates in the formation of SNARE complexes. Phylum-specific molecular regulation of YKT6 may be evolved to allow more efficient SNARE-assembly in different eukaryotic cells.
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Affiliation(s)
- Ting Ma
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Jun-Ru Tan
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jin-Yu Lu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Sha Li
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yan Zhang
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China.
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156
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Yadav K, Vijayalakshmi R, Kumar Sahu K, Sure P, Chahal K, Yadav R, Sucheta, Dubey A, Jha M, Pradhan M. Exosome-Based Macromolecular neurotherapeutic drug delivery approaches in overcoming the Blood-Brain barrier for treating brain disorders. Eur J Pharm Biopharm 2024:114298. [PMID: 38642716 DOI: 10.1016/j.ejpb.2024.114298] [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: 02/03/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Delivering drugs to the brain is a complex challenge in medical research, particularly for disorders like Alzheimer's and Parkinson's. The blood-brain barrier restricts the entry of many therapeutic molecules, hindering their effectiveness. Nanoparticles, a potential solution, face issues like toxicity and limited approvals. A new avenue explores the use of small extracellular vesicles (sEVs), i.e., exosomes, as natural carriers for drug delivery. sEVs, tiny structures below 150 nm, show promise due to their minimal immune response and ability to precisely deliver drugs. This review focuses on the potential of sEVs-based drug delivery systems for treating neurological disorders, brain cancers, and other brain-related issues. Notably, bioengineered sEVs-carrying therapeutic compounds exhibit promise in early studies. The unique features of sEVs, such as their small size and natural properties, position them as candidates to overcome challenges in drug delivery to the brain. Ongoing clinical trials and research into sEVs behavior within the body further highlight their potential for revolutionizing drug delivery and addressing complex brain conditions.
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Affiliation(s)
- Krishna Yadav
- Raipur Institute of Pharmaceutical Education and Research, Sarona, Raipur, Chhattisgarh 492010, India
| | - R Vijayalakshmi
- Department of Pharmaceutical Analysis, GIET School of Pharmacy, Chaitanya Knowledge City, Rajahmundry, AP, 533296, India
| | - Kantrol Kumar Sahu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Pavani Sure
- Department of Pharmaceutics, Vignan Institute of Pharmaceutical Sciences, Hyderabad, Telangana, India
| | - Kavita Chahal
- Department of Botany, Government Model Science College Jabalpur, Madhya Pradesh, India
| | - Renu Yadav
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana, 122103, India
| | - Sucheta
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana, 122103, India
| | - Akhilesh Dubey
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics, Mangaluru 575018, Karnataka, India
| | - Megha Jha
- Department of Life Science, Mansarovar Global University, Sehore, M.P., India
| | - Madhulika Pradhan
- Gracious College of Pharmacy, Abhanpur, Chhattisgarh, 493661, India.
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157
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Jiang L, Wan Y, Pan J, Mao X, Sun X, Zan L, Wang H. Transcriptomic analysis reveals the inhibitory effect of beta-sitosterol on proliferation of bovine preadipocytes. Anim Biotechnol 2024:2339406. [PMID: 38634284 DOI: 10.1080/10495398.2024.2339406] [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] [Indexed: 04/19/2024]
Abstract
Fat deposition affects beef quantity and quality via preadipocyte proliferation. Beta-sitosterol, a natural small molecular compound, has various functions, such as anti-inflammation, antibacterial, and anticancer properties. The mechanism of action of Beta-sitosterol on bovine preadipocytes remains unclear. This study, based on RNA-seq, reveals the impact of Beta -sitosterol on the proliferation of bovine preadipocytes. Compared to the control group, Beta-sitosterol demonstrated a more pronounced inhibitory effect on cell proliferation after 48 hours of treatment than after 24 hours, as evidenced by the results of EdU staining and flow cytometry. RNA-seq and Western Blot analyses further substantiated these findings. Our results suggest that the impact of Beta-sitosterol on the proliferation of bovine preadipocytes is not significant after a 24-hour treatment. It is only after extending the treatment time to 48 hours that Beta-sitosterol may induce cell cycle arrest at the G2/M phase by suppressing the expression of CCNB1, thereby inhibiting the proliferation of bovine preadipocytes.
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Affiliation(s)
- Lei Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuan Wan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinhai Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyu Mao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaolei Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- National Beef Cattle Improvement Centre, Yangling, Shaanxi, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- National Beef Cattle Improvement Centre, Yangling, Shaanxi, China
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158
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Ye H, Li T, Rigden DJ, Wei Z. m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq. Nucleic Acids Res 2024:gkae280. [PMID: 38634812 DOI: 10.1093/nar/gkae280] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.
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Affiliation(s)
- Haokai Ye
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Tenglong Li
- Wisdom Lake Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Life Course and Medical Sciences, University of Liverpool, L7 8TX Liverpool, UK
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159
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Aljammal R, Saravanan T, Guan T, Rhodes S, Robichaux MA, Ramamurthy V. Excessive tubulin glutamylation leads to progressive cone-rod dystrophy and loss of outer segment integrity. Hum Mol Genet 2024; 33:802-817. [PMID: 38297980 DOI: 10.1093/hmg/ddae013] [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: 10/25/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Mutations in Cytosolic Carboxypeptidase-like Protein 5 (CCP5) are associated with vision loss in humans. To decipher the mechanisms behind CCP5-associated blindness, we generated a novel mouse model lacking CCP5. In this model, we found that increased tubulin glutamylation led to progressive cone-rod dystrophy, with cones showing a more pronounced and earlier functional loss than rod photoreceptors. The observed functional reduction was not due to cell death, levels, or the mislocalization of major phototransduction proteins. Instead, the increased tubulin glutamylation caused shortened photoreceptor axonemes and the formation of numerous abnormal membranous whorls that disrupted the integrity of photoreceptor outer segments (OS). Ultimately, excessive tubulin glutamylation led to the progressive loss of photoreceptors, affecting cones more severely than rods. Our results highlight the importance of maintaining tubulin glutamylation for normal photoreceptor function. Furthermore, we demonstrate that murine cone photoreceptors are more sensitive to disrupted tubulin glutamylation levels than rods, suggesting an essential role for axoneme in the structural integrity of the cone outer segment. This study provides valuable insights into the mechanisms of photoreceptor diseases linked to excessive tubulin glutamylation.
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Affiliation(s)
- Rawaa Aljammal
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Thamaraiselvi Saravanan
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Tongju Guan
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Scott Rhodes
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Michael A Robichaux
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Visvanathan Ramamurthy
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
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160
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Feng X, Chen Y, Yan T, Lu H, Wang C, Zhao L. Effects of various living-low and training-high modes with distinct training prescriptions on sea-level performance: A network meta-analysis. PLoS One 2024; 19:e0297007. [PMID: 38635743 PMCID: PMC11025749 DOI: 10.1371/journal.pone.0297007] [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] [Received: 09/26/2023] [Accepted: 12/22/2023] [Indexed: 04/20/2024] Open
Abstract
This study aimed to separately compare and rank the effect of various living-low and training-high (LLTH) modes on aerobic and anaerobic performances in athletes, focusing on training intensity, modality, and volume, through network meta-analysis. We systematically searched PubMed, Web of Science, Embase, EBSCO, and Cochrane from their inception date to June 30, 2023. Based on the hypoxic training modality and the intensity and duration of work intervals, LLTH was divided into intermittent hypoxic exposure, continuous hypoxic training, repeated sprint training in hypoxia (RSH; work interval: 5-10 s and rest interval: approximately 30 s), interval sprint training in hypoxia (ISH; work interval: 15-30 s), short-duration high-intensity interval training (s-IHT; short work interval: 1-2 min), long-duration high-intensity interval training (l-IHT; long work interval: > 5 min), and continuous and interval training under hypoxia. A meta-analysis was conducted to determine the standardized mean differences (SMDs) among the effects of various hypoxic interventions on aerobic and anaerobic performances. From 2,072 originally identified titles, 56 studies were included in the analysis. The pooled data from 53 studies showed that only l-IHT (SMDs: 0.78 [95% credible interval; CrI, 0.52-1.05]) and RSH (SMDs: 0.30 [95% CrI, 0.10-0.50]) compared with normoxic training effectively improved athletes' aerobic performance. Furthermore, the pooled data from 29 studies revealed that active intermittent hypoxic training compared with normoxic training can effectively improve anaerobic performance, with SMDs ranging from 0.97 (95% CrI, 0.12-1.81) for l-IHT to 0.32 (95% CrI, 0.05-0.59) for RSH. When adopting a program for LLTH, sufficient duration and work intensity intervals are key to achieving optimal improvements in athletes' overall performance, regardless of the potential improvement in aerobic or anaerobic performance. Nevertheless, it is essential to acknowledge that this study incorporated merely one study on the improvement of anaerobic performance by l-IHT, undermining the credibility of the results. Accordingly, more related studies are needed in the future to provide evidence-based support. It seems difficult to achieve beneficial adaptive changes in performance with intermittent passive hypoxic exposure and continuous low-intensity hypoxic training.
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Affiliation(s)
- Xinmiao Feng
- Sports Coaching College, Beijing Sport University, Haidian, Beijing, China
| | - Yonghui Chen
- Sports Coaching College, Beijing Sport University, Haidian, Beijing, China
| | - Teishuai Yan
- Sports Coaching College, Beijing Sport University, Haidian, Beijing, China
| | - Hongyuan Lu
- Sports Coaching College, Beijing Sport University, Haidian, Beijing, China
| | - Chuangang Wang
- Sports Coaching College, Beijing Sport University, Haidian, Beijing, China
| | - Linin Zhao
- Sports Coaching College, Beijing Sport University, Haidian, Beijing, China
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161
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Tang J, Hao M, Liu J, Chen Y, Wufuer G, Zhu J, Zhang X, Zheng T, Fang M, Zhang S, Li T, Ge S, Zhang J, Xia N. Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs. Commun Chem 2024; 7:87. [PMID: 38637620 PMCID: PMC11026461 DOI: 10.1038/s42004-024-01173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the "Asn-Ala-Leu" motif and an N-terminus "Arg-Leu" as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, "Asn-Ala-Leu" and "Arg-Leu" under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.
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Affiliation(s)
- Jiabao Tang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mengling Hao
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Junxian Liu
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Yaling Chen
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Gulimire Wufuer
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Jie Zhu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, 213164, Changzhou, China
| | - Xuejie Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingquan Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mujin Fang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Shiyin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
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162
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Wang QL, Meng LC, Zhao Z, Du JF, Li P, Jiang Y, Li HJ. Ultrasensitive upconverting nanoprobes for in situ imaging of drug-induced liver injury using miR-122 as the biomarker. Talanta 2024; 274:126108. [PMID: 38640602 DOI: 10.1016/j.talanta.2024.126108] [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: 10/01/2023] [Revised: 01/09/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
Drug-induced liver injury (DILI) is a frequent adverse drug reaction. The current clinical diagnostic methods are inadequate for accurate and early detection of DILI due to the lack of effective diagnostic biomarkers. Hepatocyte-specific miR-122 is released from injured hepatocytes promptly and its efflux is significantly correlated with the progression of DILI. Therefore, achieving precise in situ detection of miR-122 with high sensitivity is vital for early visualization of DILI. Herein, a new nanoprobe, consisting of miR-122 aptamer, upconversion nanoparticles (UCNPs) and Prussian blue nanoparticles (PBNPs) was introduced for the early and sensitive detection of DILI in situ. As the nanoprobes reached in the liver, miR-122 aptamer-based entropy-driven strand displacement (ESDR) signal amplification reaction was triggered and luminescence resonance energy transfer (LRET) between UCNPs and PBNPs was responded to achieve the high-fidelity detection of DILI. A negative correlation was observed between the intensity of upconversion luminescence (UCL) and the concentration of miR-122. UCL imaging conducted both in vivo and ex vivo indicated that a reduction in miR-122 concentration led to an increase in UCL intensity, revealing a precise state of DILI. The detection technique demonstrated a positive correlation between signal intensity and severity, offering a more straightforward and intuitive method of visualizing DILI.
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Affiliation(s)
- Qiao-Lei Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Ling-Chang Meng
- Institute of Chinese Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University, Nanjing, China
| | - Zhen Zhao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Jin-Fa Du
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Jiang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Hui-Jun Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.
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163
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Balasubramanian S, Weston DA, Levin M, Davidian DCC. Electroceuticals: emerging applications beyond the nervous system and excitable tissues. Trends Pharmacol Sci 2024:S0165-6147(24)00049-X. [PMID: 38641490 DOI: 10.1016/j.tips.2024.03.001] [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: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 04/21/2024]
Abstract
Electroceuticals have evolved beyond devices manipulating neuronal signaling for symptomatic treatment, becoming more precise and disease modulating and expanding beyond the nervous system. These advancements promise transformative applications in arthritis, cancer treatment, tissue regeneration, and more. Here, we discuss these recent advances and offer insights for future research.
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Affiliation(s)
- Swarnalatha Balasubramanian
- Emerging Innovations Unit, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, Massachusetts, USA
| | - David A Weston
- Emerging Innovations Unit, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA; Wyss Institute, Harvard University, Boston, MA, USA
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164
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Zhuang Z, Li L, Yu Y, Su X, Lin S, Hu J. Targeting MicroRNA in Myopia: Current Insights. Exp Eye Res 2024:109905. [PMID: 38642599 DOI: 10.1016/j.exer.2024.109905] [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: 10/13/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Myopia, the most prevalent eye condition, has sparked notable interest regarding its origin and prevention. MicroRNAs (miRNAs) are short, non-coding RNA strands typically consisting of 18-24 nucleotides. They play a central role in post-transcriptional gene regulation and are closely associated with both normal and pathological processes in organisms. Recent advances in next-generation sequencing and bioinformatics have provided novel insights into miRNA expression and its regulatory role in myopia. This review discusses the distinct expression patterns, regulatory functions, and potential pathways of miRNAs involved in the onset and progression of myopia. The primary objective of this review was to provide valuable insights into molecular mechanisms underlying myopia and the contribution of miRNAs. These insights are expected to pave the way for further exploration of the molecular mechanisms, diagnosis, treatment, and clinical applications of myopia.
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Affiliation(s)
- Zihao Zhuang
- Department of Ophthalmology, the Second Affiliated Hospital of Fujian Medical University, Engineering Research Centre of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, Fujian, China
| | - Licheng Li
- Department of Ophthalmology, the Second Affiliated Hospital of Fujian Medical University, Engineering Research Centre of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, Fujian, China
| | - Yang Yu
- Department of Ophthalmology, the Second Affiliated Hospital of Fujian Medical University, Engineering Research Centre of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, Fujian, China
| | - Xuemei Su
- Department of Ophthalmology, the Second Affiliated Hospital of Fujian Medical University, Engineering Research Centre of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, Fujian, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, the Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China; Group of Neuroendocrinology, Garvan Institute of Medical Research, 384 Victoria St, Sydney, Australia.
| | - Jianmin Hu
- Department of Ophthalmology, the Second Affiliated Hospital of Fujian Medical University, Engineering Research Centre of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, Fujian, China; The School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, Fujian, China.
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165
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Zhang YW, Wu SX, Wang GW, Wan RD, Yang QE. Single-cell analysis identifies critical regulators of spermatogonial development and differentiation in cattle-yak bulls. J Dairy Sci 2024:S0022-0302(24)00759-8. [PMID: 38642661 DOI: 10.3168/jds.2023-24442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/11/2024] [Indexed: 04/22/2024]
Abstract
Spermatogenesis is a continuous process in which functional sperm are produced through a series of mitotic and meiotic divisions and morphological changes in germ cells. The aberrant development and fate transitions of spermatogenic cells cause hybrid sterility in mammals. Cattle-yak, a hybrid animal between taurine cattle (Bos taurus) and yak (Bos grunniens), exhibits male-specific sterility due to spermatogenic failure. In the present study, we performed single-cell RNA sequencing analysis to identify differences in testicular cell composition and the developmental trajectory of spermatogenic cells between yak and cattle-yak. The composition and molecular signatures of spermatogonial subtypes were dramatically different between these 2 animals, and the expression of genes associated with stem cell maintenance, cell differentiation and meiotic entry was altered in cattle-yak, indicating the impairment of undifferentiated spermatogonial fate decisions. Cell communication analysis revealed that signaling within different spermatogenic cell subpopulations was weakened, and progenitor spermatogonia were unable or delayed receiving and sending signals for transformation to the next stage in cattle-yak. Simultaneously, the communication between niche cells and germ cells was also abnormal. Collectively, we obtained the expression profiles of transcriptome signatures of different germ cells and testicular somatic cell populations at the single-cell level and identified critical regulators of spermatogonial differentiation and meiosis in yak and sterile cattle-yak. The findings of this study shed light on the genetic mechanisms that lead to hybrid sterility and speciation in bovid species.
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Affiliation(s)
- Yi-Wen Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Xin Wu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Wen Wang
- Qinghai Academy of Animal Husbandry and Veterinary Sciences, Xining, Qinghai 810016, China
| | - Rui-Dong Wan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810000, China; University of Chinese Academy of Sciences, Beijing 100049, China; Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China.
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166
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Gaussmann S, Peschel R, Ott J, Zak KM, Sastre J, Delhommel F, Popowicz GM, Boekhoven J, Schliebs W, Erdmann R, Sattler M. Modulation of peroxisomal import by the PEX13 SH3 domain and a proximal FxxxF binding motif. Nat Commun 2024; 15:3317. [PMID: 38632234 PMCID: PMC11024197 DOI: 10.1038/s41467-024-47605-w] [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: 01/05/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. By combining biochemical methods and structural biology, we show that the C-terminal SH3 domain of PEX13 mediates intramolecular interactions with a proximal FxxxF motif. The SH3 domain also binds WxxxF peptide motifs in the import receptor PEX5, demonstrating evolutionary conservation of such interactions from yeast to human. Strikingly, intramolecular interaction of the PEX13 FxxxF motif regulates binding of PEX5 WxxxF/Y motifs to the PEX13 SH3 domain. Crystal structures reveal how FxxxF and WxxxF/Y motifs are recognized by a non-canonical surface on the SH3 domain. The PEX13 FxxxF motif also mediates binding to PEX14. Surprisingly, the potential PxxP binding surface of the SH3 domain does not recognize PEX14 PxxP motifs, distinct from its yeast ortholog. Our data show that the dynamic network of PEX13 interactions with PEX5 and PEX14, mediated by diaromatic peptide motifs, modulates peroxisomal matrix import.
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Affiliation(s)
- Stefan Gaussmann
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Rebecca Peschel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Julia Ott
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Krzysztof M Zak
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Judit Sastre
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Florent Delhommel
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Job Boekhoven
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany.
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany.
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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167
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Hilditch AT, Romanyuk A, Hodgson LR, Mantell J, Neal CR, Verkade P, Obexer R, Serpell LC, McManus JJ, Woolfson DN. Maturation and Conformational Switching of a De Novo Designed Phase-Separating Polypeptide. J Am Chem Soc 2024; 146:10240-10245. [PMID: 38578222 PMCID: PMC11027135 DOI: 10.1021/jacs.4c00256] [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: 01/07/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Cellular compartments formed by biomolecular condensation are widespread features of cell biology. These organelle-like assemblies compartmentalize macromolecules dynamically within the crowded intracellular environment. However, the intermolecular interactions that produce condensed droplets may also create arrested states and potentially pathological assemblies such as fibers, aggregates, and gels through droplet maturation. Protein liquid-liquid phase separation is a metastable process, so maturation may be an intrinsic property of phase-separating proteins, where nucleation of different phases or states arises in supersaturated condensates. Here, we describe the formation of both phase-separated droplets and proteinaceous fibers driven by a de novo designed polypeptide. We characterize the formation of supramolecular fibers in vitro and in bacterial cells. We show that client proteins can be targeted to the fibers in cells using a droplet-forming construct. Finally, we explore the interplay between phase separation and fiber formation of the de novo polypeptide, showing that the droplets mature with a post-translational switch to largely β conformations, analogous to models of pathological phase separation.
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Affiliation(s)
- Alexander T. Hilditch
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Andrey Romanyuk
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Lorna R. Hodgson
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Judith Mantell
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Christopher R. Neal
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Richard Obexer
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K.
| | - Louise C. Serpell
- School
of Life Sciences, University of Sussex, Falmer, Brighton, JMS 3B17, U.K.
| | - Jennifer J. McManus
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- HH Wills
Physics Laboratory, School of Physics, University
of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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168
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Bakhsh T, Alhazmi S, Farsi A, Yusuf AS, Alharthi A, Qahl SH, Alghamdi MA, Alzahrani FA, Elgaddar OH, Ibrahim MA, Bahieldin A. Molecular detection of exosomal miRNAs of blood serum for prognosis of colorectal cancer. Sci Rep 2024; 14:8902. [PMID: 38632250 PMCID: PMC11024162 DOI: 10.1038/s41598-024-58536-3] [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: 10/15/2023] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer affecting people. The discovery of new, non-invasive, specific, and sensitive molecular biomarkers for CRC may assist in the diagnosis and support therapeutic decision making. Exosomal miRNAs have been demonstrated in carcinogenesis and CRC development, which makes these miRNAs strong biomarkers for CRC. Deep sequencing allows a robust high-throughput informatics investigation of the types and abundance of exosomal miRNAs. Thus, exosomal miRNAs can be efficiently examined as diagnostic biomarkers for disease screening. In the present study, a number of 660 mature miRNAs were detected in patients diagnosed with CRC at different stages. Of which, 29 miRNAs were differentially expressed in CRC patients compared with healthy controls. Twenty-nine miRNAs with high abundance levels were further selected for subsequent analysis. These miRNAs were either highly up-regulated (e.g., let-7a-5p, let-7c-5p, let-7f-5p, let-7d-3p, miR-423-5p, miR-3184-5p, and miR-584) or down-regulated (e.g., miR-30a-5p, miR-99-5p, miR-150-5p, miR-26-5p and miR-204-5p). These miRNAs influence critical genes in CRC, leading to either tumor growth or suppression. Most of the reported diagnostic exosomal miRNAs were shown to be circulating in blood serum. The latter is a novel miRNA that was found in exosomal profile of blood serum. Some of the predicted target genes of highly expressed miRNAs participate in several cancer pathways, including CRC pathway. These target genes include tumor suppressor genes, oncogenes and DNA repair genes. Main focus was given to multiple critical signaling cross-talking pathways including transforming growth factor β (TGFβ) signaling pathways that are directly linked to CRC. In conclusion, we recommend further analysis in order to experimentally confirm exact relationships between selected differentially expressed miRNAs and their predicted target genes and downstream functional consequences.
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Affiliation(s)
- Tahani Bakhsh
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia.
| | - Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, 80200, Jedaah, Saudi Arabia
- Neuroscience and Geroscience Research Unit, King Fahad Medical Research Centre, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
- Central lab of biological Sciences, Faculty of Sciences, King Abdulaziz University, 80200, Jeddah, Saudi Arabia
| | - Ali Farsi
- Department of Surgery, Faculty of Medicine, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abdulaziz S Yusuf
- Department of Biochemistry, Faculty of science, Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Medical Laboratory Sciences Department, Fakeeh College for Medical Sciences, 21461, Jeddah, Saudi Arabia
| | - Amani Alharthi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, 11952, Majmaah, Saudi Arabia
| | - Safa H Qahl
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Maha Ali Alghamdi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Faisal A Alzahrani
- Department of Biochemistry, Faculty of science, Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Ola H Elgaddar
- Department of Chemical Pathology, Alexandria University, Alexandria, Egypt
| | - Mohanad A Ibrahim
- Data Science Program, King Abdullah International Medical Research Center, 11481, Riyadh, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.
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169
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Okur Z, Schlauri N, Bitsikas V, Panopoulou M, Ortiz R, Schwaiger M, Karmakar K, Schreiner D, Scheiffele P. Control of neuronal excitation-inhibition balance by BMP-SMAD1 signalling. Nature 2024:10.1038/s41586-024-07317-z. [PMID: 38632412 DOI: 10.1038/s41586-024-07317-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
Throughout life, neuronal networks in the mammalian neocortex maintain a balance of excitation and inhibition, which is essential for neuronal computation1,2. Deviations from a balanced state have been linked to neurodevelopmental disorders, and severe disruptions result in epilepsy3-5. To maintain balance, neuronal microcircuits composed of excitatory and inhibitory neurons sense alterations in neural activity and adjust neuronal connectivity and function. Here we identify a signalling pathway in the adult mouse neocortex that is activated in response to increased neuronal network activity. Overactivation of excitatory neurons is signalled to the network through an increase in the levels of BMP2, a growth factor that is well known for its role as a morphogen in embryonic development. BMP2 acts on parvalbumin-expressing (PV) interneurons through the transcription factor SMAD1, which controls an array of glutamatergic synapse proteins and components of perineuronal nets. PV-interneuron-specific disruption of BMP2-SMAD1 signalling is accompanied by a loss of glutamatergic innervation in PV cells, underdeveloped perineuronal nets and decreased excitability. Ultimately, this impairment of the functional recruitment of PV interneurons disrupts the cortical excitation-inhibition balance, with mice exhibiting spontaneous epileptic seizures. Our findings suggest that developmental morphogen signalling is repurposed to stabilize cortical networks in the adult mammalian brain.
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Affiliation(s)
- Zeynep Okur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Nadia Schlauri
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | - Raul Ortiz
- Biozentrum, University of Basel, Basel, Switzerland
| | - Michaela Schwaiger
- Swiss Institute of Bioinformatics, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Kajari Karmakar
- Biozentrum, University of Basel, Basel, Switzerland
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
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170
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Patel MA, Fraser DD, Daley M, Cepinskas G, Veraldi N, Grazioli S. The plasma proteome differentiates the multisystem inflammatory syndrome in children (MIS-C) from children with SARS-CoV-2 negative sepsis. Mol Med 2024; 30:51. [PMID: 38632526 PMCID: PMC11022403 DOI: 10.1186/s10020-024-00806-x] [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: 08/11/2023] [Accepted: 03/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The Multi-System Inflammatory Syndrome in Children (MIS-C) can develop several weeks after SARS-CoV-2 infection and requires a distinct treatment protocol. Distinguishing MIS-C from SARS-CoV-2 negative sepsis (SCNS) patients is important to quickly institute the correct therapies. We performed targeted proteomics and machine learning analysis to identify novel plasma proteins of MIS-C for early disease recognition. METHODS A case-control study comparing the expression of 2,870 unique blood proteins in MIS-C versus SCNS patients, measured using proximity extension assays. The 2,870 proteins were reduced in number with either feature selection alone or with a prior COMBAT-Seq batch effect adjustment. The leading proteins were correlated with demographic and clinical variables. Organ system and cell type expression patterns were analyzed with Natural Language Processing (NLP). RESULTS The cohorts were well-balanced for age and sex. Of the 2,870 unique blood proteins, 58 proteins were identified with feature selection (FDR-adjusted P < 0.005, P < 0.0001; accuracy = 0.96, AUC = 1.00, F1 = 0.95), and 15 proteins were identified with a COMBAT-Seq batch effect adjusted feature selection (FDR-adjusted P < 0.05, P < 0.0001; accuracy = 0.92, AUC = 1.00, F1 = 0.89). All of the latter 15 proteins were present in the former 58-protein model. Several proteins were correlated with illness severity scores, length of stay, and interventions (LTA4H, PTN, PPBP, and EGF; P < 0.001). NLP analysis highlighted the multi-system nature of MIS-C, with the 58-protein set expressed in all organ systems; the highest levels of expression were found in the digestive system. The cell types most involved included leukocytes not yet determined, lymphocytes, macrophages, and platelets. CONCLUSIONS The plasma proteome of MIS-C patients was distinct from that of SCNS. The key proteins demonstrated expression in all organ systems and most cell types. The unique proteomic signature identified in MIS-C patients could aid future diagnostic and therapeutic advancements, as well as predict hospital length of stays, interventions, and mortality risks.
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Affiliation(s)
- Maitray A Patel
- Epidemiology and Biostatistics, Western University, N6A 3K7, London, ON, Canada
| | - Douglas D Fraser
- Lawson Health Research Institute, N6C 2R5, London, ON, Canada.
- Children's Health Research Institute, N6C 4V3, London, ON, Canada.
- Pediatrics, Western University, N6A 3K7, London, ON, Canada.
- Clinical Neurological Sciences, Western University, N6A 3K7, London, ON, Canada.
- Physiology & Pharmacology, Western University, N6A 3K7, London, ON, Canada.
- London Health Sciences Centre, Room C2-C82, 800 Commissioners Road East, N6A 5W9, London, ON, Canada.
| | - Mark Daley
- Epidemiology and Biostatistics, Western University, N6A 3K7, London, ON, Canada
- Computer Science, Western University, N6A 3K7, London, ON, Canada
| | - Gediminas Cepinskas
- Lawson Health Research Institute, N6C 2R5, London, ON, Canada
- Medical Biophysics, Western University, N6A 3K7, London, ON, Canada
| | - Noemi Veraldi
- Department of Pediatrics, Gynaecology and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Serge Grazioli
- Department of Pediatrics, Gynaecology and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Neonatal and Pediatric Intensive Care, Department of Child, Woman, and Adolescent Medicine, Geneva University Hospitals, Geneva, Switzerland
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171
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Sun Q, Zhang L, Huang X, Wang M. Salidroside prevents gestational hypertension-induced impairment of offspring learning and memory via Wnt/Skp2 pathway. Neurosci Lett 2024:137787. [PMID: 38641312 DOI: 10.1016/j.neulet.2024.137787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/29/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Salidroside (Sal) has been found to protect against multiple impairments caused by diabetes, and we designed this study to investigate the effect of Sal on gestational hypertension (GHP)-induced impairment of offspring learning and memory. METHODS We established a GHP rat model by intraperitoneal injection of NG-nitro-L-arginine methyl ester (L-NAME), and treated with Sal by daily gavage. We used Morris Water Maze test to evaluate the learning and memory ability of offspring rats. HE staining was used to measured the pathological changes in hippocampus of offspring. Immunohistochemistry, cellular immunofluorescence and western blot were used to detect the protein expression. RESULTS The learning and memory abilities of GHP offspring rats were significantly lower than those of normal rat offspring, while Sal treatment could significantly improve the learning and memory abilities of GHP offspring rats. HE staining did not reveal pathological differences in the hippocampus of normal rats, GHP rats and Sal-treated GHP offspring rats. However, Sal treatment can significantly increase the expression of Wnt1 and Skp2 protein, and decrease the expression of P27kiwf and P21waf1 protein in the hippocampus of GHP offspring rats. In vitro, Sal significantly promoted the proliferation and differentiation on neural stem cell, while Wnt1 knockdown could reverse these promotions by Sal. In the hippocampus of GHP offspring rats, Sal treatment significantly increased the expression of Tuj1, SOX2, Ki67 and DCX protein. CONCLUSION Salidroside significantly improves the learning and memory impairment of offspring caused by GHP, and its mechanism may be related to the fact that Salidroside promotes the proliferation and differentiation of neural stem cells by activating the Wnt1/Skp2 signaling pathway.
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Affiliation(s)
- Qian Sun
- Department of Gynaecology and Obstetrics, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University Jinan, Shandong 250001, China
| | - Li Zhang
- Department of Gynaecology and Obstetrics, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University Jinan, Shandong 250001, China
| | - Xiuyan Huang
- Department of Gynaecology and Obstetrics, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University Jinan, Shandong 250001, China
| | - Min Wang
- Department of Gynaecology and Obstetrics, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University Jinan, Shandong 250001, China.
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172
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Liu HY, Sun XJ, Xiu SY, Zhang XY, Wang ZQ, Gu YL, Yi CX, Liu JY, Dai YS, Yuan X, Liao HP, Liu ZM, Pang XC, Li TC. Frizzled receptors (FZDs) in Wnt signaling: potential therapeutic targets for human cancers. Acta Pharmacol Sin 2024:10.1038/s41401-024-01270-3. [PMID: 38632318 DOI: 10.1038/s41401-024-01270-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/24/2024] [Indexed: 04/19/2024] Open
Abstract
Frizzled receptors (FZDs) are key contributors intrinsic to the Wnt signaling pathway, activation of FZDs triggering the Wnt signaling cascade is frequently observed in human tumors and intimately associated with an aggressive carcinoma phenotype. It has been shown that the abnormal expression of FZD receptors contributes to the manifestation of malignant characteristics in human tumors such as enhanced cell proliferation, metastasis, chemotherapy resistance as well as the acquisition of cancer stemness. Given the essential roles of FZD receptors in the Wnt signaling in human tumors, this review aims to consolidate the prevailing knowledge on the specific status of FZD receptors (FZD1-10) and elucidate their respective functions in tumor progression. Furthermore, we delineate the structural basis for binding of FZD and its co-receptors to Wnt, and provide a better theoretical foundation for subsequent studies on related mechanisms. Finally, we describe the existing biological classes of small molecule-based FZD inhibitors in detail in the hope that they can provide useful assistance for design and development of novel drug candidates targeted FZDs.
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Affiliation(s)
- Hui-Yu Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Xiao-Jiao Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Si-Yu Xiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xiang-Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhi-Qi Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yan-Lun Gu
- Department of Pharmacy, Peking University First Hospital, Beijing, 100034, China
| | - Chu-Xiao Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jun-Yan Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Yu-Song Dai
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Hua-Peng Liao
- Yizhang County People's Hospital, Chenzhou, 424200, China
| | - Zhen-Ming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Xiao-Cong Pang
- Department of Pharmacy, Peking University First Hospital, Beijing, 100034, China.
| | - Tian-Cheng Li
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China.
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100034, China.
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173
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Chen S, Barritt JD, Cascella R, Bigi A, Cecchi C, Banchelli M, Gallo A, Jarvis JA, Chiti F, Dobson CM, Fusco G, De Simone A. Structure-Toxicity Relationship in Intermediate Fibrils from α-Synuclein Condensates. J Am Chem Soc 2024; 146:10537-10549. [PMID: 38567991 PMCID: PMC11027145 DOI: 10.1021/jacs.3c14703] [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: 12/26/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/18/2024]
Abstract
The aberrant aggregation of α-synuclein (αS) into amyloid fibrils is associated with a range of highly debilitating neurodegenerative conditions, including Parkinson's disease. Although the structural properties of mature amyloids of αS are currently understood, the nature of transient protofilaments and fibrils that appear during αS aggregation remains elusive. Using solid-state nuclear magnetic resonance (ssNMR), cryogenic electron microscopy (cryo-EM), and biophysical methods, we here characterized intermediate amyloid fibrils of αS forming during the aggregation from liquid-like spherical condensates to mature amyloids adopting the structure of pathologically observed aggregates. These transient amyloid intermediates, which induce significant levels of cytotoxicity when incubated with neuronal cells, were found to be stabilized by a small core in an antiparallel β-sheet conformation, with a disordered N-terminal region of the protein remaining available to mediate membrane binding. In contrast, mature amyloids that subsequently appear during the aggregation showed different structural and biological properties, including low levels of cytotoxicity, a rearranged structured core embedding also the N-terminal region, and a reduced propensity to interact with the membrane. The characterization of these two fibrillar forms of αS, and the use of antibodies and designed mutants, enabled us to clarify the role of critical structural elements endowing intermediate amyloid species with the ability to interact with membranes and induce cytotoxicity.
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Affiliation(s)
- Serene
W. Chen
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Joseph D. Barritt
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Roberta Cascella
- Department
of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence 50134, Italy
| | - Alessandra Bigi
- Department
of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence 50134, Italy
| | - Cristina Cecchi
- Department
of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence 50134, Italy
| | - Martina Banchelli
- Institute
of Applied Physics “Nello Carrara” National Research
Council of Italy, Sesto Fiorentino, Florence 50019, Italy
| | - Angelo Gallo
- Department
of Chemistry, University of Turin, Turin 10124, Italy
| | - James A. Jarvis
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
- Randall
Centre for Cell and Molecular Biophysics and Centre for Biomolecular
Spectroscopy, King’s College London, London SE1 9RT, U.K.
| | - Fabrizio Chiti
- Department
of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence 50134, Italy
| | | | - Giuliana Fusco
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Department
of Pharmacy, University of Naples, Naples 80131, Italy
| | - Alfonso De Simone
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
- Department
of Pharmacy, University of Naples, Naples 80131, Italy
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174
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Das I, Shay-Winkler K, Emmert ME, Goh Q, Cornwall R. The Relative Efficacy of Available Proteasome Inhibitors in Preventing Muscle Contractures Following Neonatal Brachial Plexus Injury. J Bone Joint Surg Am 2024; 106:727-734. [PMID: 38194588 PMCID: PMC11023787 DOI: 10.2106/jbjs.23.00513] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
BACKGROUND Contractures following neonatal brachial plexus injury (NBPI) are associated with growth deficits in denervated muscles. This impairment is mediated by an increase in muscle protein degradation, as contractures can be prevented in an NBPI mouse model with bortezomib (BTZ), a proteasome inhibitor (PI). However, BTZ treatment causes substantial toxicity (0% to 80% mortality). The current study tested the hypothesis that newer-generation PIs can prevent contractures with less severe toxicity than BTZ. METHODS Unilateral brachial plexus injuries were surgically created in postnatal (5-day-old) mice. Following NBPI, mice were treated with either saline solution or various doses of 1 of 3 different PIs: ixazomib (IXZ), carfilzomib (CFZ), or marizomib (MRZ). Four weeks post-NBPI, mice were assessed for bilateral passive range of motion at the shoulder and elbow joints, with blinding to the treatment group, through an established digital photography technique to determine contracture severity. Drug toxicity was assessed with survival curves. RESULTS All PIs prevented contractures at both the elbow and shoulder (p < 0.05 versus saline solution controls), with the exception of IXZ, which did not prevent shoulder contractures. However, their efficacies and toxicity profiles differed. At lower doses, CFZ was limited by toxicity (30% to 40% mortality), whereas MRZ was limited by efficacy. At higher doses, CFZ was limited by loss of efficacy, MRZ was limited by toxicity (50% to 60% mortality), and IXZ was limited by toxicity (80% to 100% mortality) and loss of efficacy. Comparisons of the data on these drugs as well as data on BTZ generated in prior studies revealed BTZ to be optimal for preventing contractures, although it, too, was limited by toxicity. CONCLUSIONS All of the tested second-generation PIs were able to reduce NBPI-induced contractures, offering further proof of concept for a regulatory role of the proteasome in contracture formation. However, the narrow dose ranges of efficacy for all PIs highlight the necessity of precise proteasome regulation for preventing contractures. Finally, the substantial toxicity stemming from proteasome inhibition underscores the importance of identifying muscle-targeted strategies to suppress protein degradation and prevent contractures safely. CLINICAL RELEVANCE Although PIs offer unique opportunities to establish critical mechanistic insights into contracture pathophysiology, their clinical use is contraindicated in patients with NPBI at this time.
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Affiliation(s)
- Indranshu Das
- Department of Medical Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Kritton Shay-Winkler
- Division of Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Marianne E Emmert
- Division of Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Qingnian Goh
- Division of Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Orthopaedic Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Roger Cornwall
- Division of Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Orthopaedic Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
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175
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Jia N, Zhang B, Huo Z, Qin J, Ji Q, Geng Y. Binding patterns of inhibitors to different pockets of kinesin Eg5. Arch Biochem Biophys 2024:109998. [PMID: 38641233 DOI: 10.1016/j.abb.2024.109998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
The kinesin-5 family member, Eg5, plays very important role in the mitosis. As a mitotic protein, Eg5 is the target of various mitotic inhibitors. There are two targeting pockets in the motor domain of Eg5, which locates in the α2/L5/α3 region and the α4/α6 region respectively. We investigated the interactions between the different inhibitors and the two binding pockets of Eg5 by using all-atom molecular dynamics method. Combined the conformational analysis with the free-energy calculation, the binding patterns of inhibitors to the two binding pockets are shown. The α2/L5/α3 pocket can be divided into 4 regions. The structures and binding conformations of inhibitors in region 1 and 2 are highly conserved. The shape of α4/α6 pocket is alterable. The space of this pocket in ADP-binding state of Eg5 is larger than that in ADP·Pi-binding state due to the limitation of a hydrogen bond formed in the ADP·Pi-binding state. The results of this investigation provide the structural basis of the inhibitor-Eg5 interaction and offer a reference for the Eg5-targeted drug design.
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Affiliation(s)
- Ning Jia
- School of Science, Hebei University of Technology, Tianjin, China; Institute of Biophysics, Hebei University of Technology, Tianjin, China
| | - Bingbing Zhang
- School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin, China; Institute of Biophysics, Hebei University of Technology, Tianjin, China
| | - Ziling Huo
- School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin, China; Institute of Biophysics, Hebei University of Technology, Tianjin, China
| | - Jingyu Qin
- College of Electrical and Information Engineering, Quzhou University, Quzhou, China
| | - Qing Ji
- School of Science, Hebei University of Technology, Tianjin, China; Institute of Biophysics, Hebei University of Technology, Tianjin, China
| | - Yizhao Geng
- School of Science, Hebei University of Technology, Tianjin, China; Institute of Biophysics, Hebei University of Technology, Tianjin, China.
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176
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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Wei C, Jiang W, Wang R, Zhong H, He H, Gao X, Zhong S, Yu F, Guo Q, Zhang L, Schiffelers LDJ, Zhou B, Trepel M, Schmidt FI, Luo M, Shao F. Brain endothelial GSDMD activation mediates inflammatory BBB breakdown. Nature 2024:10.1038/s41586-024-07314-2. [PMID: 38632402 DOI: 10.1038/s41586-024-07314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
The blood-brain barrier (BBB) protects the central nervous system from infections or harmful substances1; its impairment can lead to or exacerbate various diseases of the central nervous system2-4. However, the mechanisms of BBB disruption during infection and inflammatory conditions5,6 remain poorly defined. Here we find that activation of the pore-forming protein GSDMD by the cytosolic lipopolysaccharide (LPS) sensor caspase-11 (refs. 7-9), but not by TLR4-induced cytokines, mediates BBB breakdown in response to circulating LPS or during LPS-induced sepsis. Mice deficient in the LBP-CD14 LPS transfer and internalization pathway10-12 resist BBB disruption. Single-cell RNA-sequencing analysis reveals that brain endothelial cells (bECs), which express high levels of GSDMD, have a prominent response to circulating LPS. LPS acting on bECs primes Casp11 and Cd14 expression and induces GSDMD-mediated plasma membrane permeabilization and pyroptosis in vitro and in mice. Electron microscopy shows that this features ultrastructural changes in the disrupted BBB, including pyroptotic endothelia, abnormal appearance of tight junctions and vasculature detachment from the basement membrane. Comprehensive mouse genetic analyses, combined with a bEC-targeting adeno-associated virus system, establish that GSDMD activation in bECs underlies BBB disruption by LPS. Delivery of active GSDMD into bECs bypasses LPS stimulation and opens the BBB. In CASP4-humanized mice, Gram-negative Klebsiella pneumoniae infection disrupts the BBB; this is blocked by expression of a GSDMD-neutralizing nanobody in bECs. Our findings outline a mechanism for inflammatory BBB breakdown, and suggest potential therapies for diseases of the central nervous system associated with BBB impairment.
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Affiliation(s)
- Chao Wei
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Wei Jiang
- National Institute of Biological Sciences, Beijing, P. R. China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, P. R. China
| | - Ruiyu Wang
- National Institute of Biological Sciences, Beijing, P. R. China
| | - Haoyu Zhong
- National Institute of Biological Sciences, Beijing, P. R. China
| | - Huabin He
- National Institute of Biological Sciences, Beijing, P. R. China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, P. R. China
| | - Xinwei Gao
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Shilin Zhong
- National Institute of Biological Sciences, Beijing, P. R. China
| | - Fengting Yu
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Qingchun Guo
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Lisa D J Schiffelers
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Bin Zhou
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Martin Trepel
- Department of Hematology and Medical Oncology, University Medical Center Augsburg, Augsburg, Germany
| | - Florian I Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Minmin Luo
- Chinese Institute for Brain Research, Beijing, P. R. China.
- National Institute of Biological Sciences, Beijing, P. R. China.
- Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, P. R. China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, P. R. China.
- New Cornerstone Science Laboratory, Shenzhen, P. R. China.
| | - Feng Shao
- National Institute of Biological Sciences, Beijing, P. R. China.
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, P. R. China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, P. R. China.
- New Cornerstone Science Laboratory, Shenzhen, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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178
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Karimi A, Aga M, Khan T, D'costa SD, Thaware O, White E, Kelley MJ, Gong H, Acott TS. Comparative Analysis of Traction Forces in Normal and Glaucomatous Trabecular Meshwork Cells within a 3D, Active Fluid-Structure Interaction Culture Environment. Acta Biomater 2024:S1742-7061(24)00194-6. [PMID: 38641184 DOI: 10.1016/j.actbio.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/26/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
This study presents a 3D in vitro cell culture model, meticulously 3D printed to replicate the conventional aqueous outflow pathway anatomical structure, facilitating the study of trabecular meshwork (TM) cellular responses under glaucomatous conditions. Glaucoma affects TM cell functionality, leading to extracellular matrix (ECM) stiffening, enhanced cell-ECM adhesion, and obstructed aqueous humor outflow. Our model, reconstructed from polyacrylamide gel with elastic moduli of 1.5 and 21.7 kPa, is based on serial block-face scanning electron microscopy images of the outflow pathway. It allows for quantifying 3D, depth-dependent, dynamic traction forces exerted by both normal and glaucomatous TM cells within an active fluid-structure interaction (FSI) environment. In our experimental design, we designed two scenarios: a control group with TM cells observed over 20 hours without flow (static setting), focusing on intrinsic cellular contractile forces, and a second scenario incorporating active FSI to evaluate its impact on traction forces (dynamic setting). Our observations revealed that active FSI results in higher traction forces (normal: 1.83-fold and glaucoma: 2.24-fold) and shear strains (normal: 1.81-fold and glaucoma: 2.41-fold), with stiffer substrates amplifying this effect. Glaucomatous cells consistently exhibited larger forces than normal cells. Increasing gel stiffness led to enhanced stress fiber formation in TM cells, particularly in glaucomatous cells. Exposure to active FSI dramatically altered actin organization in both normal and glaucomatous TM cells, particularly affecting cortical actin stress fiber arrangement. This model while preliminary offers a new method in understanding TM cell biomechanics and ECM stiffening in glaucoma, highlighting the importance of FSI in these processes. STATEMENT OF SIGNIFICANCE: : This pioneering project presents an advanced 3D in vitro model, meticulously replicating the human trabecular meshwork's anatomy for glaucoma research. It enables precise quantification of cellular forces in a dynamic fluid-structure interaction, a leap forward from existing 2D models. This advancement promises significant insights into trabecular meshwork cell biomechanics and the stiffening of the extracellular matrix in glaucoma, offering potential pathways for innovative treatments. This research is positioned at the forefront of ocular disease study, with implications that extend to broader biomedical applications.
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Affiliation(s)
- Alireza Karimi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States; Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, United States.
| | - Mini Aga
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States.
| | - Taaha Khan
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States.
| | - Siddharth Daniel D'costa
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States.
| | - Omkar Thaware
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States; Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, United States.
| | - Elizabeth White
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States.
| | - Mary J Kelley
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States; Department Integrative Biosciences, School of Dentistry, Oregon Health & Science University, Portland, Oregon, United States.
| | - Haiyan Gong
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, United States; Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States.
| | - Ted S Acott
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States; Department Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, Oregon, United States.
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179
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Huo D, Liu S, Zhang L, Yang H, Sun L. Importance of the ECM-receptor interaction for adaptive response to hypoxia based on integrated transcription and translation analysis. Mol Ecol 2024:e17352. [PMID: 38624130 DOI: 10.1111/mec.17352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Low dissolved oxygen (LO) conditions represent a major environmental challenge to marine life, especially benthic animals. For these organisms, drastic declines in oxygen availability (hypoxic events) can trigger mass mortality events and thus, act as agents of selection influencing the evolution of adaptations. In sea cucumbers, one of the most successful groups of benthic invertebrates, the exposure to hypoxic conditions triggers adaptive adjustments in metabolic rates and behaviour. It is unclear, however, how these adaptive responses are regulated and the genetic mechanisms underpinning them. Here, we addressed this knowledge gap by assessing the genetic regulation (transcription and translation) of hypoxia exposure in the sea cucumber Apostichopus japonicus. Transcriptional and translational gene expression profiles under short- and long-term exposure to low oxygen conditions are tightly associated with extracellular matrix (ECM)-receptor interaction in which laminin and collagen likely have important functions. Finding revealed that genes with a high translational efficiency (TE) had a relatively short upstream open reading frame (uORF) and a high uORF normalized minimal free energy, suggesting that sea cucumbers may respond to hypoxic stress via altered TE. These results provide valuable insights into the regulatory mechanisms that confer adaptive capacity to holothurians to survive oxygen deficiency conditions and may also be used to inform the development of strategies for mitigating the harmful effects of hypoxia on other marine invertebrates facing similar challenges.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
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180
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Xia Q, Meng X, Wang Y, Yuan R, Li P, Liu L, Li YM. A cell-permeable Ub-Dha probe for profiling E1-E2-E3 enzymes in live cells. Chem Commun (Camb) 2024; 60:4342-4345. [PMID: 38545842 DOI: 10.1039/d4cc00415a] [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: 04/17/2024]
Abstract
Activity-based ubiquitin probes (Ub-ABPs) have recently been developed as effective tools for studying the capabilities of E1-E2-E3 enzymes, but most of them can only be used in cell lysates. Here, we report the first cell-penetrating Ub-Dha probes based on thiazolidine-protected cysteines, which enable successful delivery into cells confirmed by a fluorophore at the N-terminus of Ub and live-cell fluorescence microscopy. A total of 18 E1-E2-E3 enzymes in live cells were labelled and enriched in combination with label-free quantification (LFQ) mass spectrometry. This work provided a new cell-penetrating Ub tool for studying the activity and function of Ub-related enzymes.
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Affiliation(s)
- Qiong Xia
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Wang
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Rujing Yuan
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Pincheng Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Liwen Liu
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
| | - Yi-Ming Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, China.
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181
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Miyoshi G, Ueta Y, Yagasaki Y, Kishi Y, Fishell G, Machold RP, Miyata M. Developmental trajectories of GABAergic cortical interneurons are sequentially modulated by dynamic FoxG1 expression levels. Proc Natl Acad Sci U S A 2024; 121:e2317783121. [PMID: 38588430 PMCID: PMC11032493 DOI: 10.1073/pnas.2317783121] [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: 10/18/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
GABAergic inhibitory interneurons, originating from the embryonic ventral forebrain territories, traverse a convoluted migratory path to reach the neocortex. These interneuron precursors undergo sequential phases of tangential and radial migration before settling into specific laminae during differentiation. Here, we show that the developmental trajectory of FoxG1 expression is dynamically controlled in these interneuron precursors at critical junctures of migration. By utilizing mouse genetic strategies, we elucidate the pivotal role of precise changes in FoxG1 expression levels during interneuron specification and migration. Our findings underscore the gene dosage-dependent function of FoxG1, aligning with clinical observations of FOXG1 haploinsufficiency and duplication in syndromic forms of autism spectrum disorders. In conclusion, our results reveal the finely tuned developmental clock governing cortical interneuron development, driven by temporal dynamics and the dose-dependent actions of FoxG1.
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Affiliation(s)
- Goichi Miyoshi
- Department of Developmental Genetics and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi city, Gunma371-8511, Japan
- Department of Neurophysiology, Tokyo Women’s Medical University, Shinjuku, Tokyo162-8666, Japan
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY10016
| | - Yoshifumi Ueta
- Department of Neurophysiology, Tokyo Women’s Medical University, Shinjuku, Tokyo162-8666, Japan
| | - Yuki Yagasaki
- Department of Neurophysiology, Tokyo Women’s Medical University, Shinjuku, Tokyo162-8666, Japan
| | - Yusuke Kishi
- Laboratory of Molecular Neurobiology, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Tokyo113-0032, Japan
- Laboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo, Tokyo113-0033, Japan
| | - Gord Fishell
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY10016
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Stanley Center at the Broad Institute, Cambridge, MA02142
| | - Robert P. Machold
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY10016
| | - Mariko Miyata
- Department of Neurophysiology, Tokyo Women’s Medical University, Shinjuku, Tokyo162-8666, Japan
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182
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Lee WG, Asuelime GE, Asuelime-Smith MBT, Chen SY, Kim ES. Differential RNA Expression Between Metastatic and Primary Neuroblastoma Cells. J Surg Res 2024; 298:240-250. [PMID: 38631173 DOI: 10.1016/j.jss.2024.03.032] [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: 10/18/2023] [Revised: 02/01/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Abstract
INTRODUCTION Neuroblastoma (NB) is the most common extra-cranial malignancy in children. Poor survival in high-risk NB is attributed to recurrent metastatic disease. To better study metastatic disease, we used a novel mouse model to investigate differential gene expression between primary tumor cells and metastatic cells. We hypothesized that metastatic NB cells have a different gene expression profile from primary tumor cells and cultured cells. METHODS Using three human NB cell lines (NGP, CHLA255, and SH-SY5Y), orthotopic xenografts were established in immunodeficient nod/scid gamma mice via subcapsular renal injection. Mice were sacrificed and NB cells were isolated from the primary tumor and from sites of metastasis (bone marrow, liver). RNA sequencing, gene set analysis, and pathway analysis were performed to identify differentially expressed genes and molecular pathways in the metastatic cells compared to primary tumor cells. RESULTS There were 266 differentially expressed genes in metastatic tumor cells (bone marrow and liver combined) compared to primary tumor cells. The top upregulated gene was KCNK1 and the top downregulated genes were PDE7B and NEBL. Top upregulated pathways in the metastatic cells were involved in ion transport, cell signaling, and cell proliferation. Top downregulated pathways were involved in DNA synthesis, transcription, and cellular metabolism. CONCLUSIONS In metastatic NB cells, our study identified the upregulation of biologic processes involved in cell cycle regulation, cell proliferation, migration, and invasion. Ongoing studies aim to validate downstream translation of these genomic alterations, as well as target these pathways to more effectively suppress and inhibit recurrent metastatic disease in NB.
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Affiliation(s)
- William G Lee
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Grace E Asuelime
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California
| | | | - Stephanie Y Chen
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Eugene S Kim
- Division of Pediatric Surgery, Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Cedars-Sinai Medical Center, Los Angeles, California; Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.
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183
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Bulangalire N, Claeyssen C, Agbulut O, Cieniewski-Bernard C. Impact of MG132 induced-proteotoxic stress on αB-crystallin and desmin phosphorylation and O-GlcNAcylation and their partition towards cytoskeleton. Biochimie 2024:S0300-9084(24)00079-8. [PMID: 38636798 DOI: 10.1016/j.biochi.2024.04.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/19/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Small Heat Shock Proteins are considered as the first line of defense when proteostasis fails. Among them, αB-crystallin is expressed in striated muscles in which it interacts with desmin intermediate filaments to stabilize them, maintaining cytoskeleton's integrity and muscular functionalities. Desmin is a key actor for muscle health; its targeting by αB-crystallin is thus crucial, especially in stress conditions. αB-crystallin is phosphorylated and O-GlcNAcylated. Its phosphorylation increases consecutively to various stresses, correlated with its recruitment for cytoskeleton's safeguarding. However, phosphorylation as unique signal for cytoskeleton translocation remains controversial; indeed, O-GlcNAcylation was also proposed to be involved. Thus, there are still some gaps for a deeper comprehension of how αB-crystallin functions are finely regulated by post-translational modifications. Furthermore, desmin also bears both post-translational modifications; while desmin phosphorylation is closely linked to desmin intermediates filaments turnover, it is unclear whereas its O-GlcNAcylation could impact its proper function. In the herein paper, we aim at identifying whether phosphorylation and/or O-GlcNAcylation are involved in αB-crystallin targeting towards cytoskeleton in proteotoxic stress induced by proteasome inhibition in C2C12 myotubes. We demonstrated that proteotoxicity led to αB-crystallin's phosphorylation and O-GlcNAcylation patterns changes, both presenting a dynamic interplay depending on protein subfraction. Importantly, both post-translational modifications showed a spatio-temporal variation correlated with αB-crystallin translocation towards cytoskeleton. In contrast, we did not detect any change of desmin's phosphorylation and O-GlcNAcylation. All together, these data strongly support that αB-crystallin's phosphorylation/O-GlcNAcylation interplay rather than changes on desmin is a key regulator for its cytoskeleton translocation, preserving it towards stress.
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Affiliation(s)
- Nathan Bulangalire
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000 Lille, France; Université de Lille, CHU Lille, F-59000 Lille, France
| | - Charlotte Claeyssen
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000 Lille, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005, Paris, France
| | - Caroline Cieniewski-Bernard
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d'Opale, ULR 7369 - URePSSS - Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000 Lille, France.
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184
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Hayashi Y, Hashimoto M, Takaoka K, Takemoto T, Takakura N, Kidoya H. Tumor endothelial cell-derived Sfrp1 supports the maintenance of cancer stem cells via Wnt signaling. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00899-y. [PMID: 38625488 DOI: 10.1007/s11626-024-00899-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/17/2024]
Abstract
Cancer stem cells (CSCs), which are critical targets for cancer therapy as they are involved in drug resistance to anticancer drugs, and metastasis, are maintained by angiocrine factors produced by particular niches that form within tumor tissue. Secreted frizzled-related protein 1 (Sfrp1) is an extracellular protein that modulates Wnt signaling. However, the cells that produce Sfrp1 in the tumor environment and its function remain unclear. We aimed to elucidate angiocrine factors related to CSC maintenance, focusing on Sfrp1. Although Sfrp1 is a Wnt pathway-related factor, its impact on tumor tissues remains unknown. We investigated the localization of Sfrp1 in tumors and found that it is expressed in some tumor vessels. Analysis of mice lacking Sfrp1 showed that tumor growth was suppressed in Sfrp1-deficient tumor tissues. Flow cytometry analysis indicated that CSCs were maintained in the early tumor growth phase in the Sfrp1 knockout (KO) mouse model of tumor-bearing cancer. However, tumor growth was inhibited in the late tumor growth phase because of the inability to maintain CSCs. Real-time PCR results from tumors of Sfrp1 KO mice showed that the expression of Wnt signaling target genes significantly decreased in the late stage of tumor growth. This suggests that Sfrp1, an angiocrine factor produced by the tumor vascular niche, is involved in Wnt signaling-mediated mechanisms in tumor tissues.
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Affiliation(s)
- Yumiko Hayashi
- Department of Integrative Vascular Biology, Faculty of Medical Science, Fukui University, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Yoshida, Fukui, 910-1193, Japan
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masakazu Hashimoto
- Laboratory for Embryogenesis, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Katsuyoshi Takaoka
- Laboratory for Embryology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Tatsuya Takemoto
- Laboratory for Embryology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- World Premier Institute Immunology Frontier Research Center, Integrated Frontier Research for Medical Science Division, Osaka University, Suita, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hiroyasu Kidoya
- Department of Integrative Vascular Biology, Faculty of Medical Science, Fukui University, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Yoshida, Fukui, 910-1193, Japan.
- Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
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185
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Wang R, Shi Y, Lv Y, Xie C, Hu Y. The novel insights of epithelial-derived exosomes in various fibrotic diseases. Biomed Pharmacother 2024; 174:116591. [PMID: 38631144 DOI: 10.1016/j.biopha.2024.116591] [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: 01/14/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The characteristics of fibrosis include the abnormal accumulation of extracellular matrix proteins and abnormal tissue repair caused by injury, infection, and inflammation, leading to a significant increase in organ failure and mortality. Effective and precise treatments are urgently needed to halt and reverse the progression of fibrotic diseases. Exosomes are tiny vesicles derived from endosomes, spanning from 40 to 160 nanometers in diameter, which are expelled into the extracellular matrix environment by various cell types. They play a crucial role in facilitating cell-to-cell communication by transporting a variety of cargoes, including proteins, RNA, and DNA. Epithelial cells serve as the primary barrier against diverse external stimuli that precipitate fibrotic diseases. Numerous research suggests that exosomes from epithelial cells have a significant impact on several fibrotic diseases. An in-depth comprehension of the cellular and molecular mechanisms of epithelial cell-derived exosomes in fibrosis holds promise for advancing the exploration of novel diagnostic biomarkers and clinical drug targets. In this review, we expand upon the pathogenic mechanisms of epithelium-derived exosomes and highlight their role in the fibrotic process by inducing inflammation and activating fibroblasts. In addition, we are particularly interested in the bioactive molecules carried by epithelial-derived exosomes and their potential value in the diagnosis and treatment of fibrosis and delineate the clinical utility of exosomes as an emerging therapeutic modality, highlighting their potential application in addressing various medical conditions.
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Affiliation(s)
- Rifu Wang
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Yuxin Shi
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Yonglin Lv
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
| | - Changqing Xie
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China.
| | - Yanjia Hu
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, Hunan, China.
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186
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Xia GQ, Xu M, Sun C, Zhang ZL, Li XQ. Elevated microRNA-214-3p level ameliorates neuroinflammation after spinal cord ischemia-reperfusion injury by inhibiting Nmb/Cav3.2 pathway. Int Immunopharmacol 2024; 133:112031. [PMID: 38631219 DOI: 10.1016/j.intimp.2024.112031] [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: 01/09/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Neuromedin B (Nmb) plays a pivotal role in the transmission of neuroinflammation, particularly during spinal cord ischemia-reperfusion injury (SCII). However, the detailed molecular mechanisms underlying this process remain elusive. METHODS The SCII model was established by clamping the abdominal aorta of male Sprague-Dawley (SD) rats for 60 min. The protein expression levels of Nmb, Cav3.2, and IL-1β were detected by Western blotting, while miR-214-3p expression was quantified by qRT-PCR. The targeted regulation between miR-214-3p and Nmb was investigated using a dual-luciferase reporter gene assay. The cellular localization of Nmb and Cav3.2 with cell-specific markers was visualized by immunofluorescence staining. The specific roles of miR-214-3p on the Nmb/Cav3.2 interactions in SCII-injured rats were explored by intrathecal injection of Cav3.2-siRNA, PD168368 (a specific NmbR inhibitor) and synthetic miR-214-3p agomir and antagomir in separate experiments. Additionally, hind-limb motor function was evaluated using the modified Tarlov scores. RESULTS Compared to the Sham group, the protein expression levels of Nmb, Cav3.2, and the proinflammatory factor Interleukin(IL)-1β were significantly elevated at 24 h post-SCII. Intrathecal injection of PD168368 and Cav3.2-siRNA significantly suppressed the expression of Cav3.2 and IL-1β compared to the SCII group. The miRDB database and dual-luciferase reporter gene assay identified Nmb as a direct target of miR-214-3p. As expected, in vivo overexpression of miR-214-3p by agomir-214-3p pretreatment significantly inhibited the increases in Nmb, Cav3.2 and IL-1β expression and improved lower limb motor function in SCII-injured rats, while antagomiR-214-3p pretreatment reversed these effects. CONCLUSIONS Nmb protein levels positively correlated with Cav3.2 expression in SCII rats. Upregulating miR-214-3p ameliorated hind-limb motor function and protected against neuroinflammation via inhibiting the aberrant Nmb/Cav3.2 interactions and downstream IL-1β release. These findings provide novel therapeutic targets for clinical prevention and treatment of SCII.
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Affiliation(s)
- Guo-Qiang Xia
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Miao Xu
- Department of Pain Medicine, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Cong Sun
- Department of Pain Medicine, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Zai-Li Zhang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China.
| | - Xiao-Qian Li
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China.
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187
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Lienig P, Banerjee S, Kenneweg F, Thum T, Kirschning A, Dräger G. Dextrans, Pullulan and Lentinan, New Scaffold Materials for Use as Hydrogels in Tissue Engineering. Chemistry 2024; 30:e202303843. [PMID: 38217885 DOI: 10.1002/chem.202303843] [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: 11/19/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/15/2024]
Abstract
The development of hydrogels based on dextrans, pullulan and lentinan to be used in biomedical applications including tissue engineering is reported. Despite the fact that selected polysaccharides such as hyaluronic acid are well established, little is known, how these polysaccharides can be chemically modified to create hydrogels under controlled conditions. In this study we present a small library of chemically modified polysaccharides which are used for a divergent approach to achieve biomedical relevant hydrogels. In this case the crosslinking is based on thio ether formation between thiol modified donor and vinylsulfone or maleimide modified acceptor components. Successful synthesis of the linker systems and coupling at the polysaccharides, hydrogel formation takes place under physiological conditions. We extended the study by coupling small molecules like adhesion factors for increasing cell compatibility as well as a dye for further studies. The different hydrogels were studied to their rheological properties, water uptake, their permeability, biodegrability and their cytotoxicity.
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Affiliation(s)
- Pascal Lienig
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Samhita Banerjee
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Franziska Kenneweg
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Gerald Dräger
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
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188
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Pio-Lopez L, Levin M. Aging as a loss of morphostatic information: a developmental bioelectricity perspective. Ageing Res Rev 2024:102310. [PMID: 38636560 DOI: 10.1016/j.arr.2024.102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/21/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
Maintaining order at the tissue level is crucial throughout the lifespan, as failure can lead to cancer and an accumulation of molecular and cellular disorders. Perhaps, the most consistent and pervasive result of these failures is aging, which is characterized by the progressive loss of function and decline in the ability to maintain anatomical homeostasis and reproduce. This leads to organ malfunction, diseases, and ultimately death. The traditional understanding of aging is that it is caused by the accumulation of molecular and cellular damage. In this article, we propose a complementary view of aging from the perspective of endogenous bioelectricity which has not yet been integrated into aging research. We propose a view of aging as a morphostasis defect, a loss of biophysical prepattern information, encoding anatomical setpoints used for dynamic tissue and organ homeostasis. We hypothesize that this is specifically driven by abrogation of the endogenous bioelectric signaling that normally harnesses individual cell behaviors toward the creation and upkeep of complex multicellular structures in vivo. Herein, we first describe bioelectricity as the physiological software of life, and then identify and discuss the links between bioelectricity and life extension strategies and age-related diseases. We develop a bridge between aging and regeneration via bioelectric signaling that suggests a research program for healthful longevity via morphoceuticals. Finally, we discuss the broader implications of the homologies between development, aging, cancer and regeneration and how morphoceuticals can be developed for aging.
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Affiliation(s)
- Léo Pio-Lopez
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA02115, USA.
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189
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Khochare SD, Li X, Yang X, Shi Y, Feng G, Ruchhoeft P, Shih WC, Shan X. Functional Plasmonic Microscope: Characterizing the Metabolic Activity of Single Cells via Sub-nm Membrane Fluctuations. Anal Chem 2024; 96:5771-5780. [PMID: 38563229 DOI: 10.1021/acs.analchem.3c04301] [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: 04/04/2024]
Abstract
Metabolic abnormalities are at the center of many diseases, and the capability to film and quantify the metabolic activities of a single cell is important for understanding the heterogeneities in these abnormalities. In this paper, a functional plasmonic microscope (FPM) is used to image and measure metabolic activities without fluorescent labels at a single-cell level. The FPM can accurately image and quantify the subnanometer membrane fluctuations with a spatial resolution of 0.5 μm in real time. These active cell membrane fluctuations are caused by metabolic activities across the cell membrane. A three-dimensional (3D) morphology of the bottom cell membrane was imaged and reconstructed with FPM to illustrate the capability of the microscope for cell membrane characterization. Then, the subnanometer cell membrane fluctuations of single cells were imaged and quantified with the FPM using HeLa cells. Cell metabolic heterogeneity is analyzed based on membrane fluctuations of each individual cell that is exposed to similar environmental conditions. In addition, we demonstrated that the FPM could be used to evaluate the therapeutic responses of metabolic inhibitors (glycolysis pathway inhibitor STF 31) on a single-cell level. The result showed that the metabolic activities significantly decrease over time, but the nature of this response varies, depicting cell heterogeneity. A low-concentration dose showed a reduced fluctuation frequency with consistent fluctuation amplitudes, while the high-concentration dose showcased a decreasing trend in both cases. These results have demonstrated the capabilities of the functional plasmonic microscope to measure and quantify metabolic activities for drug discovery.
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Affiliation(s)
- Suraj D Khochare
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Xiaoliang Li
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Xu Yang
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Yaping Shi
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Guangxia Feng
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Paul Ruchhoeft
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Wei-Chuan Shih
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
| | - Xiaonan Shan
- Advanced Imaging and Sensing Lab, Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, United States
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190
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Liao H, Lu D, Reisinger SN, Kleeman EA, van de Garde N, Gubert C, Hannan AJ. Mimicking bacterial infection in male mice changes sperm small RNA profiles and multigenerationally alters offspring behavior and physiology. Brain Behav Immun 2024:S0889-1591(24)00362-3. [PMID: 38636562 DOI: 10.1016/j.bbi.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024] Open
Abstract
Paternal pre-conceptual exposures, including stress, diet, substance abuse, parasite infection, and viral immune activation via Poly I:C, have been reported to influence the brains and behavior of offspring through sperm epigenetic changes. However, the effects of paternal (F0) pre-conceptual exposure to bacterial-induced immune activation on the behavior and physiology of F1 and F2 generations remain unexplored. We examined this using C57BL/6J mice. Eight-week-old males (F0) received a single intraperitoneal injection of the bacterial mimetic lipopolysaccharide (LPS: 5 mg/kg) or 0.9 % saline (vehicle control) before mating with naïve females at four weeks post-injection. Comprehensive behavioral assessments were conducted to investigate anxiety, social behaviors, depressive-like behaviors and cognition in both the F1 and F2 generations within the age range of 8 to 14 weeks. Results demonstrated that only female offspring of LPS-exposed fathers exhibited reduced anxiety levels in the light/dark box, large open field, and novelty-suppressed feeding test. These F1 female offspring also exhibited heightened sociability in the 3-chambered social interaction test and a reduced preference for saccharin in the saccharin preference test. Additionally, the F1 male offspring of LPS-challenged males demonstrated an increased total distance traveled in the light/dark box and a longer distance covered in the light zone. They also exhibited diminished preference for social novelty in the 3-chambered social interaction test and an elevated novel arm preference index in the Y-maze. In the F2 generation, male descendants of LPS-treated fathers showed reduced latency to feed in the novelty-suppressed feeding test. Additionally, the F2 generation of LPS challenged fathers, but not the F1 generation, displayed enhanced immune response in both sexes after an acute LPS immune challenge (5 mg/kg). Analysis of sperm small noncoding RNA profiles from LPS-treated F0 mice revealed significant changes at 4 weeks after administration of LPS. These changes included three microRNAs, eight PIWI-interacting RNAs, and two transfer RNAs, exhibiting significant upregulation (mmu-miR-146a-5p, mmu-piR-27082 and mmu-piR-29102) or downregulation (mmu-miR-5110, mmu-miR-467e-3p, mmu-piR-22583, mmu-piR-23548, mmu-piR-36341, mmu-piR-50293, mmu-piR-16583, mmu-piR-36507, Mus_musculus_tRNA-Ile-AAT-2-1 and Mus_musculus_tRNA-Tyr-GTA-1-1). Additionally, we detected 52 upregulated small noncoding RNAs (including 9 miRNAs, 41 piRNAs, and 2 tRNAs) and 7 downregulated small noncoding RNAs (3 miRNAs, 3 piRNAs, and 1 tRNA) in the sperm of F1 offspring from LPS-treated males. These findings provide compelling evidence for the involvement of epigenetic mechanisms in the modulation of brain function and immunity, and associated behavioral and immunological traits, across generations, in response to bacterial infection.
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Affiliation(s)
- Huan Liao
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.
| | - Da Lu
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Sonali N Reisinger
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth A Kleeman
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Nicholas van de Garde
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Carolina Gubert
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia; Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia.
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191
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Domingo E, Martínez-González B, García-Crespo C, Somovilla P, de Ávila AI, Soria ME, Durán-Pastor A, Perales C. Reply to Qu et al., "Quasispecies are constantly selected through virus-encoded intracellular reproductive population bottlenecking". J Virol 2024; 98:e0004624. [PMID: 38445886 PMCID: PMC11019780 DOI: 10.1128/jvi.00046-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Brenda Martínez-González
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - María Eugenia Soria
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Antoni Durán-Pastor
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
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192
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Flippot R, Teixeira M, Rey-Cardenas M, Carril-Ajuria L, Rainho L, Naoun N, Jouniaux JM, Boselli L, Naigeon M, Danlos FX, Escudier B, Scoazec JY, Cassard L, Albiges L, Chaput N. B cells and the coordination of immune checkpoint inhibitor response in patients with solid tumors. J Immunother Cancer 2024; 12:e008636. [PMID: 38631710 PMCID: PMC11029261 DOI: 10.1136/jitc-2023-008636] [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] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
Immunotherapy profoundly changed the landscape of cancer therapy by providing long-lasting responses in subsets of patients and is now the standard of care in several solid tumor types. However, immunotherapy activity beyond conventional immune checkpoint inhibition is plateauing, and biomarkers are overall lacking to guide treatment selection. Most studies have focused on T cell engagement and response, but there is a growing evidence that B cells may be key players in the establishment of an organized immune response, notably through tertiary lymphoid structures. Mechanisms of B cell response include antibody-dependent cellular cytotoxicity and phagocytosis, promotion of CD4+ and CD8+ T cell activation, maintenance of antitumor immune memory. In several solid tumor types, higher levels of B cells, specific B cell subpopulations, or the presence of tertiary lymphoid structures have been associated with improved outcomes on immune checkpoint inhibitors. The fate of B cell subpopulations may be widely influenced by the cytokine milieu, with versatile roles for B-specific cytokines B cell activating factor and B cell attracting chemokine-1/CXCL13, and a master regulatory role for IL-10. Roles of B cell-specific immune checkpoints such as TIM-1 are emerging and could represent potential therapeutic targets. Overall, the expanding field of B cells in solid tumors of holds promise for the improvement of current immunotherapy strategies and patient selection.
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Affiliation(s)
- Ronan Flippot
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Marcus Teixeira
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Macarena Rey-Cardenas
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Lucia Carril-Ajuria
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
- Medical Oncology, CHU Brugmann, Brussels, Belgium
| | - Larissa Rainho
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Natacha Naoun
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Jean-Mehdi Jouniaux
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Lisa Boselli
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Marie Naigeon
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Francois-Xavier Danlos
- LRTI, INSERM U1015, Gustave Roussy, Villejuif, France
- Drug Development Department, Gustave Roussy, Villejuif, France
| | - Bernard Escudier
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
| | | | - Lydie Cassard
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Laurence Albiges
- Department of Medical Oncology, Gustave Roussy, Université Paris Saclay, Villejuif, France
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
| | - Nathalie Chaput
- Immunomonitoring Laboratory, CNRS3655 & INSERM US23, Université Paris-Saclay, Villejuif, France
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193
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Song Y. Liquid-liquid phase separation-inspired design of biomaterials. Biomater Sci 2024; 12:1943-1949. [PMID: 38465963 DOI: 10.1039/d3bm02008h] [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: 03/12/2024]
Abstract
Liquid-liquid phase separation (LLPS) is a crucial biological process that governs biomolecular condensation, assembly, and functionality within phase-separated aqueous environments. This phenomenon serves as a source of inspiration for the creation of artificial designs in both structured and functional biomaterials, presenting novel strategies for manipulating the structures of functional protein aggregates in a wide range of biomedical applications. This mini review summarizes my past research endeavors, offering a panoramic overview of LLPS-inspired biomaterials utilized in the design of structured materials, the development of cell mimetics, and the advancement of intelligent biomaterials.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Metal Matrix Composites, School of Material Science & Engineering, Shanghai Jiao Tong University, China.
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194
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Kang M, Yao Y. Oligodendrocyte-derived laminin-γ1 regulates the blood-brain barrier and CNS myelination in mice. Cell Rep 2024; 43:114123. [PMID: 38635399 DOI: 10.1016/j.celrep.2024.114123] [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: 08/05/2023] [Revised: 02/15/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
Although oligodendrocytes (OLs) synthesize laminin-γ1, the most widely used γ subunit, its functional significance in the CNS remains unknown. To answer this important question, we generated a conditional knockout mouse line with laminin-γ1 deficiency in OL lineage cells (γ1-OKO). γ1-OKO mice exhibit weakness/paralysis and die by post-natal day 33. Additionally, they develop blood-brain barrier (BBB) disruption in the cortex and striatum. Subsequent studies reveal decreased major facilitator superfamily domain containing 2a expression and increased endothelial caveolae vesicles, but unaltered tight junction protein expression and tight junction ultrastructure, indicating a transcellular, rather than a paracellular, mechanism of BBB breakdown. Furthermore, significantly reduced OL lineage cells, OL precursor cells (OPCs), proliferating OPCs, and mature OLs are observed in γ1-OKO brains in a region-specific manner. Consistent with this finding, various defects in myelination are detected in γ1-OKO brains at biochemical and ultrastructural levels. Overall, these results highlight important roles of OL-derived laminin-γ1 in BBB maintenance and OL biology (proliferation, differentiation, and myelination).
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Affiliation(s)
- Minkyung Kang
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Yao Yao
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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195
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Zelikson N, Ben S, Caspi M, Tarabe R, Shaleve Y, Pri-Paz Basson Y, Tayer-Shifman O, Goldberg E, Kivity S, Rosin-Arbesfeld R. Wnt signaling regulates chemokine production and cell migration of circulating human monocytes. Cell Commun Signal 2024; 22:229. [PMID: 38622714 PMCID: PMC11020454 DOI: 10.1186/s12964-024-01608-8] [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: 02/10/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The β-catenin dependent canonical Wnt signaling pathway plays a crucial role in maintaining normal homeostasis. However, when dysregulated, Wnt signaling is closely associated with various pathological conditions, including inflammation and different types of cancer.Here, we show a new connection between the leukocyte inflammatory response and the Wnt signaling pathway. Specifically, we demonstrate that circulating human primary monocytes express distinct Wnt signaling components and are susceptible to stimulation by the classical Wnt ligand-Wnt-3a. Although this stimulation increased the levels of β-catenin protein, the expression of the classical Wnt-target genes was not affected. Intriguingly, treating circulating human monocytes with Wnt-3a induces the secretion of cytokines and chemokines, enhancing monocyte migration. Mechanistically, the enhanced monocyte migration in response to Wnt stimuli is mediated through CCL2, a strong monocyte-chemoattractant.To further explore the physiological relevance of these findings, we conducted ex-vivo experiments using blood samples of patients with rheumatic joint diseases (RJD) - conditions where monocytes are known to be dysfunctional. Wnt-3a generated a unique cytokine expression profile, which was significantly distinct from that observed in monocytes obtained from healthy donors.Thus, our results provide the first evidence that Wnt-3a may serve as a potent stimulator of monocyte-driven immune processes. These findings contribute to our understanding of inflammatory diseases and, more importantly, shed light on the role of a core signaling pathway in the circulation.
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Affiliation(s)
- Natalie Zelikson
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaina Ben
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Raneen Tarabe
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yonatan Shaleve
- Department of Medicine F, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Pri-Paz Basson
- Rheumatology Unit, Meir Medical Center, Kfar Saba, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oshrat Tayer-Shifman
- Rheumatology Unit, Meir Medical Center, Kfar Saba, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elad Goldberg
- Department of Medicine F, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shaye Kivity
- Rheumatology Unit, Meir Medical Center, Kfar Saba, Israel
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel.
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196
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Jiao N, Xu J, Wang Y, Li D, Chen F, Chen Y, Chen J. Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera. BMC Genomics 2024; 25:372. [PMID: 38627613 PMCID: PMC11022335 DOI: 10.1186/s12864-024-10300-7] [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: 08/13/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio's SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera. RESULTS We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA's role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis. CONCLUSIONS This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.
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Affiliation(s)
- Nanbo Jiao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Jieru Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Yue Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Dunxi Li
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Feifei Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Yu Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China.
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China.
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197
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Ming L, Tang J, Qin F, Qin Y, Wang D, Huang L, Cao Y, Huang Z, Yin Y. Exosome secretion related gene signature predicts chemoresistance in patients with colorectal cancer. Pathol Res Pract 2024; 257:155313. [PMID: 38642509 DOI: 10.1016/j.prp.2024.155313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/14/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Colorectal cancer (CRC) is a highly heterogeneous malignancy, and patients often have different responses to treatment. In this study, the genetic characteristics related to exosome formation and secretion procedure were used to predict chemoresistance and guide the individualized treatment of patients. METHODS Firstly, seven microarray datasets in Gene Expression Omnibus (GEO) and RNA-Seq dataset from the Cancer Genome Atlas (TCGA) were used to analysis the transcriptome profiles and associated characteristics of CRC patients. Then, a predictive model based on gene features linked to exosome formation and secretion was created and validated using Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) machine learning. Finally, we evaluated the model using chemoresistant/chemosensitive cells and tissues by immunofluorescence (IF), western blot (WB), quantitative real-time PCR (qRT-PCR) and immunocytochemistry (IHC) experiments, and the predictive value of integrated model in the clinical validation cohort were performed by Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) curves analyses. RESULTS We established a risk score signature based on three genes related to exosome secretion in CRC. Better Overall Survival (OS) and greater chemosensitivity were seen in the low-risk group, whereas the high-risk group exhibited chemoresistance and a subpar response to immune checkpoint blockade (ICB) therapy. Higher expression of the model genes EXOC2, EXOC3 and STX4 were observed in chemoresistant cells and specimens. The AUC of 5-year disease-free survival (DFS) was 0.804. Compared with that in the low-risk group, patients' DFS was found to be significantly worse in the high-risk group. CONCLUSIONS In summary, the gene signature related to exosome formation and secretion could reliably predict patients' chemosensitivity and ICB treatment response, which providing new independent biomarkers for the treatment of CRC.
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Affiliation(s)
- Liang Ming
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junhui Tang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Feiyu Qin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Qin
- Department of Pathology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China
| | - Duo Wang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Liuying Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yulin Cao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuan Yin
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214062, China; Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China.
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198
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Vasavan B, Das N, Kahnamouei P, Trombley C, Swan A. Skp2-Cyclin A Interaction Is Necessary for Mitotic Entry and Maintenance of Diploidy. J Mol Biol 2024; 436:168505. [PMID: 38423454 DOI: 10.1016/j.jmb.2024.168505] [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: 10/01/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Skp2, the substrate recognition component of the SCFSkp2 ubiquitin ligase, has been implicated in the targeted destruction of a number of key cell cycle regulators and the promotion of S-phase. One of its critical targets is the Cyclin dependent kinase (Cdk) inhibitor p27, and indeed the overexpression of Skp2 in a number of cancers is directly correlated with the premature degradation of p27. Skp2 was first identified as a protein that interacts with Cyclin A in transformed cells, but its role in this complex has remained unclear. In this paper, we demonstrate that Skp2 interacts with Cyclin A in Drosophila and is required to maintain Cyclin A levels and permit mitotic entry. Failure of mitotic entry in Skp2 mutant cells results in polyploidy. If these cells enter mitosis again they are unable to properly segregate their chromosomes, leading to checkpoint dependent cell cycle arrest or apoptosis. Thus, Skp2 is required for mitosis and for maintaining diploidy and genome stability.
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Affiliation(s)
- Biju Vasavan
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 2P1, Canada
| | - Nilanjana Das
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 2P1, Canada
| | - Paria Kahnamouei
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 2P1, Canada
| | - Chantelle Trombley
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 2P1, Canada
| | - Andrew Swan
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 2P1, Canada.
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199
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Symonds K, Teresinski HJ, Hau B, Dwivedi V, Belausov E, Bar-Sinai S, Tominaga M, Haraguchi T, Sadot E, Ito K, Snedden WA. Functional characterization of calmodulin-like proteins, CML13 and CML14, as novel light chains of Arabidopsis class VIII myosins. J Exp Bot 2024; 75:2313-2329. [PMID: 38280207 DOI: 10.1093/jxb/erae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 01/29/2024]
Abstract
Myosins are important motor proteins that associate with the actin cytoskeleton. Structurally, myosins function as heteromeric complexes where smaller light chains, such as calmodulin (CaM), bind to isoleucine-glutamine (IQ) domains in the neck region to facilitate mechano-enzymatic activity. We recently identified Arabidopsis CaM-like (CML) proteins CML13 and CML14 as interactors of proteins containing multiple IQ domains, including a myosin VIII. Here, we demonstrate that CaM, CML13, and CML14 bind the neck region of all four Arabidopsis myosin VIII isoforms. Among CMLs tested for binding to myosins VIIIs, CaM, CML13, and CML14 gave the strongest signals using in planta split-luciferase protein interaction assays. In vitro, recombinant CaM, CML13, and CML14 showed specific, high-affinity, calcium-independent binding to the IQ domains of myosin VIIIs. CaM, CML13, and CML14 co-localized to plasma membrane-bound puncta when co-expressed with red fluorescent protein-myosin fusion proteins containing IQ and tail domains of myosin VIIIs. In vitro actin motility assays using recombinant myosin VIIIs demonstrated that CaM, CML13, and CML14 function as light chains. Suppression of CML13 or CML14 expression using RNA silencing resulted in a shortened-hypocotyl phenotype, similar to that observed in a quadruple myosin mutant, myosin viii4KO. Collectively, our data indicate that Arabidopsis CML13 and CML14 are novel myosin VIII light chains.
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Affiliation(s)
- Kyle Symonds
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Bryan Hau
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Vikas Dwivedi
- Institute of Plant Sciences, Volcani Institute, ARO, Rishon LeZion 7528809, Israel
| | - Eduard Belausov
- Institute of Plant Sciences, Volcani Institute, ARO, Rishon LeZion 7528809, Israel
| | - Sefi Bar-Sinai
- Institute of Plant Sciences, Volcani Institute, ARO, Rishon LeZion 7528809, Israel
| | - Motoki Tominaga
- Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Takeshi Haraguchi
- Department of Biology, Graduate School of Science, Chiba University, Inage-ku, Chiba 263-8522, Japan
| | - Einat Sadot
- Institute of Plant Sciences, Volcani Institute, ARO, Rishon LeZion 7528809, Israel
| | - Kohji Ito
- Department of Biology, Graduate School of Science, Chiba University, Inage-ku, Chiba 263-8522, Japan
| | - Wayne A Snedden
- Department of Biology, Queen's University, Kingston, ON, Canada
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200
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Li Q, Li F, Song X, Lu N, Jing X, Wen H, Ma P, Zhang H, Yao W, Wang X, Zhang M. Pan-cancer analysis of ARFs family and ARF5 promoted the progression of hepatocellular carcinoma. Heliyon 2024; 10:e29099. [PMID: 38617932 PMCID: PMC11015141 DOI: 10.1016/j.heliyon.2024.e29099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/16/2024] Open
Abstract
Background ARF family proteins are a kind of small GTPases, which are involved in regulating a variety of basic functions of cells. In recent years, the role and molecular regulatory mechanisms of ARFs in tumor progression have received increasing attention, and research reports on most of their family members are increasing. However, research on the clinical and pathological relevance of ARF5 in cancer, especially in hepatocellular carcinoma, still needs to be improved. Methods RNA-seq data in the Cancer Genome Atlas (TCGA) and genome tissue expression (GTEx) databases were used to analyze the expression and pathological data of ARFs family in Pan-cancer. Kaplan-Meier and Cox regression were used for prognostic analysis of ARF5 and Pan-cancer. Combined with ImmuCellAI database and TIMER2 database, the relationship between ARF5 expression and immune cell tumor infiltration in hepatocellular carcinoma (HCC) was analyzed. WGCNA is used to construct the co-expression gene network related to ARF5 expression in HCC and screen important modules and central genes. GO and KEGG path enrichment analysis were carried out for the genes in the modules with clinical significance. GSEA analysis was performed to take into account the role of genes with small differences. Finally, ceRNA network analysis was used to explore the molecular mechanism of miRNAs and lncRNAs regulating ARF5 expression. Results ARFs family (ARF1, ARF3, ARF4, ARF5, ARF6) are generally highly expressed in Pan-cancer. ARF5 is significantly highly expressed in 29 cancers, and the high expression of ARF5 in HCC patients is significantly negatively correlated with OS, DFI, PFI and DSS, which may lead to cancer deterioration by participating in tumor immune infiltration of HCC. Through WGCNA analysis, the expression of ARF5 in HCC may be involved in many cellular processes that consume a lot of energy, such as ribosome formation, RNA and protein synthesis and lipids, as well as COVID-19, nonalcoholic fatty liver, neurodegenerative diseases and other disease pathways. Conclusion ARFs, especially ARF5, are overexpressed in many human tumors. This study shows for the first time that ARF5 is significantly correlated with the poor prognosis of HCC patients, which may play a role as an oncogene, suggesting that ARF5 has the potential as a biomarker for the diagnosis and treatment of HCC.
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Affiliation(s)
- Qian Li
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Fang Li
- Institute of Genetics and Development Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Xinqiu Song
- Medical College of Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Ning Lu
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Xintao Jing
- Institute of Genetics and Development Biology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Hua Wen
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Peihan Ma
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Hua Zhang
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
| | - Wenzhu Yao
- Xi'an Medical University, Xi'an, 710021, Shaanxi, China
| | - Xiaofei Wang
- Biomedical Experimental Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Mingxin Zhang
- The First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, Shaanxi, China
- Shaanxi University of Traditional Chinese Medicine, Xianyang, 712046, Shaanxi, China
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