1
|
Sehgal M, Nayak SP, Sahoo S, Somarelli JA, Jolly MK. Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma. Cancer Biol Ther 2024; 25:2301802. [PMID: 38230570 PMCID: PMC10795782 DOI: 10.1080/15384047.2024.2301802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Neuroblastoma is the most frequent extracranial pediatric tumor and leads to 15% of all cancer-related deaths in children. Tumor relapse and therapy resistance in neuroblastoma are driven by phenotypic plasticity and heterogeneity between noradrenergic (NOR) and mesenchymal (MES) cell states. Despite the importance of this phenotypic plasticity, the dynamics and molecular patterns associated with these bidirectional cell-state transitions remain relatively poorly understood. Here, we analyze multiple RNA-seq datasets at both bulk and single-cell resolution, to understand the association between NOR- and MES-specific factors. We observed that NOR-specific and MES-specific expression patterns are largely mutually exclusive, exhibiting a "teams-like" behavior among the genes involved, reminiscent of our earlier observations in lung cancer and melanoma. This antagonism between NOR and MES phenotypes was also associated with metabolic reprogramming and with immunotherapy targets PD-L1 and GD2 as well as with experimental perturbations driving the NOR-MES and/or MES-NOR transition. Further, these "teams-like" patterns were seen only among the NOR- and MES-specific genes, but not in housekeeping genes, possibly highlighting a hallmark of network topology enabling cancer cell plasticity.
Collapse
Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | - Sonali Priyadarshini Nayak
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
- Max Planck School Matter to Life, University of Göttingen, Göttingen, Germany
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
| |
Collapse
|
2
|
Lehrich BM, Delgado ER. Lipid Nanovesicle Platforms for Hepatocellular Carcinoma Precision Medicine Therapeutics: Progress and Perspectives. Organogenesis 2024; 20:2313696. [PMID: 38357804 PMCID: PMC10878025 DOI: 10.1080/15476278.2024.2313696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally. HCC is highly heterogenous with diverse etiologies leading to different driver mutations potentiating unique tumor immune microenvironments. Current therapeutic options, including immune checkpoint inhibitors and combinations, have achieved limited objective response rates for the majority of patients. Thus, a precision medicine approach is needed to tailor specific treatment options for molecular subsets of HCC patients. Lipid nanovesicle platforms, either liposome- (synthetic) or extracellular vesicle (natural)-derived present are improved drug delivery vehicles which may be modified to contain specific cargos for targeting specific tumor sites, with a natural affinity for liver with limited toxicity. This mini-review provides updates on the applications of novel lipid nanovesicle-based therapeutics for HCC precision medicine and the challenges associated with translating this therapeutic subclass from preclinical models to the clinic.
Collapse
Affiliation(s)
- Brandon M. Lehrich
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Evan R. Delgado
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
3
|
Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
Collapse
Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
4
|
Chen GL, Li JY, Chen X, Liu JW, Zhang Q, Liu JY, Wen J, Wang N, Lei M, Wei JP, Yi L, Li JJ, Ling YP, Yi HQ, Hu Z, Duan J, Zhang J, Zeng B. Mechanosensitive channels TMEM63A and TMEM63B mediate lung inflation-induced surfactant secretion. J Clin Invest 2024; 134:e174508. [PMID: 38127458 PMCID: PMC10904053 DOI: 10.1172/jci174508] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023] Open
Abstract
Pulmonary surfactant is a lipoprotein complex lining the alveolar surface to decrease the surface tension and facilitate inspiration. Surfactant deficiency is often seen in premature infants and in children and adults with respiratory distress syndrome. Mechanical stretch of alveolar type 2 epithelial (AT2) cells during lung expansion is the primary physiological factor that stimulates surfactant secretion; however, it is unclear whether there is a mechanosensor dedicated to this process. Here, we show that loss of the mechanosensitive channels TMEM63A and TMEM63B (TMEM63A/B) resulted in atelectasis and respiratory failure in mice due to a deficit of surfactant secretion. TMEM63A/B were predominantly localized at the limiting membrane of the lamellar body (LB), a lysosome-related organelle that stores pulmonary surfactant and ATP in AT2 cells. Activation of TMEM63A/B channels during cell stretch facilitated the release of surfactant and ATP from LBs fused with the plasma membrane. The released ATP evoked Ca2+ signaling in AT2 cells and potentiated exocytic fusion of more LBs. Our study uncovered a vital physiological function of TMEM63 mechanosensitive channels in preparing the lungs for the first breath at birth and maintaining respiration throughout life.
Collapse
Affiliation(s)
- Gui-Lan Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jing-Yi Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Xin Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jia-Wei Liu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Qian Zhang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jie-Yu Liu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jing Wen
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Na Wang
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Ming Lei
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jun-Peng Wei
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Li Yi
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Jia-Jia Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - Yu-Peng Ling
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| | - He-Qiang Yi
- Department of Cardiothoracic Surgery, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Zhenying Hu
- Human Aging Research Institute and School of Life Sciences and
| | - Jingjing Duan
- Human Aging Research Institute and School of Life Sciences and
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Bo Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, and
| |
Collapse
|
5
|
Paquet E, Soleymani F, Viktor HL, Michalowski W. Annealed fractional Lévy-Itō diffusion models for protein generation. Comput Struct Biotechnol J 2024; 23:1641-1653. [PMID: 38680869 PMCID: PMC11047197 DOI: 10.1016/j.csbj.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024] Open
Abstract
Protein generation has numerous applications in designing therapeutic antibodies and creating new drugs. Still, it is a demanding task due to the inherent complexities of protein structures and the limitations of current generative models. Proteins possess intricate geometry, and sampling their conformational space is challenging due to its high dimensionality. This paper introduces novel Markovian and non-Markovian generative diffusion models based on fractional stochastic differential equations and the Lévy distribution, allowing for a more effective exploration of the conformational space. The approach is applied to a dataset of 40 , 000 proteins and evaluated in terms of Fréchet distance, fidelity, and diversity, outperforming the state-of-the-art by 25.4%, 35.8%, and 11.8%, respectively.
Collapse
Affiliation(s)
- Eric Paquet
- National Research Council, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
- School of Electrical Engineering and Computer Science, University of Ottawa, ON, K1N 6N5, Canada
| | - Farzan Soleymani
- Telfer School of Management, University of Ottawa, ON, K1N 6N5, Canada
| | - Herna Lydia Viktor
- School of Electrical Engineering and Computer Science, University of Ottawa, ON, K1N 6N5, Canada
| | | |
Collapse
|
6
|
Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
Collapse
Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
7
|
Trus M, Atlas D. Non-ionotropic voltage-gated calcium channel signaling. Channels (Austin) 2024; 18:2341077. [PMID: 38601983 PMCID: PMC11017947 DOI: 10.1080/19336950.2024.2341077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
Voltage-gated calcium channels (VGCCs) are the major conduits for calcium ions (Ca2+) within excitable cells. Recent studies have highlighted the non-ionotropic functionality of VGCCs, revealing their capacity to activate intracellular pathways independently of ion flow. This non-ionotropic signaling mode plays a pivotal role in excitation-coupling processes, including gene transcription through excitation-transcription (ET), synaptic transmission via excitation-secretion (ES), and cardiac contraction through excitation-contraction (EC). However, it is noteworthy that these excitation-coupling processes require extracellular calcium (Ca2+) and Ca2+ occupancy of the channel ion pore. Analogous to the "non-canonical" characterization of the non-ionotropic signaling exhibited by the N-methyl-D-aspartate receptor (NMDA), which requires extracellular Ca2+ without the influx of ions, VGCC activation requires depolarization-triggered conformational change(s) concomitant with Ca2+ binding to the open channel. Here, we discuss the contributions of VGCCs to ES, ET, and EC coupling as Ca2+ binding macromolecules that transduces external stimuli to intracellular input prior to elevating intracellular Ca2+. We emphasize the recognition of calcium ion occupancy within the open ion-pore and its contribution to the excitation coupling processes that precede the influx of calcium. The non-ionotropic activation of VGCCs, triggered by the upstroke of an action potential, provides a conceptual framework to elucidate the mechanistic aspects underlying the microseconds nature of synaptic transmission, cardiac contractility, and the rapid induction of first-wave genes.
Collapse
Affiliation(s)
- Michael Trus
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daphne Atlas
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
8
|
Bello-Madruga R, Torrent Burgas M. The limits of prediction: Why intrinsically disordered regions challenge our understanding of antimicrobial peptides. Comput Struct Biotechnol J 2024; 23:972-981. [PMID: 38404711 PMCID: PMC10884422 DOI: 10.1016/j.csbj.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/10/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
Antimicrobial peptides (AMPs) are molecules found in most organisms, playing a vital role in innate immune defense against pathogens. Their mechanism of action involves the disruption of bacterial cell membranes, causing leakage of cellular contents and ultimately leading to cell death. While AMPs typically lack a defined structure in solution, they often assume a defined conformation when interacting with bacterial membranes. Given this structural flexibility, we investigated whether intrinsically disordered regions (IDRs) with AMP-like properties could exhibit antimicrobial activity. We tested 14 peptides from different IDRs predicted to have antimicrobial activity and found that nearly all of them did not display the anticipated effects. These peptides failed to adopt a defined secondary structure and had compromised membrane interactions, resulting in a lack of antimicrobial activity. We hypothesize that evolutionary constraints may prevent IDRs from folding, even in membrane-like environments, limiting their antimicrobial potential. Moreover, our research reveals that current antimicrobial predictors fail to accurately capture the structural features of peptides when dealing with intrinsically unstructured sequences. Hence, the results presented here may have far-reaching implications for designing and improving antimicrobial strategies and therapies against infectious diseases.
Collapse
Affiliation(s)
- Roberto Bello-Madruga
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marc Torrent Burgas
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| |
Collapse
|
9
|
Xu Y, Das P, McCord RP, Shen T. Node features of chromosome structure networks and their connections to genome annotation. Comput Struct Biotechnol J 2024; 23:2240-2250. [PMID: 38827231 PMCID: PMC11140560 DOI: 10.1016/j.csbj.2024.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/04/2024] Open
Abstract
The 3D conformations of chromosomes can encode biological significance, and the implications of such structures have been increasingly appreciated recently. Certain chromosome structural features, such as A/B compartmentalization, are frequently extracted from Hi-C pairwise genome contact information (physical association between different regions of the genome) and compared with linear annotations of the genome, such as histone modifications and lamina association. We investigate how additional properties of chromosome structure can be deduced using an abstract graph representation of the contact heatmap, and describe specific network properties that can have a strong connection with some of these biological annotations. We constructed chromosome structure networks (CSNs) from bulk Hi-C data and calculated a set of site-resolved (node-based) network properties. These properties are useful for characterizing certain aspects of chromosomal structure. We examined the ability of network properties to differentiate several scenarios, such as haploid vs diploid cells, partially inverted nuclei vs conventional architecture, depletion of chromosome architectural proteins, and structural changes during cell development. We also examined the connection between network properties and a series of other linear annotations, such as histone modifications and chromatin states including poised promoter and enhancer labels. We found that semi-local network properties exhibit greater capability in characterizing genome annotations compared to diffusive or ultra-local node features. For example, the local square clustering coefficient can be a strong classifier of lamina-associated domains. We demonstrated that network properties can be useful for highlighting large-scale chromosome structure differences that emerge in different biological situations.
Collapse
Affiliation(s)
- Yingjie Xu
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Priyojit Das
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
10
|
Basu S, Kurgan L. Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses. Comput Struct Biotechnol J 2024; 23:1968-1977. [PMID: 38765610 PMCID: PMC11098722 DOI: 10.1016/j.csbj.2024.04.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.
Collapse
Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| |
Collapse
|
11
|
Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
Collapse
Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| |
Collapse
|
12
|
Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Comput Struct Biotechnol J 2024; 23:537-548. [PMID: 38235361 PMCID: PMC10791570 DOI: 10.1016/j.csbj.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.
Collapse
Affiliation(s)
- Shuixiu Wen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Yuxin Zhao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Xinyu Qi
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Mingzhu Cai
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Kaisheng Huang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Hui Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| |
Collapse
|
13
|
Hu M, Ge J, Jiang Y, Sun X, Guo D, Gu Y. Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica. Synth Syst Biotechnol 2024; 9:618-626. [PMID: 38784195 PMCID: PMC11109602 DOI: 10.1016/j.synbio.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.
Collapse
Affiliation(s)
- Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Dongshen Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| |
Collapse
|
14
|
Elbahnsi A, Dudas B, Cisternino S, Declèves X, Miteva MA. Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations. Comput Struct Biotechnol J 2024; 23:2548-2564. [PMID: 38989058 PMCID: PMC11233806 DOI: 10.1016/j.csbj.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
P-glycoprotein (P-gp) plays a crucial role in cellular detoxification and drug efflux processes, transitioning between inward-facing (IF) open, occluded, and outward-facing (OF) states to facilitate substrate transport. Its role is critical in cancer therapy, where P-gp contributes to the multidrug resistance phenotype. In our study, classical and enhanced molecular dynamics (MD) simulations were conducted to dissect the structural and functional features of the P-gp conformational states. Our advanced MD simulations, including kinetically excited targeted MD (ketMD) and adiabatic biasing MD (ABMD), provided deeper insights into state transition and translocation mechanisms. Our findings suggest that the unkinking of TM4 and TM10 helices is a prerequisite for correctly achieving the outward conformation. Simulations of the IF-occluded conformations, characterized by kinked TM4 and TM10 helices, consistently demonstrated altered communication between the transmembrane domains (TMDs) and nucleotide binding domain 2 (NBD2), suggesting the implication of this interface in inhibiting P-gp's efflux function. A particular emphasis was placed on the unstructured linker segment connecting the NBD1 to TMD2 and its role in the transporter's dynamics. With the linker present, we specifically noticed a potential entrance of cholesterol (CHOL) through the TM4-TM6 portal, shedding light on crucial residues involved in accommodating CHOL. We therefore suggest that this entry mechanism could be employed for some P-gp substrates or inhibitors. Our results provide critical data for understanding P-gp functioning and developing new P-gp inhibitors for establishing more effective strategies against multidrug resistance.
Collapse
Affiliation(s)
- Ahmad Elbahnsi
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Salvatore Cisternino
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Xavier Declèves
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Maria A. Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| |
Collapse
|
15
|
Rao J, Wang X, Chen X, Liu Y, Jiang J, Wang Z. Multi-omics analysis reveals that Cas13d contributes to PI3K-AKT signaling and facilitates cell proliferation via PFKFB4 upregulation. Gene 2024; 927:148760. [PMID: 38992762 DOI: 10.1016/j.gene.2024.148760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
The CRISPR-Cas system is a powerful gene editing technology, the clinical application of which is currently constrained due to safety concerns. A substantial body of safety research concerning Cas9 exists; however, scant attention has been directed toward investigating the safety profile of the emergent Cas13 system, which confers RNA editing capabilities. In particular, uncertainties persist regarding the potential cellular impacts of Cas13d in the absence of reliance on a cleavage effect. In this study, we conducted an initial exploration of the effects of Cas13d on HeLa cells. Total RNA and protein samples were extracted after transfection with a Cas13d-expressing plasmid construct, followed by transcriptomic and proteomic sequencing. Differential gene expression analysis identified 94 upregulated and 847 downregulated genes, while differential protein expression analysis identified 185 upregulated and 231 downregulated proteins. Subsequently, enrichment analysis was conducted on the transcriptome and proteome sequencing data, revealing that the PI3K-Akt signaling pathway is a common term. After intersecting the differentially expressed genes enriched in the PI3K-Akt signaling pathway with all the differentially expressed proteins, it was found that the expression of the related regulatory gene PFKFB4 was upregulated. Moreover, western blot analysis demonstrated that Cas13d can mediate PI3K-Akt signaling upregulation through overexpression of PFKFB4. CCK-8 assay, colony formation, and EdU experiments showed that Cas13d can promote cell proliferation. Our data demonstrate, for the first time, that Cas13d significantly impacts the transcriptomic and proteomic profiles, and proliferation phenotype, of HeLa cells, thus offering novel insights into safety considerations regarding gene editing systems.
Collapse
Affiliation(s)
- Jin Rao
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xuefu Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiangyu Chen
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yudi Liu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Junfeng Jiang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China; Histology and Embryology Department, Naval Medical University, Shanghai, China.
| | - Zhinong Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China.
| |
Collapse
|
16
|
Zheng YB, Lu S, Chu TB, Pang GF, Yang LY, Zhang Q. Investigate the potential impact of Hemagglutinin from the H1N1 strain on severe pneumonia. Gene 2024; 926:148559. [PMID: 38740352 DOI: 10.1016/j.gene.2024.148559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The most prevalent glycoprotein on the influenza virus envelope is called hemagglutinin (HA), yet little is known about its involvement in the pathophysiology and etiology of severe influenza pneumonia. Here, after stimulating human bronchial epithelial cells (16-HBE) and mice with HA of H1N1 for 12 h, we investigated the proliferation, migration, inflammatory cytokines expression, and apoptosis in 16-HBE and the pathological damage in mouse lung tissue. The expression of inflammatory cytokines plasminogen activator inhibitor 1(PAI-1), urokinase-type (uPA) and tissue-type (tPA) plasminogen activators, and apoptosis were all enhanced by HA, which also prevented the proliferation and migration of bronchial epithelial cells. HA enhanced up-regulated PAI-1, uPA, and tPA protein expression within mouse lung tissue and caused lung injury. In conclusion, HA alone, but not the whole H1N1 virus, induces lung tissue injury by inhibiting cell proliferation and migration, while promoting the expression of inflammatory cytokines and apoptosis.
Collapse
Affiliation(s)
- Yu-Bi Zheng
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China.
| | - Song Lu
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Tian-Bao Chu
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Gui-Feng Pang
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Lin-Ying Yang
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China
| | - Qing Zhang
- Affiliated Hospital of Chengde Medical University, Department of Respiratory and Critical Care Medicine, Chengde 067000, Hebei, China.
| |
Collapse
|
17
|
Zhu M, Xu H, Jin Y, Kong X, Xu B, Liu Y, Yu H. Synaptotagmin-1 undergoes phase separation to regulate its calcium-sensitive oligomerization. J Cell Biol 2024; 223:e202311191. [PMID: 38980206 PMCID: PMC11232894 DOI: 10.1083/jcb.202311191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/17/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Synaptotagmin-1 (Syt1) is a calcium sensor that regulates synaptic vesicle fusion in synchronous neurotransmitter release. Syt1 interacts with negatively charged lipids and the SNARE complex to control the fusion event. However, it remains incompletely understood how Syt1 mediates Ca2+-trigged synaptic vesicle fusion. Here, we discovered that Syt1 undergoes liquid-liquid phase separation (LLPS) to form condensates both in vitro and in living cells. Syt1 condensates play a role in vesicle attachment to the PM and efficiently recruit SNAREs and complexin, which may facilitate the downstream synaptic vesicle fusion. We observed that Syt1 condensates undergo a liquid-to-gel-like phase transition, reflecting the formation of Syt1 oligomers. The phase transition can be blocked or reversed by Ca2+, confirming the essential role of Ca2+ in Syt1 oligomer disassembly. Finally, we showed that the Syt1 mutations causing Syt1-associated neurodevelopmental disorder impair the Ca2+-driven phase transition. These findings reveal that Syt1 undergoes LLPS and a Ca2+-sensitive phase transition, providing new insights into Syt1-mediated vesicle fusion.
Collapse
Affiliation(s)
- Min Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Han Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yulei Jin
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoxu Kong
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bingkuan Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yinghui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haijia Yu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| |
Collapse
|
18
|
Dong F, Lojko P, Bazzone A, Bernhard F, Borodina I. Transporter function characterization via continuous-exchange cell-free synthesis and solid supported membrane-based electrophysiology. Bioelectrochemistry 2024; 159:108732. [PMID: 38810322 DOI: 10.1016/j.bioelechem.2024.108732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Functional characterization of transporters is impeded by the high cost and technical challenges of current transporter assays. Thus, in this work, we developed a new characterization workflow that combines cell-free protein synthesis (CFPS) and solid supported membrane-based electrophysiology (SSME). For this, membrane protein synthesis was accomplished in a continuous exchange cell-free system (CECF) in the presence of nanodiscs. The resulting transporters expressed in nanodiscs were incorporated into proteoliposomes and assayed in the presence of different substrates using the surface electrogenic event reader. As a proof of concept, we validated this workflow to express and characterize five diverse transporters: the drug/H+-coupled antiporters EmrE and SugE, the lactose permease LacY, the Na+/H+ antiporter NhaA from Escherichia coli, and the mitochondrial carrier AAC2 from Saccharomyces cerevisiae. For all transporters kinetic parameters, such as KM, IMAX, and pH dependency, were evaluated. This robust and expedite workflow (e.g., can be executed within only five workdays) offers a convenient direct functional assessment of transporter protein activity and has the ability to facilitate applications of transporters in medical and biotechnological research.
Collapse
Affiliation(s)
- Fang Dong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Pawel Lojko
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | | | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| |
Collapse
|
19
|
Xu S, Lee I, Kwon SJ, Kim E, Nevo L, Straight L, Murata H, Matyjaszewski K, Dordick JS. Split fluorescent protein-mediated multimerization of cell wall binding domain for highly sensitive and selective bacterial detection. N Biotechnol 2024; 82:54-64. [PMID: 38750815 DOI: 10.1016/j.nbt.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
Cell wall peptidoglycan binding domains (CBDs) of cell lytic enzymes, including bacteriocins, autolysins and bacteriophage endolysins, enable highly selective bacterial binding, and thus, have potential as biorecognition molecules for nondestructive bacterial detection. Here, a novel design for a self-complementing split fluorescent protein (FP) complex is proposed, where a multimeric FP chain fused with specific CBDs ((FP-CBD)n) is assembled inside the cell, to improve sensitivity by enhancing the signal generated upon Staphylococcus aureus or Bacillus anthracis binding. Flow cytometry shows enhanced fluorescence on the cell surface with increasing FP stoichiometry and surface plasmon resonance reveals nanomolar binding affinity to isolated peptidoglycan. The breadth of function of these complexes is demonstrated through the use of CBD modularity and the ability to attach enzymatic detection modalities. Horseradish peroxidase-coupled (FP-CBD)n complexes generate a catalytic amplification, with the degree of amplification increasing as a function of FP length, reaching a limit of detection (LOD) of 103 cells/droplet (approximately 0.1 ng S. aureus or B. anthracis) within 15 min on a polystyrene surface. These fusion proteins can be multiplexed for simultaneous detection. Multimeric split FP-CBD fusions enable use as a biorecognition molecule with enhanced signal for use in bacterial biosensing platforms.
Collapse
Affiliation(s)
- Shirley Xu
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Inseon Lee
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Eunsol Kim
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Liv Nevo
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Lorelli Straight
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA
| | - Hironobu Murata
- Department of Chemistry, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA
| | | | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA; Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY, USA.
| |
Collapse
|
20
|
Niu M, Whang H, Wu Z, Jiang S, Chen L. Deletion of Asb15b gene can lead to a significant decrease in zebrafish intermuscular bone. Gene 2024; 923:148561. [PMID: 38754570 DOI: 10.1016/j.gene.2024.148561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Intermuscular bones, which are present in numerous economically significant fish species, have a negative impact on the development of aquaculture. The Asb15b gene, primarily expressed in skeletal muscle, plays a crucial role in regulating protein turnover and the development of muscle fibers. It stimulates protein synthesis and controls the differentiation of muscle fibers. In this study, we employed CRISPR/Cas9 technology to generate homozygous zebrafish strains with 7 bp and 49 bp deletions in the Asb15b gene. Subsequent analyses using skeleton staining demonstrated a substantial reduction in the number of intermuscular bones in adult Asb15b-/- -7 bp and Asb15b-/- -49 bp mutants compared to the wild-type zebrafish, with decreases of 30 % (P < 0.001) and 40 % (P < 0.0001), respectively. Histological experiments further revealed that the diameter and number of muscle fibers in adult Asb15b-/- mutants did not exhibit significant changes when compared to wild-type zebrafish. Moreover, qRT-PCR experiments demonstrated significant differences in the expression of bmp6 and runx2b genes, which are key regulators of intermuscular bone development, during different stages of intermuscular bone development in Asb15b-/- mutants. This study strongly suggests that the Asb15b gene plays a crucial role in regulating intermuscular bone development in fish and lays the groundwork for further exploration of the role of the Asb15b gene in zebrafish intermuscular bone development.
Collapse
Affiliation(s)
- Minghui Niu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Huamin Whang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Zhichao Wu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Shouwen Jiang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Liangbiao Chen
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China.
| |
Collapse
|
21
|
Liu Y, Du M, Shu S, Wei J, Zhu K, Wang G. Bacterial surface properties and transport behavior actively respond to an extracellular polymeric substance gradient in saturated porous media. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173889. [PMID: 38876335 DOI: 10.1016/j.scitotenv.2024.173889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
The transport and retention of bacteria in porous media, such as aquifer, are governed by the solid-liquid interface characteristics and bacterial mobility. The secretion of extracellular polymeric substance (EPS) by bacteria modifies their surface property, and thereby has effects on their adhesion to surface. The role of EPS in bacterial mobility within saturated quartz sand media is uncertain, as both promoting and inhibitory effects have been reported, and underlying mechanisms remain unclear. In this study, the effects of EPS on bacterial transport behavior and possible underlying mechanism were investigated at 4 concentrations (0 mg L-1, 50 mg L-1, 200 mg L-1 and 1000 mg L-1) using laboratory simulation experiments in conjunction with Extend Derjaguin-Landau-Verweu-Overbeek (XDLVO) modeling. The results showed that EPS facilitated bacterial mobility at all tested concentrations. It could be partially explained by the increased energy barrier between bacterial cells and quartz sand surface in the presence of EPS. The XDLVO sphere-plate model predicted that EPS induced a higher electrostatic double layer (EDL) repulsive force, Lewis acid-base (AB) and steric stabilization (ST), as well as a lower Lifshitz-van der Waals (LW) attractive force. However, at the highest EPS concentration (1000 mg L-1), the promotion of EPS on bacterial mobility weakened as a result of lower repulsive interactions between cells, which was supported by observed enhanced bacterial aggregation. Consequently, the increased aggregation led to greater bio-colloidal straining and ripening in the sand column, weakening the positive impact of EPS on bacterial transport. These findings suggested that EPS exhibited concentration-dependent effects on bacterial surface properties and transport behavior and revealed non-intuitive dual effects of EPS on those processes.
Collapse
Affiliation(s)
- Ying Liu
- Department of Soil and Water Sciences, National Black Soil & Agriculture Research, China Agricultural University, Beijing 100193, China
| | - Mengya Du
- Department of Soil and Water Sciences, National Black Soil & Agriculture Research, China Agricultural University, Beijing 100193, China
| | - Shangyi Shu
- Department of Soil and Water Sciences, National Black Soil & Agriculture Research, China Agricultural University, Beijing 100193, China
| | - Jian Wei
- Department of Soil and Water Sciences, National Black Soil & Agriculture Research, China Agricultural University, Beijing 100193, China
| | - Kun Zhu
- Department of Soil and Water Sciences, National Black Soil & Agriculture Research, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- Department of Soil and Water Sciences, National Black Soil & Agriculture Research, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
22
|
Li X, Gamuyao R, Wu ML, Cho WJ, King SV, Petersen R, Stabley DR, Lindow C, Climer LK, Shirinifard A, Ferrara F, Throm RE, Robinson CG, Zhou Y, Carisey AF, Tebo AG, Chang CL. A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction. J Cell Biol 2024; 223:e202311126. [PMID: 38949658 PMCID: PMC11215687 DOI: 10.1083/jcb.202311126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
Contact sites between lipid droplets and other organelles are essential for cellular lipid and energy homeostasis upon metabolic demands. Detection of these contact sites at the nanometer scale over time in living cells is challenging. We developed a tool kit for detecting contact sites based on fluorogen-activated bimolecular complementation at CONtact sites, FABCON, using a reversible, low-affinity split fluorescent protein, splitFAST. FABCON labels contact sites with minimal perturbation to organelle interaction. Via FABCON, we quantitatively demonstrated that endoplasmic reticulum (ER)- and mitochondria (mito)-lipid droplet contact sites are dynamic foci in distinct metabolic conditions, such as during lipid droplet biogenesis and consumption. An automated analysis pipeline further classified individual contact sites into distinct subgroups based on size, likely reflecting differential regulation and function. Moreover, FABCON is generalizable to visualize a repertoire of organelle contact sites including ER-mito. Altogether, FABCON reveals insights into the dynamic regulation of lipid droplet-organelle contact sites and generates new hypotheses for further mechanistical interrogation during metabolic regulation.
Collapse
Affiliation(s)
- Xiao Li
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Rico Gamuyao
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ming-Lun Wu
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Woo Jung Cho
- Cell and Tissue Imaging Center, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sharon V. King
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - R.A. Petersen
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Daniel R. Stabley
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Caleb Lindow
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Leslie K. Climer
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Francesca Ferrara
- Vector Production and Development Laboratory, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Robert E. Throm
- Vector Production and Development Laboratory, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Camenzind G. Robinson
- Cell and Tissue Imaging Center, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yiwang Zhou
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Alexandre F. Carisey
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Alison G. Tebo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Chi-Lun Chang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| |
Collapse
|
23
|
Neahring L, Cho NH, He Y, Liu G, Fernandes J, Rux CJ, Nakos K, Subramanian R, Upadhyayula S, Yildiz A, Dumont S. Torques within and outside the human spindle balance twist at anaphase. J Cell Biol 2024; 223:e202312046. [PMID: 38869473 PMCID: PMC11176257 DOI: 10.1083/jcb.202312046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are together required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.
Collapse
Affiliation(s)
- Lila Neahring
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Nathan H. Cho
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Yifei He
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jonathan Fernandes
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Caleb J. Rux
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Konstantinos Nakos
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ahmet Yildiz
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Physics Department, University of California Berkeley, Berkeley, CA, USA
| | - Sophie Dumont
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
- UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
24
|
Chao X, Yang Y, Gong W, Zou S, Tu H, Li D, Feng W, Cai H. Leep2A and Leep2B function as a RasGAP complex to regulate macropinosome formation. J Cell Biol 2024; 223:e202401110. [PMID: 38888895 PMCID: PMC11187982 DOI: 10.1083/jcb.202401110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/12/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Macropinocytosis mediates the non-selective bulk uptake of extracellular fluid, enabling cells to survey the environment and obtain nutrients. A conserved set of signaling proteins orchestrates the actin dynamics that lead to membrane ruffling and macropinosome formation across various eukaryotic organisms. At the center of this signaling network are Ras GTPases, whose activation potently stimulates macropinocytosis. However, how Ras signaling is initiated and spatiotemporally regulated during macropinocytosis is not well understood. By using the model system Dictyostelium and a proteomics-based approach to identify regulators of macropinocytosis, we uncovered Leep2, consisting of Leep2A and Leep2B, as a RasGAP complex. The Leep2 complex specifically localizes to emerging macropinocytic cups and nascent macropinosomes, where it modulates macropinosome formation by regulating the activities of three Ras family small GTPases. Deletion or overexpression of the complex, as well as disruption or sustained activation of the target Ras GTPases, impairs macropinocytic activity. Our data reveal the critical role of fine-tuning Ras activity in directing macropinosome formation.
Collapse
Affiliation(s)
- Xiaoting Chao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yihong Yang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weibin Gong
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Songlin Zou
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hui Tu
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Peking University, Beijing, China
| | - Dong Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Feng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huaqing Cai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
25
|
Fuller KB, Jacobs RQ, Carter ZI, Cuny ZG, Schneider DA, Lucius AL. Global kinetic mechanism describing single nucleotide incorporation for RNA polymerase I reveals fast UMP incorporation. Biophys Chem 2024; 312:107281. [PMID: 38889653 PMCID: PMC11260521 DOI: 10.1016/j.bpc.2024.107281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
RNA polymerase I (Pol I) is responsible for synthesizing ribosomal RNA, which is the rate limiting step in ribosome biogenesis. We have reported wide variability in the magnitude of the rate constants defining the rate limiting step in sequential nucleotide additions catalyzed by Pol I. in this study we sought to determine if base identity impacts the rate limiting step of nucleotide addition catalyzed by Pol I. To this end, we report a transient state kinetic interrogation of AMP, CMP, GMP, and UMP incorporations catalyzed by Pol I. We found that Pol I uses one kinetic mechanism to incorporate all nucleotides. However, we found that UMP incorporation is faster than AMP, CMP, and GMP additions. Further, we found that endonucleolytic removal of a dimer from the 3' end was fastest when the 3' terminal base is a UMP. It has been previously shown that both downstream and upstream template sequence identity impacts the kinetics of nucleotide addition. The results reported here show that the incoming base identity also impacts the magnitude of the observed rate limiting step.
Collapse
Affiliation(s)
- Kaila B Fuller
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA
| | | | - Zachary G Cuny
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, AL 35294, USA.
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
26
|
Reyhani-Ardabili M, Ghafouri-Fard S. CRISPR/Cas9 technology in the modeling of and treatment of mucopolysaccharidosis. Biochem Biophys Rep 2024; 39:101771. [PMID: 39044769 PMCID: PMC11263496 DOI: 10.1016/j.bbrep.2024.101771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/22/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024] Open
Abstract
Mucopolysaccharidosis (MPS) syndromes are a group of heterogeneous genetic disorders in terms of genetic basis and clinical manifestations, ranging from mild to fatal forms. There are a number of applied or prospective treatment modalities for MPS, including bone marrow transplantation, enzyme replacement therapy, targeted gene therapy and substrate reduction therapy. Recently, CRISPR/Cas9 technology has emerged as a novel tool for several metabolic disorders, such as MPS. This review concentrates on the application of this technique in the treatment of MPS, particularly MPS I, and modeling of disease-causing mutations.
Collapse
Affiliation(s)
- Mehran Reyhani-Ardabili
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
27
|
Wang Y, Gao M, Zhu S, Li Z, Zhang T, Jiang Y, Zhu L, Zhan X. Glycerol-driven adaptive evolution for the production of low-molecular-weight Welan gum: Characterization and activity evaluation. Carbohydr Polym 2024; 339:122292. [PMID: 38823937 DOI: 10.1016/j.carbpol.2024.122292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 06/03/2024]
Abstract
Through adaptive laboratory evolution (ALE) of Sphingomonas sp. ATCC 31555, fermentation for production of low-molecular-weight welan gum (LMW-WG) was performed using glycerol as sole carbon source. During ALE, GPC-MALS analysis revealed a gradual decrease in WG molecular weight with the increase of adaptation cycles, accompanied by changes in solution conformation. LMW-WG was purified and structurally analyzed using GPC-MALS, monosaccharide composition analysis, infrared spectroscopy, NMR analysis, atomic force microscopy, and scanning electron microscopy. Subsequently, LMW-WG obtains hydration, transparency, antioxidant activity, and rheological properties. Finally, an in vitro simulation colon reactor was used to evaluate potential prebiotic properties of LMW-WG as dietary fiber. Compared with WG produced using sucrose as substrate, LMW-WG exhibited a fourfold reduction in molecular weight while maintaining moderate viscosity. Structurally, L-Rha nearly completely replaced L-Man. Furthermore, LMW-WG demonstrated excellent hydration, antioxidant activity, and high transparency. It also exhibited resistance to saliva and gastrointestinal digestion, showcasing a favorable colonization effect on Bifidobacterium, making it a promising symbiotic agent.
Collapse
Affiliation(s)
- Yuying Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Minjie Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shengyong Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhitao Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tiantian Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yun Jiang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Zhu
- A & F Biotech. Ltd., Burnaby, BC V5A3P6, Canada
| | - Xiaobei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
28
|
Richardson B, Goedert T, Quraishe S, Deinhardt K, Mudher A. How do neurons age? A focused review on the aging of the microtubular cytoskeleton. Neural Regen Res 2024; 19:1899-1907. [PMID: 38227514 DOI: 10.4103/1673-5374.390974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 01/17/2024] Open
Abstract
Aging is the leading risk factor for Alzheimer's disease and other neurodegenerative diseases. We now understand that a breakdown in the neuronal cytoskeleton, mainly underpinned by protein modifications leading to the destabilization of microtubules, is central to the pathogenesis of Alzheimer's disease. This is accompanied by morphological defects across the somatodendritic compartment, axon, and synapse. However, knowledge of what occurs to the microtubule cytoskeleton and morphology of the neuron during physiological aging is comparatively poor. Several recent studies have suggested that there is an age-related increase in the phosphorylation of the key microtubule stabilizing protein tau, a modification, which is known to destabilize the cytoskeleton in Alzheimer's disease. This indicates that the cytoskeleton and potentially other neuronal structures reliant on the cytoskeleton become functionally compromised during normal physiological aging. The current literature shows age-related reductions in synaptic spine density and shifts in synaptic spine conformation which might explain age-related synaptic functional deficits. However, knowledge of what occurs to the microtubular and actin cytoskeleton, with increasing age is extremely limited. When considering the somatodendritic compartment, a regression in dendrites and loss of dendritic length and volume is reported whilst a reduction in soma volume/size is often seen. However, research into cytoskeletal change is limited to a handful of studies demonstrating reductions in and mislocalizations of microtubule-associated proteins with just one study directly exploring the integrity of the microtubules. In the axon, an increase in axonal diameter and age-related appearance of swellings is reported but like the dendrites, just one study investigates the microtubules directly with others reporting loss or mislocalization of microtubule-associated proteins. Though these are the general trends reported, there are clear disparities between model organisms and brain regions that are worthy of further investigation. Additionally, longitudinal studies of neuronal/cytoskeletal aging should also investigate whether these age-related changes contribute not just to vulnerability to disease but also to the decline in nervous system function and behavioral output that all organisms experience. This will highlight the utility, if any, of cytoskeletal fortification for the promotion of healthy neuronal aging and potential protection against age-related neurodegenerative disease. This review seeks to summarize what is currently known about the physiological aging of the neuron and microtubular cytoskeleton in the hope of uncovering mechanisms underpinning age-related risk to disease.
Collapse
Affiliation(s)
- Brad Richardson
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Thomas Goedert
- Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Shmma Quraishe
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Katrin Deinhardt
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Amritpal Mudher
- School of Biological Sciences, University of Southampton, Southampton, UK
| |
Collapse
|
29
|
Yuce M, Ates B, Yasar NI, Sungur FA, Kurkcuoglu O. A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome. J Mol Graph Model 2024; 131:108817. [PMID: 38976944 DOI: 10.1016/j.jmgm.2024.108817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the E. coli ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligand-rRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for in vitro studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.
Collapse
Affiliation(s)
- Merve Yuce
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Beril Ates
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Nesrin Isil Yasar
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Fethiye Aylin Sungur
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Ozge Kurkcuoglu
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| |
Collapse
|
30
|
Parihar K, Ko SHB, Bradley RP, Taylor P, Ramakrishnan N, Baumgart T, Guo W, Weaver VM, Janmey PA, Radhakrishnan R. Asymmetric crowders and membrane morphology at the nexus of intracellular trafficking and oncology. MECHANOBIOLOGY IN MEDICINE 2024; 2:100071. [PMID: 38899029 PMCID: PMC11185830 DOI: 10.1016/j.mbm.2024.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A definitive understanding of the interplay between protein binding/migration and membrane curvature evolution is emerging but needs further study. The mechanisms defining such phenomena are critical to intracellular transport and trafficking of proteins. Among trafficking modalities, exosomes have drawn attention in cancer research as these nano-sized naturally occurring vehicles are implicated in intercellular communication in the tumor microenvironment, suppressing anti-tumor immunity and preparing the metastatic niche for progression. A significant question in the field is how the release and composition of tumor exosomes are regulated. In this perspective article, we explore how physical factors such as geometry and tissue mechanics regulate cell cortical tension to influence exosome production by co-opting the biophysics as well as the signaling dynamics of intracellular trafficking pathways and how these exosomes contribute to the suppression of anti-tumor immunity and promote metastasis. We describe a multiscale modeling approach whose impact goes beyond the fundamental investigation of specific cellular processes toward actual clinical translation. Exosomal mechanisms are critical to developing and approving liquid biopsy technologies, poised to transform future non-invasive, longitudinal profiling of evolving tumors and resistance to cancer therapies to bring us one step closer to the promise of personalized medicine.
Collapse
Affiliation(s)
- Kshitiz Parihar
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Seung-Hyun B. Ko
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan P. Bradley
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Taylor
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - N. Ramakrishnan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Tobias Baumgart
- Department of Chemistry, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Guo
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Valerie M. Weaver
- Department of Surgery, Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA, USA
| | - Paul A. Janmey
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
31
|
Tong M, Zhai K, Duan Y, Xia W, Zhao B, Zhang L, Chu J, Yao X. Selenium alleviates the adverse effects of microplastics on kale by regulating photosynthesis, redox homeostasis, secondary metabolism and hormones. Food Chem 2024; 450:139349. [PMID: 38631205 DOI: 10.1016/j.foodchem.2024.139349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Kale is a functional food with anti-cancer, antioxidant, and anemia prevention properties. The harmful effects of the emerging pollutant microplastic (MP) on plants have been widely studied, but there is limited research how to mitigate MP damage on plants. Numerous studies have shown that Se is involved in regulating plant resistance to abiotic stresses. The paper investigated impact of MP and Se on kale growth, photosynthesis, reactive oxygen species (ROS) metabolism, phytochemicals, and endogenous hormones. Results revealed that MP triggered a ROS burst, which led to breakdown of antioxidant system in kale, and had significant toxic effects on photosynthetic system, biomass, and accumulation of secondary metabolites, as well as a significant decrease in IAA and a significant increase in GA. Under MP supply, Se mitigated the adverse effects of MP on kale by increasing photosynthetic pigment content, stimulating function of antioxidant system, enhancing secondary metabolite synthesis, and modulating hormonal networks.
Collapse
Affiliation(s)
- Mengting Tong
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Kuizhi Zhai
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Yusui Duan
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Wansheng Xia
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Bingnan Zhao
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Lulu Zhang
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Jianzhou Chu
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xiaoqin Yao
- School of Life Sciences, Hebei University, Baoding 071002, China; Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China; Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding 071002, China.
| |
Collapse
|
32
|
Nabi IR, Cardoen B, Khater IM, Gao G, Wong TH, Hamarneh G. AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. J Cell Biol 2024; 223:e202311073. [PMID: 38865088 PMCID: PMC11169916 DOI: 10.1083/jcb.202311073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular localization tools to study molecular structure at the nanoscale level in the intact cell, bridging the mesoscale gap to classical structural biology methodologies. Analysis of super-resolution data by artificial intelligence (AI), such as machine learning, offers tremendous potential for the discovery of new biology, that, by definition, is not known and lacks ground truth. Herein, we describe the application of weakly supervised paradigms to super-resolution microscopy and its potential to enable the accelerated exploration of the nanoscale architecture of subcellular macromolecules and organelles.
Collapse
Affiliation(s)
- Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Ben Cardoen
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Ismail M. Khater
- School of Computing Science, Simon Fraser University, Burnaby, Canada
- Department of Electrical and Computer Engineering, Faculty of Engineering and Technology, Birzeit University, Birzeit, Palestine
| | - Guang Gao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Timothy H. Wong
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ghassan Hamarneh
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| |
Collapse
|
33
|
Tomar RS, Niedzwiedzki DM, Liu H. Altered excitation energy transfer between phycobilisome and photosystems in the absence of ApcG, a small linker peptide, in Synechocystis sp. PCC 6803, a cyanobacterium. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149049. [PMID: 38801856 DOI: 10.1016/j.bbabio.2024.149049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Phycobilisome (PBS) is a large pigment-protein complex in cyanobacteria and red algae responsible for capturing sunlight and transferring its energy to photosystems (PS). Spectroscopic and structural properties of various PBSs have been widely studied, however, the nature of so-called complex-complex interactions between PBS and PSs remains much less explored. In this work, we have investigated the function of a newly identified PBS linker protein, ApcG, some domain of which, together with a loop region (PB-loop in ApcE), is possibly located near the PBS-PS interface. Using Synechocystis sp. PCC 6803, we generated an ApcG deletion mutant and probed its deletion effect on the energetic coupling between PBS and photosystems. Steady-state and time-resolved spectroscopic characterization of the purified ΔApcG-PBS demonstrated that ApcG removal weakly affects the photophysical properties of PBS for which the spectroscopic properties of terminal energy emitters are comparable to those of PBS from wild-type strain. However, analysis of fluorescence decay imaging datasets reveals that ApcG deletion induces disruptions within the allophycocyanin (APC) core, resulting in the emergence (splitting) of two spectrally diverse subgroups with some short-lived APC. Profound spectroscopic changes of the whole ΔApcG mutant cell, however, emerge during state transition, a dynamic process of light scheme adaptation. The mutant cells in State I show a substantial increase in PBS-related fluorescence. On the other hand, global analysis of time-resolved fluorescence demonstrates that in general ApcG deletion does not alter or inhibit state transitions interpreted in terms of the changes of the PSII and PSI fluorescence emission intensity. The results revealed yet-to-be discovered mechanism of ApcG-docking induced excitation energy transfer regulation within PBS or to Photosystems.
Collapse
Affiliation(s)
- Rupal Singh Tomar
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Energy Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Haijun Liu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA.
| |
Collapse
|
34
|
Grimes SL, Denison MR. The Coronavirus helicase in replication. Virus Res 2024; 346:199401. [PMID: 38796132 PMCID: PMC11177069 DOI: 10.1016/j.virusres.2024.199401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
The coronavirus nonstructural protein (nsp) 13 encodes an RNA helicase (nsp13-HEL) with multiple enzymatic functions, including unwinding and nucleoside phosphatase (NTPase) activities. Attempts for enzymatic inactivation have defined the nsp13-HEL as a critical enzyme for viral replication and a high-priority target for antiviral development. Helicases have been shown to play numerous roles beyond their canonical ATPase and unwinding activities, though these functions are just beginning to be explored in coronavirus biology. Recent genetic and biochemical studies, as well as work in structurally-related helicases, have provided evidence that supports new hypotheses for the helicase's potential role in coronavirus replication. Here, we review several aspects of the coronavirus nsp13-HEL, including its reported and proposed functions in viral replication and highlight fundamental areas of research that may aid the development of helicase inhibitors.
Collapse
Affiliation(s)
- Samantha L Grimes
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark R Denison
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| |
Collapse
|
35
|
Liang W, Liang B, Yan K, Zhang G, Zhuo J, Cai Y. Low-Intensity Pulsed Ultrasound: A Physical Stimulus with Immunomodulatory and Anti-inflammatory Potential. Ann Biomed Eng 2024; 52:1955-1981. [PMID: 38683473 DOI: 10.1007/s10439-024-03523-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024]
Abstract
Ultrasound has expanded into the therapeutic field as a medical imaging and diagnostic technique. Low-intensity pulsed ultrasound (LIPUS) is a kind of therapeutic ultrasound that plays a vital role in promoting fracture healing, wound repair, immunomodulation, and reducing inflammation. Its anti-inflammatory effects are manifested by decreased pro-inflammatory cytokines and chemokines, accelerated regression of immune cell invasion, and accelerated damage repair. Although the anti-inflammatory mechanism of LIPUS is not very clear, many in vitro and in vivo studies have shown that LIPUS may play its anti-inflammatory role by activating signaling pathways such as integrin/Focal adhesion kinase (FAK)/Phosphatidylinositol 3-kinase (PI3K)/Serine threonine kinase (Akt), Vascular endothelial growth factor (VEGF)/endothelial nitric oxide synthase (eNOS), or inhibiting signaling pathways such as Toll-like receptors (TLRs)/Nuclear factor kappa-B (NF-κB) and p38-Mitogen-activated protein kinase (MAPK). As a non-invasive physical therapy, the anti-inflammatory and immunomodulatory effects of LIPUS deserve further exploration.
Collapse
Affiliation(s)
- Wenxin Liang
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of Chinese PLA General Hospital, 28 Fu Xing Road, Beijing, 100853, People's Republic of China
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Beibei Liang
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of Chinese PLA General Hospital, 28 Fu Xing Road, Beijing, 100853, People's Republic of China
| | - Kaicheng Yan
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of Chinese PLA General Hospital, 28 Fu Xing Road, Beijing, 100853, People's Republic of China
| | - Guanxuanzi Zhang
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of Chinese PLA General Hospital, 28 Fu Xing Road, Beijing, 100853, People's Republic of China
| | - Jiaju Zhuo
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of Chinese PLA General Hospital, 28 Fu Xing Road, Beijing, 100853, People's Republic of China
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Yun Cai
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of Chinese PLA General Hospital, 28 Fu Xing Road, Beijing, 100853, People's Republic of China.
| |
Collapse
|
36
|
Blondel M, Machet C, Wildemann B, Abidine Y, Swider P. Mechanobiology of bacterial biofilms: Implications for orthopedic infection. J Orthop Res 2024; 42:1861-1869. [PMID: 38432991 DOI: 10.1002/jor.25822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Postoperative bacterial infections are prevalent complications in both human and veterinary orthopedic surgery, particularly when a biofilm develops. These infections often result in delayed healing, early revision, permanent functional loss, and, in severe cases, amputation. The diagnosis and treatment pose significant challenges, and bacterial biofilm further amplifies the therapeutic difficulty as it confers protection against the host immune system and against antibiotics which are usually administered as a first-line therapeutic option. However, the inappropriate use of antibiotics has led to the emergence of numerous multidrug-resistant organisms, which largely compromise the already imperfect treatment efficiency. In this context, the study of bacterial biofilm formation allows to better target antibiotic use and to evaluate alternative therapeutic strategies. Exploration of the roles played by mechanical factors on biofilm development is of particular interest, especially because cartilage and bone tissues are reactive environments that are subjected to mechanical load. This review delves into the current landscape of biofilm mechanobiology, exploring the role of mechanical factors on biofilm development through a multiscale prism starting from bacterial microscopic scale to reach biofilm mesoscopic size and finally the macroscopic scale of the fracture site or bone-implant interface.
Collapse
Affiliation(s)
- Margaux Blondel
- Small Animal Surgery Department, Lyon University, VetAgro Sup, Marcy l'Etoile, France
| | - Camille Machet
- National Veterinary School of Toulouse, Toulouse, France
| | - Britt Wildemann
- Experimental Trauma Surgery, Department of Trauma, Hand and Reconstructive Surgery, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Yara Abidine
- Institut de Mécanique des Fluides (IMFT), CNRS & Toulouse University, Toulouse, France
| | - Pascal Swider
- Institut de Mécanique des Fluides (IMFT), CNRS & Toulouse University, Toulouse, France
| |
Collapse
|
37
|
Liu Y, Sun T, Yang J, Luo J, Zhou H. Fractionated irradiation induces radioresistant oral carcinoma cells with enhanced malignant phenotypes. Arch Oral Biol 2024; 164:105988. [PMID: 38788293 DOI: 10.1016/j.archoralbio.2024.105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE The fact that certain oral carcinoma patients experience radiotherapy failure implies that a more radioresistant and aggressive phenotype of surviving cancer cells potentially occurs during treatment. Our study aimed to establish radioresistant oral cancer cells through a fractionated irradiation protocol that mimics clinically relevant radiotherapy dosing strategies and to investigate all-round alterations in the malignant phenotype. METHODS Radioresistant oral carcinoma cells were generated by exposing Cal27 and Detroit 562 cells to 60 Gy radiation in 10 dose-escalating fractions and verified by cell immunofluorescence. Specific markers related to the epithelial-mesenchymal transition (EMT) process and the cancer stem cell (CSC) phenotype were assessed by Western blotting. Cell invasion and migration were evaluated using Matrigel-coated transwell and wound healing assays, respectively. Nontargeted metabolomics was used to mechanistically delineate the potential metabolic patterns linked to EMT and CSCs; the CSC phenotype was also examined by sphere formation assays and cell immunofluorescence. RESULTS Radioresistant oral carcinoma cell lines were successfully established and validated. These cells exhibited enhanced EMT and increase in both cell invasion and migration. These radioresistant cells further demonstrated a high metabolic profile, notably marked by lipid metabolism reprogramming and functional enrichment of ATP-binding cassette (ABC) transporters. Consistently, enhanced CSC phenotype in radioresistant cells was confirmed by elevated expression of stemness markers and increased sphere-forming capacity. CONCLUSION Radioresistant oral carcinoma cells subjected to fractionated radiation exhibit an augmented malignant phenotype. The metabolic characteristics linked to enhanced EMT and CSC phenotypes provide potential targets for improving radiotherapy in oral carcinoma.
Collapse
Affiliation(s)
- Yangfan Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Tongxu Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jin Yang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jingjing Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China.
| |
Collapse
|
38
|
Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
Collapse
Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
39
|
Yeo J, Daurer BJ, Kimanius D, Balakrishnan D, Bepler T, Tan YZ, Loh ND. Ghostbuster: A phase retrieval diffraction tomography algorithm for cryo-EM. Ultramicroscopy 2024; 262:113962. [PMID: 38642481 DOI: 10.1016/j.ultramic.2024.113962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/16/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024]
Abstract
Ewald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles, reconstruction artifacts which we refer to as ghosts can appear. By retrieving the lost phases of the electron exitwaves and accounting for the first Born approximation scattering within the particle, we show that these ghosts can be effectively eliminated. Our simulations demonstrate how such ghostbusting can improve reconstructions as compared to existing state-of-the-art software. Like ptychographic cryo-EM, our Ghostbuster algorithm uses phase retrieval to improve reconstructions, but unlike the former, we do not need to modify the existing data acquisition pipelines.
Collapse
Affiliation(s)
- Joel Yeo
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, 119077 Singapore, Singapore; Department of Physics, National University of Singapore, 117551 Singapore, Singapore; Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, 138634 Singapore, Singapore
| | - Benedikt J Daurer
- Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Diamond Light Source, Harwell Campus, Didcot, OX11 0DE, UK
| | - Dari Kimanius
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; CZ Imaging Institute, 3400 Bridge Parkway, Redwood City, CA 94065, USA
| | - Deepan Balakrishnan
- Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore; Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore; Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore; Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648 Singapore, Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, 138673 Singapore, Singapore
| | - N Duane Loh
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, 119077 Singapore, Singapore; Department of Physics, National University of Singapore, 117551 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 117558 Singapore, Singapore; Center for Bio-Imaging Sciences, National University of Singapore, 117557 Singapore, Singapore.
| |
Collapse
|
40
|
Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
Collapse
Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| |
Collapse
|
41
|
Zhong L, Wang Z, Ye X, Cui J, Wang Z, Jia S. Molecular simulations guide immobilization of lipase on nest-like ZIFs with regulatable hydrophilic/hydrophobic surface. J Colloid Interface Sci 2024; 667:199-211. [PMID: 38636222 DOI: 10.1016/j.jcis.2024.04.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/24/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
The catalytic performance of immobilized lipase is greatly influenced by functional support, which attracts growing interest for designing supports to achieve their promotive catalytic activity. Many lipases bind strongly to hydrophobic surfaces where they undergo interfacial activation. Herein, the behavioral differences of lipases with distinct lid structures on interfaces of varying hydrophobicity levels were firstly investigated by molecular simulations. It was found that a reasonable hydrophilic/hydrophobic surface could facilitate the lipase to undergo interfacial activation. Building on these findings, a novel "nest"-like superhydrophobic ZIFs (ZIFN) composed of hydrophobic ligands was prepared for the first time and used to immobilize lipase from Aspergillus oryzae (AOL@ZIFN). The AOL@ZIFN exhibited 2.0-folds higher activity than free lipase in the hydrolysis of p-Nitrophenyl palmitate (p-NPP). Especially, the modification of superhydrophobic ZIFN with an appropriate amount of hydrophilic tannic acid can significantly improve the activity of the immobilized lipase (AOL@ZIFN-TA). The AOL@ZIFN-TA exhibited 30-folds higher activity than free lipase, and still maintained 82% of its initial activity after 5 consecutive cycles, indicating good reusability. These results demonstrated that nanomaterials with rational arrangement of the hydrophilic/hydrophobic surface could facilitate the lipase to undergo interfacial activation and improve its activity, displaying the potential of the extensive application.
Collapse
Affiliation(s)
- Le Zhong
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, PR China
| | - Zhongjie Wang
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, PR China
| | - Xiaohong Ye
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, PR China
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, PR China.
| | - Ziyuan Wang
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, PR China.
| | - Shiru Jia
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, PR China
| |
Collapse
|
42
|
Li J, Huang X, An Y, Chen X, Chen Y, Xu M, Shan H, Zhang M. The role of snapin in regulation of brain homeostasis. Neural Regen Res 2024; 19:1696-1701. [PMID: 38103234 PMCID: PMC10960280 DOI: 10.4103/1673-5374.389364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/15/2023] [Accepted: 10/08/2023] [Indexed: 12/18/2023] Open
Abstract
Brain homeostasis refers to the normal working state of the brain in a certain period, which is important for overall health and normal life activities. Currently, there is a lack of effective treatment methods for the adverse consequences caused by brain homeostasis imbalance. Snapin is a protein that assists in the formation of neuronal synapses and plays a crucial role in the normal growth and development of synapses. Recently, many researchers have reported the association between snapin and neurologic and psychiatric disorders, demonstrating that snapin can improve brain homeostasis. Clinical manifestations of brain disease often involve imbalances in brain homeostasis and may lead to neurological and behavioral sequelae. This article aims to explore the role of snapin in restoring brain homeostasis after injury or diseases, highlighting its significance in maintaining brain homeostasis and treating brain diseases. Additionally, it comprehensively discusses the implications of snapin in other extracerebral diseases such as diabetes and viral infections, with the objective of determining the clinical potential of snapin in maintaining brain homeostasis.
Collapse
Affiliation(s)
- Jiawen Li
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Xinqi Huang
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Yumei An
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Xueshi Chen
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Yiyang Chen
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Mingyuan Xu
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| | - Haiyan Shan
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Mingyang Zhang
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
- Institute of Forensic Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu Province, China
| |
Collapse
|
43
|
Gemmer M, Chaillet ML, Förster F. Exploring the molecular composition of the multipass translocon in its native membrane environment. Life Sci Alliance 2024; 7:e202302496. [PMID: 38866426 PMCID: PMC11169918 DOI: 10.26508/lsa.202302496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Multispanning membrane proteins are inserted into the endoplasmic reticulum membrane by the ribosome-bound multipass translocon (MPT) machinery. Based on cryo-electron tomography and extensive subtomogram analysis, we reveal the composition and arrangement of ribosome-bound MPT components in their native membrane environment. The intramembrane chaperone complex PAT and the translocon-associated protein (TRAP) complex associate substoichiometrically with the MPT in a translation-dependent manner. Although PAT is preferentially part of MPTs bound to translating ribosomes, the abundance of TRAP is highest in MPTs associated with non-translating ribosomes. The subtomogram average of the TRAP-containing MPT reveals intermolecular contacts between the luminal domains of TRAP and an unknown subunit of the back-of-Sec61 complex. AlphaFold modeling suggests this protein is nodal modulator, bridging the luminal domains of nicalin and TRAPα. Collectively, our results visualize the variability of MPT factors in the native membrane environment dependent on the translational activity of the bound ribosome.
Collapse
Affiliation(s)
- Max Gemmer
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Marten L Chaillet
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Friedrich Förster
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
44
|
Li B, Li X, Jiang Z, Zhou D, Feng Y, Chen G, Li N. LncRNA XIST modulates miR-328-3p ectopic expression in lung injury induced by tobacco-specific lung carcinogen NNK both in vitro and in vivo. Br J Pharmacol 2024; 181:2509-2527. [PMID: 38589338 DOI: 10.1111/bph.16373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND AND PURPOSE It is well acknowledged that tobacco-derived lung carcinogens can induce lung injury and even lung cancer through a complex mechanism. MicroRNAs (MiRNAs) are differentially expressed in tobacco-derived carcinogen nicotine-derived nitrosamine ketone (NNK)-treated A/J mice. EXPERIMENTAL APPROACH RNA sequencing was used to detect the level of long non-coding RNAs (lncRNAs). Murine and human lung normal and cancer cells were used to evaluate the function of lncRNA XIST and miR-328-3p in vitro, and NNK-treated A/J mice were used to test their function in vivo. In vivo levels of miR-328-3p and lncRNA XIST were analysed, using in situ hybridization. miR-328-3p agomir and lncRNA XIST-specific siRNA were used to manipulate in vivo levels of miR-328-3p and lncRNA XIST in A/J mice. KEY RESULTS LncRNA XIST was up-regulated in NNK-induced lung injury and dominated the NNK-induced ectopic miRNA expression in NNK-induced lung injury both in vitro and in vivo. Either lncRNA XIST silencing or miR-328-3p overexpression exerted opposing effects in lung normal and cancer cells regarding cell migration. LncRNA XIST down-regulated miR-328-3p levels as a miRNA sponge, and miR-328-3p targeted the 3'-UTR of FZD7 mRNA, which is ectopically overexpressed in lung cancer patients. Both in vivo lncRNA XIST silencing and miR-328 overexpression could rescue NNK-induced lung injury and aberrant overexpression of the lung cancer biomarker CK19 in NNK-treated A/J mice. CONCLUSIONS AND IMPLICATIONS Our results highlight the promotive effect of lncRNA XIST in NNK-induced lung injury and elucidate its post-transcriptional mechanisms, indicating that targeting lncRNA XIST/miR-328-3p could be a potential therapeutic strategy to prevent tobacco carcinogen-induced lung injury in vivo.
Collapse
Affiliation(s)
- Bingxin Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuezheng Li
- Department of PIVAS, Yanbian University Hospital, Yanji, China
| | - Zhe Jiang
- Department of PIVAS, Yanbian University Hospital, Yanji, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuan Feng
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Gang Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Ning Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| |
Collapse
|
45
|
Isola D, Elazar Z. Phospholipid Supply for Autophagosome Biogenesis. J Mol Biol 2024; 436:168691. [PMID: 38944336 DOI: 10.1016/j.jmb.2024.168691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Autophagy is a cellular degradation pathway where double-membrane autophagosomes form de novo to engulf cytoplasmic material destined for lysosomal degradation. This process requires regulated membrane remodeling, beginning with the initial autophagosomal precursor and progressing to its elongation and maturation into a fully enclosed, fusion-capable vesicle. While the core protein machinery involved in autophagosome formation has been extensively studied over the past two decades, the role of phospholipids in this process has only recently been studied. This review focuses on the phospholipid composition of the phagophore membrane and the mechanisms that supply lipids to expand this unique organelle.
Collapse
Affiliation(s)
- Damilola Isola
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
| |
Collapse
|
46
|
Gao J, Gunasekar S, Xia ZJ, Shalin K, Jiang C, Chen H, Lee D, Lee S, Pisal ND, Luo JN, Griciuc A, Karp JM, Tanzi R, Joshi N. Gene therapy for CNS disorders: modalities, delivery and translational challenges. Nat Rev Neurosci 2024; 25:553-572. [PMID: 38898231 DOI: 10.1038/s41583-024-00829-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Gene therapy is emerging as a powerful tool to modulate abnormal gene expression, a hallmark of most CNS disorders. The transformative potentials of recently approved gene therapies for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and active cerebral adrenoleukodystrophy are encouraging further development of this approach. However, most attempts to translate gene therapy to the clinic have failed to make it to market. There is an urgent need not only to tailor the genes that are targeted to the pathology of interest but to also address delivery challenges and thereby maximize the utility of genetic tools. In this Review, we provide an overview of gene therapy modalities for CNS diseases, emphasizing the interconnectedness of different delivery strategies and routes of administration. Important gaps in understanding that could accelerate the clinical translatability of CNS genetic interventions are addressed, and we present lessons learned from failed clinical trials that may guide the future development of gene therapies for the treatment and management of CNS disorders.
Collapse
Affiliation(s)
- Jingjing Gao
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA.
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
| | - Swetharajan Gunasekar
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziting Judy Xia
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kiruba Shalin
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Christopher Jiang
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hao Chen
- Marine College, Shandong University, Weihai, China
| | - Dongtak Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sohyung Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nishkal D Pisal
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - James N Luo
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Ana Griciuc
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Jeffrey M Karp
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Rudolph Tanzi
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Nitin Joshi
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
47
|
Wang Y, Yang JS, Zhao M, Chen JQ, Xie HX, Yu HY, Liu NH, Yi ZJ, Liang HL, Xing L, Jiang HL. Mitochondrial endogenous substance transport-inspired nanomaterials for mitochondria-targeted gene delivery. Adv Drug Deliv Rev 2024; 211:115355. [PMID: 38849004 DOI: 10.1016/j.addr.2024.115355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Mitochondrial genome (mtDNA) independent of nuclear gene is a set of double-stranded circular DNA that encodes 13 proteins, 2 ribosomal RNAs and 22 mitochondrial transfer RNAs, all of which play vital roles in functions as well as behaviors of mitochondria. Mutations in mtDNA result in various mitochondrial disorders without available cures. However, the manipulation of mtDNA via the mitochondria-targeted gene delivery faces formidable barriers, particularly owing to the mitochondrial double membrane. Given the fact that there are various transport channels on the mitochondrial membrane used to transfer a variety of endogenous substances to maintain the normal functions of mitochondria, mitochondrial endogenous substance transport-inspired nanomaterials have been proposed for mitochondria-targeted gene delivery. In this review, we summarize mitochondria-targeted gene delivery systems based on different mitochondrial endogenous substance transport pathways. These are categorized into mitochondrial steroid hormones import pathways-inspired nanomaterials, protein import pathways-inspired nanomaterials and other mitochondria-targeted gene delivery nanomaterials. We also review the applications and challenges involved in current mitochondrial gene editing systems. This review delves into the approaches of mitochondria-targeted gene delivery, providing details on the design of mitochondria-targeted delivery systems and the limitations regarding the various technologies. Despite the progress in this field is currently slow, the ongoing exploration of mitochondrial endogenous substance transport and mitochondrial biological phenomena may act as a crucial breakthrough in the targeted delivery of gene into mitochondria and even the manipulation of mtDNA.
Collapse
Affiliation(s)
- Yi Wang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jing-Song Yang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Min Zhao
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Qi Chen
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hai-Xin Xie
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hao-Yuan Yu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Na-Hui Liu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Zi-Juan Yi
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hui-Lin Liang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Xing
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hu-Lin Jiang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China; College of Pharmacy, Yanbian University, Yanji 133002, China.
| |
Collapse
|
48
|
Wu D, Huang C, Guan K. Mechanistic and therapeutic perspectives of miRNA-PTEN signaling axis in cancer therapy resistance. Biochem Pharmacol 2024; 226:116406. [PMID: 38969299 DOI: 10.1016/j.bcp.2024.116406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Cancer, being one of the most lethal illnesses, presents an escalating clinical dilemma on a global scale. Despite significant efforts and advancements in cancer treatment over recent decades, the persistent challenge of resistance to traditional chemotherapeutic agents and/or emerging targeted drugs remains a prominent issue in the field of cancer therapies. Among the frequently inactivated tumor suppressor genes in cancer, phosphatase and Tensin Homolog (PTEN) stands out, and its decreased expression may contribute to the emergence of therapeutic resistance. MicroRNAs (miRNAs), characterized by their short length of 22 nucleotides, exert regulatory control over target mRNA expression by binding to complementary sequences. Recent findings indicate that microRNAs play varied regulatory roles, encompassing promotion, suppression, and dual functions on PTEN, and their aberration is implicated in heightened resistance to anticancer therapies. Significantly, recent research has revealed that competitive endogenous RNAs (ceRNAs) play a pivotal role in influencing PTEN expression, and the regulatory network involving circRNA/lncRNA-miRNA-PTEN is intricately linked to resistance in various cancer types to anticancer therapies. Finally, our findings showcase that diverse approaches, such as herbal medicine, small molecule inhibitors, low-intensity ultrasound, and engineered exosomes, can effectively overcome drug resistance in cancer by modulating the miRNA-PTEN axis.
Collapse
Affiliation(s)
- Di Wu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China.
| | - Kaifeng Guan
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
49
|
Ghoytasi I, Bavi O, Kaazempur Mofrad MR, Naghdabadi R. An in-silico study on the mechanical behavior of colorectal cancer cell lines in the micropipette aspiration process. Comput Biol Med 2024; 178:108744. [PMID: 38889631 DOI: 10.1016/j.compbiomed.2024.108744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/17/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
Cancer alters the structural integrity and morphology of cells. Consequently, the cell function is overshadowed. In this study, the micropipette aspiration process is computationally modeled to predict the mechanical behavior of the colorectal cancer cells. The intended cancer cells are modeled as an incompressible Neo-Hookean visco-hyperelastic material. Also, the micropipette is assumed to be rigid with no deformation. The proposed model is validated with an in-vitro study. To capture the equilibrium and time-dependent behaviors of cells, ramp, and creep tests are respectively performed using the finite element method. Through the simulations, the effects of the micropipette geometry and the aspiration pressure on the colorectal cancer cell lines are investigated. Our findings indicate that, as the inner radius of the micropipette increases, despite the increase in deformation rate and aspirated length, the time to reach the equilibrium state increases. Nevertheless, it is obvious that increasing the tip curvature radius has a small effect on the change of the aspirated length. But, due to the decrease in the stress concentration, it drastically reduces the equilibrium time and increases the deformation rate significantly. Interestingly, our results demonstrate that increasing the aspiration pressure somehow causes the cell stiffening, thereby reducing the upward trend of deformation rate, equilibrium time, and aspirated length. Our findings provide valuable insights for researchers in cell therapy and cancer treatment and can aid in developing more precise microfluidic.
Collapse
Affiliation(s)
- Ibrahim Ghoytasi
- Department of Mechanical Engineering, Sharif University of Technology, 89694-14588, Tehran, Iran
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran.
| | - Mohammad Reza Kaazempur Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Reza Naghdabadi
- Department of Mechanical Engineering, Sharif University of Technology, 89694-14588, Tehran, Iran; Institute for Nanoscience and Nanotechnology, Sharif University of Technology, 89694-14588, Tehran, Iran.
| |
Collapse
|
50
|
Mao Y, Wickström SA. Mechanical state transitions in the regulation of tissue form and function. Nat Rev Mol Cell Biol 2024; 25:654-670. [PMID: 38600372 DOI: 10.1038/s41580-024-00719-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
From embryonic development, postnatal growth and adult homeostasis to reparative and disease states, cells and tissues undergo constant changes in genome activity, cell fate, proliferation, movement, metabolism and growth. Importantly, these biological state transitions are coupled to changes in the mechanical and material properties of cells and tissues, termed mechanical state transitions. These mechanical states share features with physical states of matter, liquids and solids. Tissues can switch between mechanical states by changing behavioural dynamics or connectivity between cells. Conversely, these changes in tissue mechanical properties are known to control cell and tissue function, most importantly the ability of cells to move or tissues to deform. Thus, tissue mechanical state transitions are implicated in transmitting information across biological length and time scales, especially during processes of early development, wound healing and diseases such as cancer. This Review will focus on the biological basis of tissue-scale mechanical state transitions, how they emerge from molecular and cellular interactions, and their roles in organismal development, homeostasis, regeneration and disease.
Collapse
Affiliation(s)
- Yanlan Mao
- Laboratory for Molecular Cell Biology, University College London, London, UK.
- Institute for the Physics of Living Systems, University College London, London, UK.
| | - Sara A Wickström
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
| |
Collapse
|