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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genet 2023; 19:e1010857. [PMID: 37494383 PMCID: PMC10406323 DOI: 10.1371/journal.pgen.1010857] [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: 04/05/2023] [Revised: 08/07/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Hugo B. Brandão
- Illumina Inc., 5200 Illumina Way, San Diego, California, United States of America
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. Biol Open 2023; 12:bio059955. [PMID: 37283223 PMCID: PMC10259849 DOI: 10.1242/bio.059955] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.
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Affiliation(s)
- Rachel E. Cherney
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Christine A. Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Proteomics Core Facility, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Proteomics Core Facility, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Aki K. Braceros
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - J. Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
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53
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Veenstra BT, Veenstra TD. Proteomic applications in identifying protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:1-48. [PMID: 38220421 DOI: 10.1016/bs.apcsb.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.
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Affiliation(s)
- Benjamin T Veenstra
- Department of Math and Sciences, Cedarville University, Cedarville, OH, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH, United States.
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54
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Siris S, Gladstone CA, Guo Y, Patel R, Pinder CL, Shattock RJ, McKay PF, Langford PR, Bidmos FA. Increasing human monoclonal antibody cloning efficiency with a whole-cell modified immunoglobulin-capture assay (mICA). Front Immunol 2023; 14:1184510. [PMID: 37334357 PMCID: PMC10272928 DOI: 10.3389/fimmu.2023.1184510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
Expression cloning of fully human monoclonal antibodies (hmAbs) is seeing powerful utility in the field of vaccinology, especially for elucidating vaccine-induced B-cell responses and novel vaccine candidate antigen discovery. Precision of the hmAb cloning process relies on efficient isolation of hmAb-producing plasmablasts of interest. Previously, a novel immunoglobulin-capture assay (ICA) was developed, using single protein vaccine antigens, to enhance the pathogen-specific hmAb cloning output. Here, we report a novel modification of this single-antigen ICA using formalin-treated, fluorescently stained whole cell suspensions of the human bacterial invasive pathogens, Streptococcus pneumoniae and Neisseria meningitidis. Sequestration of IgG secreted by individual vaccine antigen-specific plasmablasts was achieved by the formation of an anti-CD45-streptavidin and biotin anti-IgG scaffold. Suspensions containing heterologous pneumococcal and meningococcal strains were then used to enrich for polysaccharide- and protein antigen-specific plasmablasts, respectively, during single cell sorting. Following application of the modified whole-cell ICA (mICA), ~61% (19/31) of anti-pneumococcal polysaccharide hmAbs were cloned compared to 14% (8/59) obtained using standard (non-mICA) methods - representing a ~4.4-fold increase in hmAb cloning precision. A more modest ~1.7-fold difference was obtained for anti-meningococcal vaccine hmAb cloning; ~88% of hmAbs cloned via mICA versus ~53% cloned via the standard method were specific for a meningococcal surface protein. VDJ sequencing revealed that cloned hmAbs reflected an anamnestic response to both pneumococcal and meningococcal vaccines; diversification within hmAb clones occurred by positive selection for replacement mutations. Thus, we have shown successful utilization of whole bacterial cells in the ICA protocol enabling isolation of hmAbs targeting multiple disparate epitopes, thereby increasing the power of approaches such as reverse vaccinology 2.0 (RV 2.0) for bacterial vaccine antigen discovery.
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Affiliation(s)
- Sara Siris
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Camilla A. Gladstone
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanping Guo
- Flow Cytometry Core Facility, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Radhika Patel
- Flow Cytometry Core Facility, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Christopher L. Pinder
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Robin J. Shattock
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul F. McKay
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Fadil A. Bidmos
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
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Kim A, Martinez-Valbuena I, Li J, Lang AE, Kovacs GG. Disease-Specific α-Synuclein Seeding in Lewy Body Disease and Multiple System Atrophy Are Preserved in Formaldehyde-Fixed Paraffin-Embedded Human Brain. Biomolecules 2023; 13:936. [PMID: 37371515 DOI: 10.3390/biom13060936] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Recent studies have been able to detect α-synuclein (αSyn) seeding in formaldehyde-fixed paraffin-embedded (FFPE) tissues from patients with synucleinopathies using seed amplification assays (SAAs), but with relatively low sensitivity due to limited protein extraction efficiency. With the aim of introducing an alternative option to frozen tissues, we developed a streamlined protein extraction protocol for evaluating disease-specific seeding in FFPE human brain. We evaluated the protein extraction efficiency of different tissue preparations, deparaffinizations, and protein extraction buffers using formaldehyde-fixed and FFPE tissue of a single Lewy body disease (LBD) subject. Alternatively, we incorporated heat-induced antigen retrieval and dissociation using a commercially available kit. Our novel protein extraction protocol has been optimized to work with 10 sections of 4.5-µm-thickness or 2-mm-diameter micro-punch of FFPE tissue that can be used to seed SAAs. We demonstrated that extracted proteins from FFPE still preserve seeding potential and further show disease-specific seeding in LBD and multiple system atrophy. To the best of our knowledge, our study is the first to recapitulate disease-specific αSyn seeding behaviour in FFPE human brain. Our findings open new perspectives in re-evaluating archived human brain tissue, extending the disease-specific seeding assays to larger cohorts to facilitate molecular subtyping of synucleinopathies.
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Affiliation(s)
- Ain Kim
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ivan Martinez-Valbuena
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Jun Li
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Anthony E Lang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S6, Canada
| | - Gabor G Kovacs
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S6, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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56
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Marine polysaccharide-based hydrogels for critical materials selective removal and recovery: A review. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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57
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Ghimici L, Ghiorghiță CA, Năfureanu MM. Abatement of some commercial fungicide content from model dispersions by a new thiourea-graft-polyethyleneimine derivative. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67539-67551. [PMID: 37115448 DOI: 10.1007/s11356-023-27260-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/23/2023] [Indexed: 05/25/2023]
Abstract
A new derivative of polyethyleneimine (PEI) with 9% degree of substitution of its primary and secondary amino groups with thiourea moieties (TU9-PEI) has been synthesized and investigated as flocculant in model suspensions of commercial fungicide formulations Dithane M45, Melody Compact 49 WG, Cabrio®Top, and their mixtures. The structure of TU9-PEI, obtained by an aqueous one-pot strategy involving formaldehyde mediated coupling of PEI and TU, was confirmed by FTIR and 1H NMR spectroscopy as well as the streaming potential measurements. The settling time, polymer dose, and fungicide type and concentration were the parameters used for assessing the flocculation ability of the new polycation sample. The UV-Vis spectroscopy measurements revealed a good removal efficiency of TU9-PEI for all of the fungicides investigated, between 88 and 94%. Slightly higher removal percent was found for greater fungicide concentrations. The charge neutralization was indicated by zeta potential measurements (values close to zero recorded at the optimum polymer dose) as the main mechanism which contributed to the Dithane and Cabrio®Top particle removal and a combined effect of the TU9-PEI/fungicide particle electrostatic attractions and hydrogen bonds between both the amine and thiourea groups of the polycation chains and the hydroxyl ones on the copper oxychloride particles (negative values) in case of the Melody Compact 49 WG particle separation. Particle size and surface morphology analysis data gave supplementary evidences regarding the TU9-PEI ability to separate the fungicides investigated from simulated wastewater.
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Affiliation(s)
- Luminita Ghimici
- "Petru Poni" Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487, Iasi, Romania.
| | | | - Maria-Magdalena Năfureanu
- "Petru Poni" Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487, Iasi, Romania
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58
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Guo AD, Yan KN, Hu H, Zhai L, Hu TF, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu YJ, Zhang J, Tan M, Chen XH. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem 2023:10.1038/s41557-023-01196-z. [PMID: 37106095 DOI: 10.1038/s41557-023-01196-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Precise dissection of DNA-protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA-protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA-protein interactions. Harnessing unique abilities to capture weak and transient DNA-protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA-protein profiling toolbox and map accurate DNA-protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.
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Affiliation(s)
- An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Teng-Fei Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yijia Chi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongxin Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Jiang Xu
- School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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59
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Liu J, Duan Q, Shao Z, Chen K, Zhu Y, Li J, Tan W. Formaldehyde Cross-Linking-Assisted Phase Separation for Protein Aptamer Selection. Anal Chem 2023; 95:6700-6708. [PMID: 37052573 DOI: 10.1021/acs.analchem.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
With the merits of easy synthesis, strong modifiability, and high affinity, aptamers have been broadly applied for protein targeting in bioanalysis, diagnosis, and therapeutics. The selection of protein-targeted aptamers is currently largely dependent on solid-liquid separation by using different types of nano- or micro-beads. However, the use of beads inescapably introduces unwanted nonspecific binding and thus affects selection efficiency. In order to sidestep this obstacle, we herein report an integrated technique to facilitate the discovery and development of protein-targeting aptamers by incorporating formaldehyde cross-linking with phase separation (FCPS). The feasibility and universality of FCPS were confirmed by the successful selection of two aptamers that could target various antibodies. Unlike traditional approaches, the proposed technique avoids the use of beads and enables the rapid generation of aptamers after only one to three rounds of selection. The as-selected aptamers were further used to regulate and control antibody activity, showing potential applications in biomedicine.
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Affiliation(s)
- Jia Liu
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiao Duan
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhentao Shao
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Kaiming Chen
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yingdi Zhu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Juan Li
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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60
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Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535391. [PMID: 37066147 PMCID: PMC10103960 DOI: 10.1101/2023.04.03.535391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.
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61
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Marwarha G, Slagsvold KH, Høydal MA. NF-κB Transcriptional Activity Indispensably Mediates Hypoxia–Reoxygenation Stress-Induced microRNA-210 Expression. Int J Mol Sci 2023; 24:ijms24076618. [PMID: 37047592 PMCID: PMC10095479 DOI: 10.3390/ijms24076618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Ischemia–reperfusion (I-R) injury is a cardinal pathophysiological hallmark of ischemic heart disease (IHD). Despite significant advances in the understanding of what causes I-R injury and hypoxia–reoxygenation (H-R) stress, viable molecular strategies that could be targeted for the treatment of the deleterious biochemical pathways activated during I-R remain elusive. The master hypoxamiR, microRNA-210 (miR-210), is a major determinant of protective cellular adaptation to hypoxia stress but exacerbates apoptotic cell death during cellular reoxygenation. While the hypoxia-induced transcriptional up-regulation of miR-210 is well delineated, the cellular mechanisms and molecular entities that regulate the transcriptional induction of miR-210 during the cellular reoxygenation phase have not been elucidated yet. Herein, in immortalized AC-16 cardiomyocytes, we delineated the indispensable role of the ubiquitously expressed transcription factor, NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) in H-R-induced miR-210 expression during cellular reoxygenation. Using dominant negative and dominant active expression vectors encoding kinases to competitively inhibit NF-κB activation, we elucidated NF-κB activation as a significant mediator of H-R-induced miR-210 expression. Ensuing molecular assays revealed a direct NF-κB-mediated transcriptional up-regulation of miR-210 expression in response to the H-R challenge that is characterized by the NF-κB-mediated reorchestration of the entire repertoire of histone modification changes that are a signatory of a permissive actively transcribed miR-210 promoter. Our study confers a novel insight identifying NF-κB as a potential novel molecular target to combat H-R-elicited miR-210 expression that fosters augmented cardiomyocyte cell death.
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Affiliation(s)
- Gurdeep Marwarha
- Group of Molecular and Cellular Cardiology, Department of Circulation and Medical Imaging, Faculty of Medicine and Health, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
| | - Katrine Hordnes Slagsvold
- Group of Molecular and Cellular Cardiology, Department of Circulation and Medical Imaging, Faculty of Medicine and Health, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Department of Cardiothoracic Surgery, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Morten Andre Høydal
- Group of Molecular and Cellular Cardiology, Department of Circulation and Medical Imaging, Faculty of Medicine and Health, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
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Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533031. [PMID: 36993219 PMCID: PMC10055122 DOI: 10.1101/2023.03.16.533031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or "omes," measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen repositories. However, these biospecimens have been underutilized for multi-omic analysis due to the low throughput of current analytical technologies that impede large-scale studies. Methods Tissue sampling, preparation, and downstream analysis were integrated into a 96-well format multi-omics workflow, MultiomicsTracks96. Frozen mouse organs were sampled using the CryoGrid system, and matched FFPE samples were processed using a microtome. The 96-well format sonicator, PIXUL, was adapted to extract DNA, RNA, chromatin, and protein from tissues. The 96-well format analytical platform, Matrix, was used for chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), methylated RNA immunoprecipitation (MeRIP), and RNA reverse transcription (RT) assays followed by qPCR and sequencing. LC-MS/MS was used for protein analysis. The Segway genome segmentation algorithm was used to identify functional genomic regions, and linear regressors based on the multi-omics data were trained to predict protein expression. Results MultiomicsTracks96 was used to generate 8-dimensional datasets including RNA-seq measurements of mRNA expression; MeRIP-seq measurements of m6A and m5C; ChIP-seq measurements of H3K27Ac, H3K4m3, and Pol II; MeDIP-seq measurements of 5mC; and LC-MS/MS measurements of proteins. We observed high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles (ChIP-seq: H3K27Ac, H3K4m3, Pol II; MeDIP-seq: 5mC) was able to recapitulate and predict organ-specific super-enhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic expression profiles can be more accurately predicted by the full suite of multi-omics data, compared to using epigenomic, transcriptomic, or epitranscriptomic measurements individually. Conclusions The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies - for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.
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Sharma AK, Fitieh AM, Locke AJ, Ali JYH, Ismail IH. Quantification of protein enrichment at site-specific DNA double-strand breaks by chromatin immunoprecipitation in cultured human cells. STAR Protoc 2023; 4:101917. [PMID: 36520630 PMCID: PMC9758495 DOI: 10.1016/j.xpro.2022.101917] [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: 06/04/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Here, we present a chromatin-immunoprecipitation-based protocol to quantify the recruitment of proteins adjacent to site-specific DNA double-strand breaks (DSBs), such as proteins involved in DSB repair. We describe steps to induce DSBs in U2OS osteosarcoma cells stably expressing the restriction endonucleases FokI or AsiSI. We then detail the procedures of chromatin isolation and immunoprecipitation, followed by protein elution and quantitative-PCR-based quantification of DNA. This protocol cannot be used on DSBs generated at random loci by DNA damaging agents. For complete details on the use and execution of this protocol, please refer to Fitieh et al. (2022).1.
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Affiliation(s)
- Ajit K Sharma
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Amira Mohammed Fitieh
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada; Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Andrew J Locke
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Jana Yasser Hafez Ali
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Ismail Hassan Ismail
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada; Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt.
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Ma Y, Steinmetz NF. Potato Virus X Inactivation and Characterization. Methods Mol Biol 2023; 2671:257-271. [PMID: 37308650 DOI: 10.1007/978-1-0716-3222-2_15] [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] [Indexed: 06/14/2023]
Abstract
The nucleoprotein components of plant viruses self-assemble into monodisperse, nanoscale structures with a high degree of symmetry and polyvalency. Of particular interest are the filamentous plant viruses which provide uniform high aspect ratio nanostructures-such structures remain challenging to obtain using purely synthetic approaches. Potato virus X (PVX) has drawn interest by the materials science community because of its filamentous structure measuring 515 × 13 nm; and both genetic engineering and chemical conjugation methods have been reported to impart new functionalities and develop PVX-based nanomaterials for applications in the health and materials sector. Toward environmentally safe materials-i.e., materials that are not infectious toward crops, such as potato, we reported methods to inactivate PVX. In this chapter, we describe the three methods to inactivate PVX and render it non-infectious toward plants, while maintaining structure and function.
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Affiliation(s)
- Yifeng Ma
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Radiology, University of California San Diego, La Jolla, CA, USA.
- Center for Nano-ImmunoEngineering, University of California San Diego, La Jolla, CA, USA.
- Institute for Materials Discovery and Design, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Center for Engineering in Cancer, Institute for Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
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65
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Kahiapo JK, Monahan K. Chromatin Immunoprecipitation from Formaldehyde Cross-Linked Olfactory Sensory Neurons. Methods Mol Biol 2023; 2710:71-82. [PMID: 37688725 DOI: 10.1007/978-1-0716-3425-7_6] [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] [Indexed: 09/11/2023]
Abstract
Chromatin immunoprecipitation (ChIP) allows a researcher to determine the genomic occupancy of nuclear proteins, providing insight into the roles of transcription factors, chromatin modifiers, histone modifications, and other factors bound to DNA. Protein-DNA interactions are first fixed in vivo by chemical cross-linking, and then a target protein is captured together with any associated DNA by an antibody mediated pull-down. The co-immunoprecipitated DNA can then be assayed by quantitative PCR or deep sequencing. Here, we demonstrate this technique using murine olfactory sensory neurons (OSNs) purified using fluorescence-activated cell sorting (FACS) and antibodies for the ubiquitous chromatin protein CTCF.
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Affiliation(s)
- Jerome K Kahiapo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Rapid Downregulation of H3K4me3 Binding to Immunoregulatory Genes in Altered Gravity in Primary Human M1 Macrophages. Int J Mol Sci 2022; 24:ijms24010603. [PMID: 36614046 PMCID: PMC9820304 DOI: 10.3390/ijms24010603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
The sensitivity of human immune system cells to gravity changes has been investigated in numerous studies. Human macrophages mediate innate and thus rapid immune defense on the one hand and activate T- and B-cell-based adaptive immune response on the other hand. In this process they finally act as immunoeffector cells, and are essential for tissue regeneration and remodeling. Recently, we demonstrated in the human Jurkat T cell line that genes are differentially regulated in cluster structures under altered gravity. In order to study an in vivo near system of immunologically relevant human cells under physically real microgravity, we performed parabolic flight experiments with primary human M1 macrophages under highly standardized conditions and performed chromatin immunoprecipitation DNA sequencing (ChIP-Seq) for whole-genome epigenetic detection of the DNA-binding loci of the main transcription complex RNA polymerase II and the transcription-associated epigenetic chromatin modification H3K4me3. We identified an overall downregulation of H3K4me3 binding loci in altered gravity, which were unequally distributed inter- and intrachromosomally throughout the genome. Three-quarters of all affected loci were located on the p arm of the chromosomes chr5, chr6, chr9, and chr19. The genomic distribution of the downregulated H3K4me3 loci corresponds to a substantial extent to immunoregulatory genes. In microgravity, analysis of RNA polymerase II binding showed increased binding to multiple loci at coding sequences but decreased binding to central noncoding regions. Detection of altered DNA binding of RNA polymerase II provided direct evidence that gravity changes can lead to altered transcription. Based on this study, we hypothesize that the rapid transcriptional response to changing gravitational forces is specifically encoded in the epigenetic organization of chromatin.
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Le HTQ, Lee EY. Insights into C1 and C3 assimilation pathways in type I methanotrophic bacterium from co-production of 1,2-propanediol and lactate. BIORESOURCE TECHNOLOGY 2022; 365:128172. [PMID: 36279980 DOI: 10.1016/j.biortech.2022.128172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Methanotrophic bacteria are attractive hosts for mining metabolic pathways of C1 assimilation to produce value-added products. Herein, the type I methanotroph Methylotuvimicrobium alcaliphilum 20Z was employed to explore the carbon flux from methane and methanol via the EMP pathway to produce 1,2-propanediol (1,2-PDO). The production of 1,2-PDO on methane was found to be mainly restricted by the lower carbon flux toward the EMP pathway. The co-utilization of C1 substrates and glycerol (C3) could contribute to enhance 1,2-PDO. Lactate was co-produced in much higher amounts than 1,2-PDO. This unexpected product was probably derived from lactaldehyde by inherent aldehyde dehydrogenases. The 1,2-PDO production without increased accumulation of lactate was observed via establishing the acetol-based pathway by propane utilization with the overexpression of pmoD. This is the first study to provide experimental insights into the operation of metabolic routes for 1,2-PDO and lactate co-production from C1 and C3 compounds in methanotrophs.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
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Dator RP, Murray KJ, Luedtke MW, Jacobs FC, Kassie F, Nguyen HD, Villalta PW, Balbo S. Identification of Formaldehyde-Induced DNA-RNA Cross-Links in the A/J Mouse Lung Tumorigenesis Model. Chem Res Toxicol 2022; 35:2025-2036. [PMID: 36356054 PMCID: PMC10336729 DOI: 10.1021/acs.chemrestox.2c00206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a potent lung carcinogen present in tobacco products, and exposure to it is likely one of the factors contributing to the development of lung cancer in cigarette smokers. To exert its carcinogenic effects, NNK must be metabolically activated into highly reactive species generating a wide spectrum of DNA damage. We have identified a new class of DNA adducts, DNA-RNA cross-links found for the first time in NNK-treated mice lung DNA using our improved high-resolution accurate mass segmented full scan data-dependent neutral loss MS3 screening strategy. The levels of these DNA-RNA cross-links were found to be significantly higher in NNK-treated mice compared to the corresponding controls, which is consistent with higher levels of formaldehyde due to NNK metabolism as compared to endogenous levels. We hypothesize that this DNA-RNA cross-linking occurs through reaction with NNK-generated formaldehyde and speculate that this phenomenon has broad implications for NNK-induced carcinogenesis. The structures of these cross-links were characterized using high-resolution LC-MS2 and LC-MS3 accurate mass spectral analysis and comparison to a newly synthesized standard. Taken together, our data demonstrate a previously unknown link between DNA-RNA cross-link adducts and NNK and provide a unique opportunity to further investigate how these novel NNK-derived DNA-RNA cross-links contribute to carcinogenesis in the future.
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Affiliation(s)
- Romel P. Dator
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
| | - Kevin J. Murray
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108
- Center for Mass Spectrometry and Proteomics, University of Minnesota, St. Paul, MN 55108
| | | | - Foster C. Jacobs
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455
| | - Fekadu Kassie
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Hai Dang Nguyen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Pharmacology, College of Medicine, University of Minnesota, Minneapolis, MN 55455
| | - Peter W. Villalta
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455
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Ugwu CE, Kenechukwu FC, Diovu EO, Udodeme HO, Momoh MA, Onuigbo EB, Attama AA. Exploitation of capsule system for colon targeted drug delivery of biopolymer-based microparticles: in vivo and in vitro applications. Heliyon 2022; 8:e11390. [PMID: 36387434 PMCID: PMC9663862 DOI: 10.1016/j.heliyon.2022.e11390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/29/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
The current study was to improve and control aceclofenac delivery prepared as biopolymer-based microparticles for effective colon-targeted drug delivery using modified gelatin capsules (MGCs) at different time intervals developed in two batches (C1 and C2). Microparticles were formulated with extracted mucuna gum using liquid paraffin oil (AC.LPO) and soybean oil (AC.SO) and evaluated in vitro for physicochemical performance and in vivo in rats. Encapsulation efficiency ranges from 54.48 ± 0.21% to 82.83 ± 0.22% for AC.LPO and 52.64 ± 0.11% to 80.36 ± 0.22% for AC.SO. SEM showed oblong and irregular shapes with porous and cracked surfaces. DSC showed low enthalpy and a very broad endothermic peak depicting high amorphous property. Delayed drug release was observed in the upper gastrointestinal tract with sustained release depicted in the lower gastrointestinal tract (GIT) using 3 and 9-h batch C1 of MGCs. AC.SO exhibited significantly (p < 0.05) higher anti-inflammatory activity (86%) than AC.LPO (77%). Hence, aceclofenac colon delivery could be improved and controlled using biopolymer-based colon-targeted microparticles delivered with MGCs.
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Affiliation(s)
- Calister E. Ugwu
- Department of Pharmaceutical Technology and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
- Corresponding author.
| | - Franklin C. Kenechukwu
- Drug Delivery Unit, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Edith O. Diovu
- Department of Pharmacognosy and Environmental Medicine, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Helen O. Udodeme
- Department of Pharmacognosy and Environmental Medicine, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Mumuni A. Momoh
- Drug Delivery Unit, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Ebele B. Onuigbo
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Anthony A. Attama
- Drug Delivery Unit, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
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Wong SL, Pandzic E, Kardia E, Allan KM, Whan RM, Waters SA. Quantifying Intracellular Viral Pathogen: Specimen Preparation, Visualization and Quantification of Multiple Immunofluorescent Signals in Fixed Human Airway Epithelium Cultured at Air-Liquid Interface. J Pers Med 2022; 12:jpm12101668. [PMID: 36294807 PMCID: PMC9605096 DOI: 10.3390/jpm12101668] [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: 07/29/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Infection control and aggressive antibiotic therapy play an important role in the management of airway infections in individuals with cystic fibrosis (CF). The responses of airway epithelial cells to pathogens are likely to contribute to the pathobiology of CF lung disease. Primary airway epithelial cells obtained from individuals with CF, cultured and differentiated at air-liquid interface (ALI), effectively mimic the structure and function of the in vivo airway epithelium. With the recent respiratory viral pandemics, ALI cultures were extensively used to model respiratory infections in vitro to facilitate physiologically relevant respiratory research. Immunofluorescence staining and imaging were used as an effective tool to provide a fundamental understanding of host–pathogen interactions and for exploring the therapeutic potential of novel or repurposed drugs. Therefore, we described an optimized quantitative fluorescence microscopy assay for the wholemount staining and imaging of epithelial cell markers to identify distinct cell populations and pathogen-specific targets in ALI cultures of human airway epithelial cells grown on permeable support insert membranes. We present a detailed methodology using a graphical user interface (GUI) package to quantify the detected signals on a tiled whole membrane. Our method provided an imaging strategy of the entire membrane, overcoming the common issue of undersampling and enabling unbiased quantitative analysis.
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Affiliation(s)
- Sharon L. Wong
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Elvis Pandzic
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Egi Kardia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katelin M. Allan
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Renee M. Whan
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shafagh A. Waters
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Respiratory Medicine, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
- Correspondence:
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Sandlin CW, Gu S, Xu J, Deshpande C, Feldman MD, Good MC. Epithelial cell size dysregulation in human lung adenocarcinoma. PLoS One 2022; 17:e0274091. [PMID: 36201559 PMCID: PMC9536599 DOI: 10.1371/journal.pone.0274091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Human cells tightly control their dimensions, but in some cancers, normal cell size control is lost. In this study we measure cell volumes of epithelial cells from human lung adenocarcinoma progression in situ. By leveraging artificial intelligence (AI), we reconstruct tumor cell shapes in three dimensions (3D) and find airway type 2 cells display up to 10-fold increases in volume. Surprisingly, cell size increase is not caused by altered ploidy, and up to 80% of near-euploid tumor cells show abnormal sizes. Size dysregulation is not explained by cell swelling or senescence because cells maintain cytoplasmic density and proper organelle size scaling, but is correlated with changes in tissue organization and loss of a novel network of processes that appear to connect alveolar type 2 cells. To validate size dysregulation in near-euploid cells, we sorted cells from tumor single-cell suspensions on the basis of size. Our study provides data of unprecedented detail for cell volume dysregulation in a human cancer. Broadly, loss of size control may be a common feature of lung adenocarcinomas in humans and mice that is relevant to disease and identification of these cells provides a useful model for investigating cell size control and consequences of cell size dysregulation.
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Affiliation(s)
- Clifford W. Sandlin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
| | - Song Gu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Jun Xu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Charuhas Deshpande
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew C. Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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Johnston AD, Lu J, Korbie D, Trau M. Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis. Sci Rep 2022; 12:16051. [PMID: 36163372 PMCID: PMC9512909 DOI: 10.1038/s41598-022-18196-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
In fragmented DNA, PCR-based methods quantify the number of intact regions at a specific amplicon length. However, the relationship between the population of DNA fragments within a sample and the likelihood they will amplify has not been fully described. To address this, we have derived a mathematical equation that relates the distribution profile of a stochastically fragmented DNA sample to the probability that a DNA fragment within that sample can be amplified by any PCR assay of arbitrary length. Two panels of multiplex PCR assays for quantifying fragmented DNA were then developed: a four-plex panel that can be applied to any human DNA sample and used to estimate the percentage of regions that are intact at any length; and a two-plex panel optimized for quantifying circulating cell-free DNA (cfDNA). For these assays, regions of the human genome least affected by copy number aberration were identified and selected; within these copy-neutral regions, each PCR assay was designed to amplify both genomic and bisulfite-converted DNA; and all assays were validated for use in both conventional qPCR and droplet-digital PCR. Finally, using the cfDNA-optimized assays we find evidence of universally conserved nucleosome positioning among individuals.
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Affiliation(s)
- Andrew D Johnston
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, Westmead, NSW, Australia
| | - Jennifer Lu
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Darren Korbie
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Matt Trau
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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74
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Wietz M, Metfies K, Bienhold C, Wolf C, Janssen F, Salter I, Boetius A. Impact of preservation method and storage period on ribosomal metabarcoding of marine microbes: Implications for remote automated samplings. Front Microbiol 2022; 13:999925. [PMID: 36160263 PMCID: PMC9490091 DOI: 10.3389/fmicb.2022.999925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Automated sampling technologies can enhance the temporal and spatial resolution of marine microbial observations, particularly in remote and inaccessible areas. A critical aspect of automated microbiome sampling is the preservation of nucleic acids over long-term autosampler deployments. Understanding the impact of preservation method on microbial metabarcoding is essential for implementing genomic observatories into existing infrastructure, and for establishing best practices for the regional and global synthesis of data. The present study evaluates the effect of two preservatives commonly used in autosampler deployments (mercuric chloride and formalin) and two extraction kits (PowerWater and NucleoSpin) on amplicon sequencing of 16S and 18S rRNA gene over 50 weeks of sample storage. Our results suggest the combination of mercuric chloride preservation and PowerWater extraction as most adequate for 16S and 18S rRNA gene amplicon-sequencing from the same seawater sample. This approach provides consistent information on species richness, diversity and community composition in comparison to control samples (nonfixed, filtered and frozen) when stored up to 50 weeks at in situ temperature. Preservation affects the recovery of certain taxa, with specific OTUs becoming overrepresented (SAR11 and diatoms) or underrepresented (Colwellia and pico-eukaryotes) after preservation. In case eukaryotic sequence information is the sole target, formalin preservation and NucleoSpin extraction performed best. Our study contributes to the design of long-term autonomous microbial observations in remote ocean areas, allowing cross-comparison of microbiome dynamics across sampling devices (e.g., water and particle samplers) and marine realms.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christian Wolf
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Felix Janssen
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Torshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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75
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Biswas P, Adhikari A, Pal U, Mondal S, Mukherjee D, Ghosh R, Obaid RJ, Moussa Z, Choudhury SS, Ahmed SA, Das R, Pal SK. A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative. Front Chem 2022; 10:978668. [PMID: 36118312 PMCID: PMC9473634 DOI: 10.3389/fchem.2022.978668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.
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Affiliation(s)
- Pritam Biswas
- Department of Microbiology, St. Xavier’s College, Kolkata, India
| | - Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Rami J. Obaid
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Sudeshna Shyam Choudhury
- Department of Microbiology, St. Xavier’s College, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Saleh A. Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
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76
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Boildieu D, Guerenne-Del Ben T, Duponchel L, Sol V, Petit JM, Champion É, Kano H, Helbert D, Magnaudeix A, Leproux P, Carré P. Coherent anti-Stokes Raman scattering cell imaging and segmentation with unsupervised data analysis. Front Cell Dev Biol 2022; 10:933897. [PMID: 36051442 PMCID: PMC9424763 DOI: 10.3389/fcell.2022.933897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
Coherent Raman imaging has been extensively applied to live-cell imaging in the last 2 decades, allowing to probe the intracellular lipid, protein, nucleic acid, and water content with a high-acquisition rate and sensitivity. In this context, multiplex coherent anti-Stokes Raman scattering (MCARS) microspectroscopy using sub-nanosecond laser pulses is now recognized as a mature and straightforward technology for label-free bioimaging, offering the high spectral resolution of conventional Raman spectroscopy with reduced acquisition time. Here, we introduce the combination of the MCARS imaging technique with unsupervised data analysis based on multivariate curve resolution (MCR). The MCR process is implemented under the classical signal non-negativity constraint and, even more originally, under a new spatial constraint based on cell segmentation. We thus introduce a new methodology for hyperspectral cell imaging and segmentation, based on a simple, unsupervised workflow without any spectrum-to-spectrum phase retrieval computation. We first assess the robustness of our approach by considering cells of different types, namely, from the human HEK293 and murine C2C12 lines. To evaluate its applicability over a broader range, we then study HEK293 cells in different physiological states and experimental situations. Specifically, we compare an interphasic cell with a mitotic (prophase) one. We also present a comparison between a fixed cell and a living cell, in order to visualize the potential changes induced by the fixation protocol in cellular architecture. Next, with the aim of assessing more precisely the sensitivity of our approach, we study HEK293 living cells overexpressing tropomyosin-related kinase B (TrkB), a cancer-related membrane receptor, depending on the presence of its ligand, brain-derived neurotrophic factor (BDNF). Finally, the segmentation capability of the approach is evaluated in the case of a single cell and also by considering cell clusters of various sizes.
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Affiliation(s)
- Damien Boildieu
- University of Limoges, CNRS, XLIM, UMR 7252, Limoges, France
- University of Poitiers, CNRS, XLIM, UMR 7252, Poitiers, France
| | | | - Ludovic Duponchel
- University of Lille, CNRS, UMR 8516, LASIRE - Laboratoire de Spectroscopie Pour Les Interactions, La Réactivité et L’Environnement, Lille, France
| | - Vincent Sol
- University of Limoges, PEIRENE, UR 22722, Limoges, France
| | | | - Éric Champion
- University of Limoges, CNRS, Institut de Recherche sur Les Céramiques, UMR 7315, Limoges, France
| | - Hideaki Kano
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - David Helbert
- University of Poitiers, CNRS, XLIM, UMR 7252, Poitiers, France
| | - Amandine Magnaudeix
- University of Limoges, CNRS, Institut de Recherche sur Les Céramiques, UMR 7315, Limoges, France
| | - Philippe Leproux
- University of Limoges, CNRS, XLIM, UMR 7252, Limoges, France
- *Correspondence: Philippe Leproux,
| | - Philippe Carré
- University of Poitiers, CNRS, XLIM, UMR 7252, Poitiers, France
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77
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Liu J, Li Y, Mo H, Xie E, Fang J, Gan W. Current utilization of waste biomass as filler for wood adhesives: A review. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2022.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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78
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Palomar VM, Jaksich S, Fujii S, Kuciński J, Wierzbicki AT. High-resolution map of plastid-encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1139-1151. [PMID: 35765883 PMCID: PMC9540123 DOI: 10.1111/tpj.15882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 05/16/2023]
Abstract
Plastids contain their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplast DNA using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq). We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with levels of RNA accumulation, which demonstrates the impact of PEP on chloroplast gene expression. Presented data are available through a publicly available Plastid Genome Visualization Tool (Plavisto) at https://plavisto.mcdb.lsa.umich.edu/.
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Affiliation(s)
- V. Miguel Palomar
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Sarah Jaksich
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Sho Fujii
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
- Department of Botany, Graduate School of ScienceKyoto UniversityKyoto606‐8502Japan
- Department of Biology, Faculty of Agriculture and Life ScienceHirosaki UniversityHirosaki036‐8561Japan
| | - Jan Kuciński
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Andrzej T. Wierzbicki
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMichigan48109USA
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79
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Harris RL, Vetter MCYL, van Heerden E, Cason E, Vermeulen JG, Taneja A, Kieft TL, DeCoste CJ, Laevsky GS, Onstott TC. FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities. MICROBIAL ECOLOGY 2022; 84:182-197. [PMID: 34406445 PMCID: PMC9250922 DOI: 10.1007/s00248-021-01809-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA+); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.
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Affiliation(s)
- Rachel L Harris
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Maggie C Y Lau Vetter
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Laboratory of Extraterrestrial Ocean Systems, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, Hainan, China.
| | - Esta van Heerden
- Centre for Water Sciences and Management, North West University, Potchefstroom, South Africa
- iWater Pty Ltd, 5 Walter Sisulu Rd, Park West, Bloemfontein, 9301, South Africa
| | - Errol Cason
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Animal-, Wildlife- and Grassland Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - Jan-G Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Virology, University of the Free State, Bloemfontein, 9301, South Africa
| | - Anjali Taneja
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
- McCourt School of Public Policy, Georgetown University, Washington, DC, 20057, USA
| | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Christina J DeCoste
- Flow Cytometry Resource Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Gary S Laevsky
- Confocal Imaging Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
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80
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Agne S, Naylor GJP, Preick M, Yang L, Thiel R, Weigmann S, Paijmans JLA, Barlow A, Hofreiter M, Straube N. Taxonomic Identification of Two Poorly Known Lantern Shark Species Based on Mitochondrial DNA From Wet-Collection Paratypes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.910009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence. In contrast, DNA sequence information has rarely been used. Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions. The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far. However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data. Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals. Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species. Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research.
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81
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Agne S, Preick M, Straube N, Hofreiter M. Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.909846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.
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82
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Mund A, Brunner AD, Mann M. Unbiased spatial proteomics with single-cell resolution in tissues. Mol Cell 2022; 82:2335-2349. [PMID: 35714588 DOI: 10.1016/j.molcel.2022.05.022] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 12/19/2022]
Abstract
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify the entire complement of proteins in cells or tissues. Here, we review challenges and recent advances in the LC-MS-based analysis of minute protein amounts, down to the level of single cells. Application of this technology revealed that single-cell transcriptomes are dominated by stochastic noise due to the very low number of transcripts per cell, whereas the single-cell proteome appears to be complete. The spatial organization of cells in tissues can be studied by emerging technologies, including multiplexed imaging and spatial transcriptomics, which can now be combined with ultra-sensitive proteomics. Combined with high-content imaging, artificial intelligence and single-cell laser microdissection, MS-based proteomics provides an unbiased molecular readout close to the functional level. Potential applications range from basic biological questions to precision medicine.
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Affiliation(s)
- Andreas Mund
- Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Andreas-David Brunner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Matthias Mann
- Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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83
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Li B, Wan Z, Zheng H, Cai S, Tian HW, Tang H, Chu X, He G, Guo DS, Xue XS, Chen G. Construction of Complex Macromulticyclic Peptides via Stitching with Formaldehyde and Guanidine. J Am Chem Soc 2022; 144:10080-10090. [PMID: 35639413 DOI: 10.1021/jacs.2c04620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is a growing interest in constructing multicyclic peptide structures to expand the chemical space of peptides. Conventional strategies for constructing large peptide structures are limited by the typical reliance on the inflexible coupling between premade templates equipped with fixed reactive handles and peptide substrates via cysteine anchors. Herein, we report the development of a facile three-component condensation reaction of primary alkyl amine, formaldehyde, and guanidine for construction of complex macromulticyclic peptides with novel topologies via lysine anchors. Moreover, the reaction sequences can be orchestrated in different anchor combinations and spatial arrangements to generate various macrocyclic structures crosslinked by distinct fused tetrahydrotriazine linkages. The macrocyclization reactions are selective, efficient, versatile, and workable in both organic and aqueous media. Thus, the condensation reaction provides a smart tool for stitching native peptides in situ using simple methylene threads and guanidine joints in a flexible and programmable manner.
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Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Han-Wen Tian
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Sheng Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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84
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Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics 2022; 22:e2100206. [PMID: 35633285 DOI: 10.1002/pmic.202100206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry-based with tailored biochemical and genetic methods to examine overall protein make-up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of chromatin function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
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85
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Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects. Int J Mol Sci 2022; 23:ijms23115923. [PMID: 35682602 PMCID: PMC9180120 DOI: 10.3390/ijms23115923] [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: 04/08/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
RNA-binding proteins (RBPs) form complex interactions with RNA to regulate the cell’s activities including cell development and disease resistance. RNA-binding proteome (RBPome) aims to profile and characterize the RNAs and proteins that interact with each other to carry out biological functions. Generally, RNA-centric and protein-centric ribonomic approaches have been successfully developed to profile RBPome in different organisms including plants and animals. Further, more and more novel methods that were firstly devised and applied in mammalians have shown great potential to unravel RBPome in plants such as RNA-interactome capture (RIC) and orthogonal organic phase separation (OOPS). Despise the development of various robust and state-of-the-art ribonomics techniques, genome-wide RBP identifications and characterizations in plants are relatively fewer than those in other eukaryotes, indicating that ribonomics techniques have great opportunities in unraveling and characterizing the RNA–protein interactions in plant species. Here, we review all the available approaches for analyzing RBPs in living organisms. Additionally, we summarize the transcriptome-wide approaches to characterize both the coding and non-coding RBPs in plants and the promising use of RBPome for booming agriculture.
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86
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Wei YB, Luo D, Xiong X, Huang YL, Xie M, Lu W, Li D. Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework. Chem Sci 2022; 13:4813-4820. [PMID: 35655868 PMCID: PMC9067591 DOI: 10.1039/d2sc00188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions induced by crosslinking agents such as formaldehyde (HCHO). Building artificial models to simulate the crosslinking process would advance our understanding of the underlying mechanisms and therefore develop coping strategies accordingly. Herein we report the design and synthesis of a Zn-based metal-organic framework with mixed ligands of 2,6-diaminopurine and amine-functionalized dicarboxylate, representing DNA and protein residues, respectively. Combined characterization techniques allow us to demonstrate the unusual efficiency of HCHO-crosslinking within the confined space of the titled MOF. Particularly, in situ single-crystal X-ray diffraction studies reveal a sequential methylene-knitting process upon HCHO addition, along with strong fluorescence that was not interfered with by other metabolites, glycine, and Tris. This work has successfully constructed a purine-based metal-organic framework with unoccupied Watson-Crick sites, serving as a crystalline model for HCHO-induced DPCs by mimicking the confinement effect of protein/DNA interactions.
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Affiliation(s)
- Yu-Bai Wei
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dong Luo
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Xiao Xiong
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Yong-Liang Huang
- Department of Chemistry, Shantou University Medical College Shantou Guangdong 515041 P. R. China
| | - Mo Xie
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Weigang Lu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dan Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
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87
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Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens. Clin Proteomics 2022; 19:10. [PMID: 35501693 PMCID: PMC9063121 DOI: 10.1186/s12014-022-09346-0] [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: 05/04/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
Objectives Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins. Methods Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS). Results Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09346-0.
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88
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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89
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Zhu BT. Biochemical mechanism underlying the pathogenesis of diabetic retinopathy and other diabetic complications in humans: the methanol-formaldehyde-formic acid hypothesis. Acta Biochim Biophys Sin (Shanghai) 2022; 54:415-451. [PMID: 35607958 PMCID: PMC9828688 DOI: 10.3724/abbs.2022012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
Hyperglycemia in diabetic patients is associated with abnormally-elevated cellular glucose levels. It is hypothesized that increased cellular glucose will lead to increased formation of endogenous methanol and/or formaldehyde, both of which are then metabolically converted to formic acid. These one-carbon metabolites are known to be present naturally in humans, and their levels are increased under diabetic conditions. Mechanistically, while formaldehyde is a cross-linking agent capable of causing extensive cytotoxicity, formic acid is an inhibitor of mitochondrial cytochrome oxidase, capable of inducing histotoxic hypoxia, ATP deficiency and cytotoxicity. Chronic increase in the production and accumulation of these toxic one-carbon metabolites in diabetic patients can drive the pathogenesis of ocular as well as other diabetic complications. This hypothesis is supported by a large body of experimental and clinical observations scattered in the literature. For instance, methanol is known to have organ- and species-selective toxicities, including the characteristic ocular lesions commonly seen in humans and non-human primates, but not in rodents. Similarly, some of the diabetic complications (such as ocular lesions) also have a characteristic species-selective pattern, closely resembling methanol intoxication. Moreover, while alcohol consumption or combined use of folic acid plus vitamin B is beneficial for mitigating acute methanol toxicity in humans, their use also improves the outcomes of diabetic complications. In addition, there is also a large body of evidence from biochemical and cellular studies. Together, there is considerable experimental support for the proposed hypothesis that increased metabolic formation of toxic one-carbon metabolites in diabetic patients contributes importantly to the development of various clinical complications.
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Affiliation(s)
- Bao Ting Zhu
- Shenzhen Key Laboratory of Steroid Drug Discovery and DevelopmentSchool of MedicineThe Chinese University of Hong KongShenzhen518172China
- Department of PharmacologyToxicology and TherapeuticsSchool of MedicineUniversity of Kansas Medical CenterKansas CityKS66160USA
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90
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Chen Y, Cao A, Li Q, Quan J. Identification of DNA aptamers that specifically targets EBV + nasopharyngeal carcinoma via binding with EphA2/CD98hc complex. Biochem Biophys Res Commun 2022; 608:135-141. [PMID: 35397426 DOI: 10.1016/j.bbrc.2022.03.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/02/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is one of the Epstein-Barr virus (EBV)-associated malignancies and has a distinct geographical distribution. The high mortality rates of NPC patients with advanced and recurrent disease highlight the urgent need for biomarkers for early diagnosis and effective treatments. In this study, we developed DNA aptamers that specifically bind to EBV positive NPC cells by the Cell-SELEX procedure. We further identified the EphA2 (ephrin type-A receptor 2)/CD98hc (CD98 heavy chain) complex as the potential target of the aptamer EA-3 by combining aptamer-based separation and mass spectrometry analysis. Our results revealed for the first time that EphA2 colocalized with CD98hc at the plasma membrane and EphA2 coimmunoprecipitated with CD98hc, which may serve as a starting point for exploring the potential functions of the complex of EphA2 and CD98hc in NPCs. Here, we demonstrated that aptamers can be useful for the identification of protein complexes on the surface of cancer cells.
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Affiliation(s)
- Yaqi Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Anqi Cao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qinkai Li
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - JunMin Quan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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91
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Cao H, Kapranov P. Methods to Analyze the Non-Coding RNA Interactome—Recent Advances and Challenges. Front Genet 2022; 13:857759. [PMID: 35368711 PMCID: PMC8969105 DOI: 10.3389/fgene.2022.857759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/15/2022] [Indexed: 12/03/2022] Open
Abstract
Most of the human genome is transcribed to generate a multitude of non-coding RNAs. However, while these transcripts have generated an immense amount of scientific interest, their biological function remains a subject of an intense debate. Understanding mechanisms of action of non-coding RNAs is a key to addressing the issue of biological relevance of these transcripts. Based on some well-understood non-coding RNAs that function inside the cell by interacting with other molecules, it is generally believed many other non-coding transcripts could also function in a similar fashion. Therefore, development of methods that can map RNA interactome is the key to understanding functionality of the extensive cellular non-coding transcriptome. Here, we review the vast progress that has been made in the past decade in technologies that can map RNA interactions with different sites in DNA, proteins or other RNA molecules; the general approaches used to validate the existence of novel interactions; and the challenges posed by interpreting the data obtained using the interactome mapping methods.
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92
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Lee M, Shin J, Kim S, Gandla S. Whey Protein Isolate Film and Laser-Ablated Textured PDMS-Based Single-Electrode Triboelectric Nanogenerator for Pressure-Sensor Application. SENSORS (BASEL, SWITZERLAND) 2022; 22:2154. [PMID: 35336324 PMCID: PMC8953929 DOI: 10.3390/s22062154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022]
Abstract
The use of biopolymers for realizing economical and eco-friendly triboelectric nanogenerators (TENGs) widens the application prospects of TENGs. Herein, an animal-sourced whey protein isolate (WPI) film, processed and prepared by a simple aqueous solution preparation and drop-casting technique, is applied to demonstrate its potential use in bio-TENGs. With the addition of formaldehyde in WPI, the films result in a free-standing and flexible film, whereas the pure WPI films are difficult to handle and lack flexibility. A TENG device based on the WPI and the laser-ablated textured polydimethylsiloxane (PDMS) for pressure-sensor application were developed. The output voltage of the TENG comprising WPI increased nearly two-fold compared to the TENG without WPI. A simple single-electrode TENG device configuration was adopted so that it could be easily integrated into a wearable electronic device. Moreover, WPI film exhibited tribo-negative-like material characteristics. This study provides new insights into the development of biocompatible and eco-friendly biopolymers for various electronic devices and sensors.
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Affiliation(s)
- Minwoo Lee
- Multifunctional Nano Bio Electronics Lab, Department of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Jonghwan Shin
- Multifunctional Nano Bio Electronics Lab, Department of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Sunkook Kim
- Multifunctional Nano Bio Electronics Lab, Department of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Srinivas Gandla
- Multifunctional Nano Bio Electronics Lab, Department of Advanced Materials and Science Engineering, Sungkyunkwan University, Suwon 16419, Korea
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93
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Permana D, Putra HE, Djaenudin D. Designed protein multimerization and polymerization for functionalization of proteins. Biotechnol Lett 2022; 44:341-365. [PMID: 35083582 PMCID: PMC8791688 DOI: 10.1007/s10529-021-03217-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/04/2021] [Indexed: 12/15/2022]
Abstract
Abstract Multimeric and polymeric proteins are large biomacromolecules consisting of multiple protein molecules as their monomeric units, connected through covalent or non-covalent bonds. Genetic modification and post-translational modifications (PTMs) of proteins offer alternative strategies for designing and creating multimeric and polymeric proteins. Multimeric proteins are commonly prepared by genetic modification, whereas polymeric proteins are usually created through PTMs. There are two methods that can be applied to create polymeric proteins: self-assembly and crosslinking. Self-assembly offers a spontaneous reaction without a catalyst, while the crosslinking reaction offers some catalyst options, such as chemicals and enzymes. In addition, enzymes are excellent catalysts because they provide site-specificity, rapid reaction, mild reaction conditions, and activity and functionality maintenance of protein polymers. However, only a few enzymes are applicable for the preparation of protein polymers. Most of the other enzymes are effective only for protein conjugation or labeling. Here, we review novel and applicable strategies for the preparation of multimeric proteins through genetic modification and self-assembly. We then describe the formation of protein polymers through site-selective crosslinking reactions catalyzed by enzymes, crosslinking reactions of non-natural amino acids, and protein-peptide (SpyCatcher/SpyTag) interactions. Finally, we discuss the potential applications of these protein polymers. Graphical abstract ![]()
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan. .,Research Unit for Clean Technology, The National Research and Innovation Agency of Republic of Indonesia, Jl. Cisitu, Bandung, 40135, Indonesia.
| | - Herlian Eriska Putra
- Research Unit for Clean Technology, The National Research and Innovation Agency of Republic of Indonesia, Jl. Cisitu, Bandung, 40135, Indonesia
| | - Djaenudin Djaenudin
- Research Unit for Clean Technology, The National Research and Innovation Agency of Republic of Indonesia, Jl. Cisitu, Bandung, 40135, Indonesia
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94
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Wang Y, Hu Y, Höti N, Huang L, Zhang H. Characterization of In Vivo Protein Complexes via Chemical Cross-Linking and Mass Spectrometry. Anal Chem 2022; 94:1537-1542. [PMID: 34962381 PMCID: PMC9006583 DOI: 10.1021/acs.analchem.1c02410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cells perform various functions by proteins via protein complexes. Characterization of protein complexes is critical to understanding their biological and clinical significance and has been one of the major efforts of functional proteomics. To date, most protein complexes are characterized by the in vitro system from protein extracts after the cells or tissues are lysed, and it has been challenging to determine which of these protein complexes are formed in intact cells. Herein, we report an approach to preserve protein complexes using in vivo cross-linking, followed by size exclusion chromatography and data-independent acquisition mass spectrometry. This approach enables the characterization of in vivo protein complexes from cells or tissues, which allows the determination of protein complexes in clinical research. More importantly, the described approach can identify protein complexes that are not detected by the in vitro system, which provide unique protein function information.
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Affiliation(s)
- Yuefan Wang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, USA
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95
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Spiniello M, Scalf M, Casamassimi A, Abbondanza C, Smith LM. Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. Int J Mol Sci 2022; 23:ijms23020942. [PMID: 35055128 PMCID: PMC8779001 DOI: 10.3390/ijms23020942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
RNA-binding proteins are crucial to the function of coding and non-coding RNAs. The disruption of RNA–protein interactions is involved in many different pathological states. Several computational and experimental strategies have been developed to identify protein binders of selected RNA molecules. Amongst these, ‘in cell’ hybridization methods represent the gold standard in the field because they are designed to reveal the proteins bound to specific RNAs in a cellular context. Here, we compare the technical features of different ‘in cell’ hybridization approaches with a focus on their advantages, limitations, and current and potential future applications.
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Affiliation(s)
- Michele Spiniello
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, 80131 Naples, Italy
- Correspondence: (M.S.); (A.C.)
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.S.); (L.M.S.)
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
- Correspondence: (M.S.); (A.C.)
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.S.); (L.M.S.)
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96
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Rak M, Reiss K. Double Labeling Fluorescent Immunocytochemistry. Methods Mol Biol 2022; 2422:147-161. [PMID: 34859404 DOI: 10.1007/978-1-0716-1948-3_10] [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] [Indexed: 06/13/2023]
Abstract
Fluorescent immunocytochemistry is a powerful technique based on detecting antigens. It leads to discoveries in cell composition and structure as well as its functioning by expanding knowledge on colocalization between its components. The potency of this method is based on findings in the areas of specific antibodies production, fluorescent labels, and microscopy. Since it merges different fields, it requires basic knowledge on all the steps that are needed in the procedure planning and implementation to be used properly and produce reliable results. Here we describe a protocol of LN-229 human glioblastoma cells double labeling of LC3 and IRS-1 proteins, highlighting the importance of some steps of the procedure and possible variables.
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Affiliation(s)
- Monika Rak
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland.
- Departments of Medicine & Neurological Cancer Research, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
| | - Krzysztof Reiss
- Departments of Medicine & Neurological Cancer Research, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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97
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Oba U, Kohashi K, Sangatsuda Y, Oda Y, Sonoda KH, Ohga S, Yoshimoto K, Arai Y, Yachida S, Shibata T, Ito T, Miura F. An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections. Biol Methods Protoc 2022; 7:bpac014. [PMID: 35937639 PMCID: PMC9351614 DOI: 10.1093/biomethods/bpac014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction" (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.
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Affiliation(s)
- Utako Oba
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
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98
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Irgen-Gioro S, Yoshida S, Walling V, Chong S. Fixation can change the appearance of phase separation in living cells. eLife 2022; 11:79903. [PMID: 36444977 PMCID: PMC9817179 DOI: 10.7554/elife.79903] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.
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Affiliation(s)
- Shawn Irgen-Gioro
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States,Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Victoria Walling
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
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99
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Blombach F, Smollett KL, Werner F. ChIP-Seq Occupancy Mapping of the Archaeal Transcription Machinery. Methods Mol Biol 2022; 2522:209-222. [PMID: 36125752 DOI: 10.1007/978-1-0716-2445-6_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genome-wide occupancy studies for RNA polymerases and their basal transcription factors deliver information about transcription dynamics and the recruitment of transcription elongation and termination factors in eukaryotes and prokaryotes. The primary method to determine genome-wide occupancies is chromatin immunoprecipitation combined with deep sequencing (ChIP-seq). Archaea possess a transcription machinery that is evolutionarily closer related to its eukaryotic counterpart but it operates in a prokaryotic cellular context. Studies on archaeal transcription brought insight into the evolution of transcription machineries and the universality of transcription mechanisms. Because of the limited resolution of ChIP-seq, the close spacing of promoters and transcription units found in archaeal genomes pose a challenge for ChIP-seq and the ensuing data analysis. The extreme growth temperature of many established archaeal model organisms necessitates further adaptations. This chapter describes a version of ChIP-seq adapted for the basal transcription machinery of thermophilic archaea and some modifications to the data analysis.
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Affiliation(s)
- Fabian Blombach
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.
| | - Kathy L Smollett
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.
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100
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Tan WX, Bok CM, Ng NHJ, Teo AKK. Chromatin Immunoprecipitation in Human Pluripotent Stem Cell-Derived 3D Organoids to Analyze DNA-Protein Interactions. Methods Mol Biol 2022; 2429:215-232. [PMID: 35507164 DOI: 10.1007/978-1-0716-1979-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chromatin immunoprecipitation (ChIP) is a technique that has been widely used to interrogate DNA-protein interactions in cells. In recent years, human pluripotent stem cell (hPSC)-derived 3D organoids have emerged as a powerful model to understand human development and diseases. Performing ChIP in hPSC-derived 3D organoids is a useful approach to dissect the roles of transcription factors or co-factors and to understand the epigenetic landscape in human development and diseases. However, performing ChIP in 3D organoids is more challenging than monolayer cultures, and an optimized protocol is needed for interpretable data. Hence, in this chapter, we describe in detail a protocol for performing ChIP in hPSC-derived islet-like cells as an example, from organoid harvest to ChIP-qPCR data analysis. This chapter also highlights potential pitfalls and provides recommendations for troubleshooting.
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Affiliation(s)
- Wei Xuan Tan
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chek Mei Bok
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Natasha Hui Jin Ng
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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