1
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Hill CJ, Datta S, McCurtin NP, Kimball HZ, Kingsley MC, Bayer AL, Martin AC, Peng Q, Weerapana E, Scheck RA. A Modular Turn-On Strategy to Profile E2-Specific Ubiquitination Events in Living Cells. Angew Chem Int Ed Engl 2024; 63:e202319579. [PMID: 38291002 DOI: 10.1002/anie.202319579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/01/2024]
Abstract
A cascade of three enzymes, E1-E2-E3, is responsible for transferring ubiquitin to target proteins, which controls many different aspects of cellular signaling. The role of the E2 has been largely overlooked, despite influencing substrate identity, chain multiplicity, and topology. Here we report a method-targeted charging of ubiquitin to E2 (tCUbE)-that can track a tagged ubiquitin through its entire enzymatic cascade in living mammalian cells. We use this approach to reveal new targets whose ubiquitination depends on UbcH5a E2 activity. We demonstrate that tCUbE can be broadly applied to multiple E2s and in different human cell lines. tCUbE is uniquely suited to examine E2-E3-substrate cascades of interest and/or piece together previously unidentified cascades, thereby illuminating entire branches of the UPS and providing critical insight that will be useful for identifying new therapeutic targets in the UPS.
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Affiliation(s)
- Caitlin J Hill
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Suprama Datta
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | | | - Hannah Z Kimball
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Molly C Kingsley
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | - Abraham L Bayer
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | | | - Qianni Peng
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Rebecca A Scheck
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
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2
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Choi HP, Yang JH, Azadzoi KM. Differential Post-Translational Modifications of Proteins in Bladder Ischemia. Biomedicines 2023; 12:81. [PMID: 38255188 PMCID: PMC10813800 DOI: 10.3390/biomedicines12010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Clinical and basic research suggests that bladder ischemia may be an independent variable in the development of lower urinary tract symptoms (LUTS). We have reported that ischemic changes in the bladder involve differential expression and post-translational modifications (PTMs) of the protein's functional domains. In the present study, we performed in-depth analysis of a previously reported proteomic dataset to further characterize proteins PTMs in bladder ischemia. Our proteomic analysis of proteins in bladder ischemia detected differential formation of non-coded amino acids (ncAAs) that might have resulted from PTMs. In-depth analysis revealed that three groups of proteins in the bladder proteome, including contractile proteins and their associated proteins, stress response proteins, and cell signaling-related proteins, are conspicuously impacted by ischemia. Differential PTMs of proteins by ischemia seemed to affect important signaling pathways in the bladder and provoke critical changes in the post-translational structural integrity of the stress response, contractile, and cell signaling-related proteins. Our data suggest that differential PTMs of proteins may play a role in the development of cellular stress, sensitization of smooth muscle cells to contractile stimuli, and deferential cell signaling in bladder ischemia. These observations may provide the foundation for future research to validate and define clinical translation of the modified biomarkers for precise diagnosis of bladder dysfunction and the development of new therapeutic targets against LUTS.
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Affiliation(s)
- Han-Pil Choi
- Proteomics Laboratory, VA Boston Healthcare System, Boston, MA 02130, USA;
| | - Jing-Hua Yang
- Proteomics Laboratory, Department of Surgery, VA Boston Healthcare System, Boston University School of Medicine, Boston, MA 02130, USA;
| | - Kazem M. Azadzoi
- Departments of Urology and Pathology, VA Boston Healthcare System, Boston University School of Medicine, Boston, MA 02130, USA
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3
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Nwabor OF, Chukamnerd A, Terbtothakun P, Nwabor LC, Surachat K, Roytrakul S, Voravuthikunchai SP, Chusri S. Synergistic effects of polymyxin and vancomycin combinations on carbapenem- and polymyxin-resistant Klebsiella pneumoniae and their molecular characteristics. Microbiol Spectr 2023; 11:e0119923. [PMID: 37905823 PMCID: PMC10715205 DOI: 10.1128/spectrum.01199-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE This study provides insights into the mechanisms of polymyxin resistance in K. pneumoniae clinical isolates and demonstrates potential strategies of polymyxin and vancomycin combinations for combating this resistance. We also identified possible mechanisms that might be associated with the treatment of these combinations against carbapenem- and polymyxin-resistant K. pneumoniae clinical isolates. The findings have significant implications for the development of alternative therapies and the effective management of infections caused by these pathogens.
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Affiliation(s)
- Ozioma Forstinus Nwabor
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Arnon Chukamnerd
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Pawarisa Terbtothakun
- Division of Biological Science, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Lois Chinwe Nwabor
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Faculty of Medicine, Translational Medicine Research Center, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Faculty of Science, Center of Antimicrobial Biomaterial Innovation-Southeast Asia and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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4
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Kafri M, Patena W, Martin L, Wang L, Gomer G, Ergun SL, Sirkejyan AK, Goh A, Wilson AT, Gavrilenko SE, Breker M, Roichman A, McWhite CD, Rabinowitz JD, Cross FR, Wühr M, Jonikas MC. Systematic identification and characterization of genes in the regulation and biogenesis of photosynthetic machinery. Cell 2023; 186:5638-5655.e25. [PMID: 38065083 PMCID: PMC10760936 DOI: 10.1016/j.cell.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 08/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Photosynthesis is central to food production and the Earth's biogeochemistry, yet the molecular basis for its regulation remains poorly understood. Here, using high-throughput genetics in the model eukaryotic alga Chlamydomonas reinhardtii, we identify with high confidence (false discovery rate [FDR] < 0.11) 70 poorly characterized genes required for photosynthesis. We then enable the functional characterization of these genes by providing a resource of proteomes of mutant strains, each lacking one of these genes. The data allow assignment of 34 genes to the biogenesis or regulation of one or more specific photosynthetic complexes. Further analysis uncovers biogenesis/regulatory roles for at least seven proteins, including five photosystem I mRNA maturation factors, the chloroplast translation factor MTF1, and the master regulator PMR1, which regulates chloroplast genes via nuclear-expressed factors. Our work provides a rich resource identifying regulatory and functional genes and placing them into pathways, thereby opening the door to a system-level understanding of photosynthesis.
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Affiliation(s)
- Moshe Kafri
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gillian Gomer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sabrina L Ergun
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Arthur K Sirkejyan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia E Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Asael Roichman
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Frederick R Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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5
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Tai L, Saffery NS, Chin SP, Cheong SK. Secretome profile of TNF-α-induced human umbilical cord mesenchymal stem cells unveils biological processes relevant to skin wound healing. Regen Med 2023; 18:839-856. [PMID: 37671699 DOI: 10.2217/rme-2023-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023] Open
Abstract
Aim: To profile and study the proteins responsible for the beneficial effect of the TNF-α-induced human umbilical cord mesenchymal stem cells (hUCMSCs) secretome in wound healing. Methods: The hUCMSCs secretome was generated with (induced) or without (uninduced) TNF-α and was subsequently analyzed by liquid chromatography-mass spectrometry, immunoassay and in vitro scratch assay. Results: Proteomic analysis revealed approximately 260 proteins, including 51 and 55 unique proteins in the induced and uninduced secretomes, respectively. Gene ontology analysis disclosed that differential proteins in the induced secretome mainly involved inflammation-related terms. The induced secretome, consisting of higher levels of FGFb, VEGF, PDGF and IL-6, significantly accelerated wound closure and enhanced MMP-13 secretion in HaCaT keratinocytes. Conclusion: The secretome from induced hUCMSCs includes factors that promote wound closure.
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Affiliation(s)
- Lihui Tai
- Cytopeutics Sdn Bhd, Suite 2-3 2nd floor, Bio-X Centre, Persiaran Cyberpoint Selatan, Cyber 8, 63000, Cyberjaya, Selangor, Malaysia
| | - Nik Syazana Saffery
- Cytopeutics Sdn Bhd, Suite 2-3 2nd floor, Bio-X Centre, Persiaran Cyberpoint Selatan, Cyber 8, 63000, Cyberjaya, Selangor, Malaysia
| | - Sze Piaw Chin
- Cytopeutics Sdn Bhd, Suite 2-3 2nd floor, Bio-X Centre, Persiaran Cyberpoint Selatan, Cyber 8, 63000, Cyberjaya, Selangor, Malaysia
| | - Soon Keng Cheong
- Cytopeutics Sdn Bhd, Suite 2-3 2nd floor, Bio-X Centre, Persiaran Cyberpoint Selatan, Cyber 8, 63000, Cyberjaya, Selangor, Malaysia
- M. Kandiah Faculty of Medicine & Health Sciences (MK FMHS), Universiti Tunku Abdul Rahman Sungai Long City Campus, Jalan Sungai Long, Bandar Sungai Long, Cheras, 43000, Kajang, Selangor, Malaysia
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6
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Nayak S, Aanice D, Andria D, Pai A, Maiti B. Polymerase chain reaction-based typing methods and protein profiling analysis of Acinetobacter baumannii isolated from environmental and clinical sources from South India. Can J Microbiol 2023; 69:449-462. [PMID: 37364377 DOI: 10.1139/cjm-2023-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Acinetobacter baumannii is an opportunistic pathogen known for causing hospital-acquired infections. The natural habitat includes soil, water, sewage, and drains, but it is also detected in infected individuals' blood, pus, and respiratory pathways. Due to its resilient nature, it is known to be a causative agent for outbreaks. Therefore, it is crucial to understand the genetic similarity between clinical and environmental isolates. The study aimed to find the genetic relationships between clinical and environmental isolates using PCR-based typing methods such as enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), random amplified polymorphic DNA (RAPD), and repetitive extragenic palindromic sequence-based PCR (Rep-PCR). Additionally, outer membrane protein (OMP) and whole cell protein (WCP) profiles were also used. The PCR-based methods, ERIC-PCR and Rep-PCR, showed decreased genetic similarity between clinical and environmental isolates (66% and 58%, respectively). However, RAPD showed relatively higher genetic similarity (91%). The OMP and WCP profiles showed varied banding patterns between the clinical and environmental isolates in the 29-43 kDa region. The PCR-based methods proved to be a reliable and reproducible technique. The OMP and WCP profiles, though not as discriminatory as the molecular typing methods, could help identify the most and least commonly occurring protein bands and thus help in typing clinical and environmental A. baumannii isolates.
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Affiliation(s)
- Srajana Nayak
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangaluru, Karnataka 575018, India
| | - D'Almeida Aanice
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangaluru, Karnataka 575018, India
| | - Dsouza Andria
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangaluru, Karnataka 575018, India
| | - Archana Pai
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangaluru, Karnataka 575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangaluru, Karnataka 575018, India
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7
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Gao Z, Li Z, Hutchins Z, Zhang Q, Zhong W. Enhancing Extracellular Vesicle Analysis by Integration of Large-Volume Sample Stacking in Capillary Electrophoresis with Asymmetrical Flow Field-Flow Fractionation. Anal Chem 2023; 95:15778-15785. [PMID: 37795969 PMCID: PMC10947528 DOI: 10.1021/acs.analchem.3c03303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Extracellular vesicles (EVs) play important roles in cell-cell communication and pathological development. Cargo profiling for the EVs present in clinical specimens can provide valuable insights into their functions and help discover effective EV-based markers for diagnostic and therapeutic purposes. However, the highly abundant and complex matrix components pose significant challenges for specific identification of low-abundance EV cargos. Herein, we combine asymmetrical flow field-flow fractionation (AF4) with large-volume sample stacking and capillary electrophoresis (LVSS/CE), to attain EVs with high purity for downstream protein profiling. This hyphenated system first separates the EVs from the contamination of smaller serum proteins by AF4, and second resolves the EVs from the coeluted, nonvesicular matrix components by CE following LVSS. The optimal LVSS condition permits the injection of 10-fold more EVs into CE compared to the nonstacking condition without compromising separation resolution. Collection and downstream analysis of the highly pure EVs after CE separation were demonstrated in the present work. The high EV purity yields a much-improved labeling efficiency when detected by fluorescent antibodies compared to those collected from the one-dimension separation of AF4, and permits the identification of more EV-specific cargos by LC-MS/MS compared to those isolated by ultracentrifugation (UC), the exoEasy Maxi Kit, and AF4. Our results strongly support that AF4-LVSS/CE can improve EV isolation and cargo analysis, opening up new opportunities for understanding EV functions and their applications in the biomedical fields.
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Affiliation(s)
- Ziting Gao
- Department of Chemistry, University of California – Riverside, Riverside, CA 92521, U.S.A
| | - Zongbo Li
- Department of Chemistry, University of California – Riverside, Riverside, CA 92521, U.S.A
| | - Zachary Hutchins
- Department of Chemistry, University of California – Riverside, Riverside, CA 92521, U.S.A
| | - Quanqing Zhang
- Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California – Riverside, Riverside, CA 92521, U.S.A
| | - Wenwan Zhong
- Department of Chemistry, University of California – Riverside, Riverside, CA 92521, U.S.A
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8
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Liu YT, Xu Z, Liu W, Ren S, Xiong HW, Jiang T, Chen J, Kang Y, Li QY, Wu ZH, Machens HG, Yang XF, Chen ZB. The circ_0002538/miR-138-5p/plasmolipin axis regulates Schwann cell migration and myelination in diabetic peripheral neuropathy. Neural Regen Res 2023; 18:1591-1600. [PMID: 36571367 PMCID: PMC10075099 DOI: 10.4103/1673-5374.355979] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Circular RNAs (circRNAs) play a vital role in diabetic peripheral neuropathy. However, their expression and function in Schwann cells in individuals with diabetic peripheral neuropathy remain poorly understood. Here, we performed protein profiling and circRNA sequencing of sural nerves in patients with diabetic peripheral neuropathy and controls. Protein profiling revealed 265 differentially expressed proteins in the diabetic peripheral neuropathy group. Gene Ontology indicated that differentially expressed proteins were mainly enriched in myelination and mitochondrial oxidative phosphorylation. A real-time polymerase chain reaction assay performed to validate the circRNA sequencing results yielded 11 differentially expressed circRNAs. circ_0002538 was markedly downregulated in patients with diabetic peripheral neuropathy. Further in vitro experiments showed that overexpression of circ_0002538 promoted the migration of Schwann cells by upregulating plasmolipin (PLLP) expression. Moreover, overexpression of circ_0002538 in the sciatic nerve in a streptozotocin-induced mouse model of diabetic peripheral neuropathy alleviated demyelination and improved sciatic nerve function. The results of a mechanistic experiment showed that circ_0002538 promotes PLLP expression by sponging miR-138-5p, while a lack of circ_0002538 led to a PLLP deficiency that further suppressed Schwann cell migration. These findings suggest that the circ_0002538/miR-138-5p/PLLP axis can promote the migration of Schwann cells in diabetic peripheral neuropathy patients, improving myelin sheath structure and nerve function. Thus, this axis is a potential target for therapeutic treatment of diabetic peripheral neuropathy.
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Affiliation(s)
- Yu-Tian Liu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zhao Xu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wei Liu
- Department of Geriatrics, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Sen Ren
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - He-Wei Xiong
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Tao Jiang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yu Kang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Qian-Yun Li
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zi-Han Wu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Hans-GüNther Machens
- Department of Plastic and Hand Surgery, Technical University of Munich, Munich, Germany
| | - Xiao-Fan Yang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zhen-Bing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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9
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Dela Cruz TEE, Behr JH, Geistlinger J, Grosch R, Witzel K. Monitoring of an Applied Beneficial Trichoderma Strain in Root-Associated Soil of Field-Grown Maize by MALDI-TOF MS. Microorganisms 2023; 11:1655. [PMID: 37512828 PMCID: PMC10384135 DOI: 10.3390/microorganisms11071655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The persistence of beneficial microorganisms in the rhizosphere or surrounding soil following their application is a prerequisite for the effective interaction with the plant or indigenous microbial communities in the respective habitats. The goal of the study was to analyze the establishment and persistence of the applied beneficial Trichoderma harzianum (OMG16) strain in the maize root-associated soil depending on agricultural practice (soil management practice, N-fertilizer intensity) in a field experiment. A rapid identification of the inoculated strain OMG16 is essential for its monitoring. We used a culture-based approach coupled to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis for the rapid identification of the inoculated Trichoderma strain as part of the beneficial microbe consortium (BMc). We isolated 428 fungal isolates from eight treatments of the field experiment. Forty eight percent of the isolated fungi equivalent to 205 fungal isolates were identified as Trichoderma, of which 87% (=179 isolates) were obtained from the fields inoculated with BMc. Gene sequence analysis showed a high similarity of the MALDI-TOF MS-identified Trichoderma, with that of the inoculated Trichoderma harzianum OMG16 confirming the re-isolation of the added beneficial fungus. This study highlighted the use of MALDI-TOF MS analysis as a quick, cost-effective detection and efficient monitoring tool for microbial-based bioinoculants in the field.
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Affiliation(s)
- Thomas Edison E Dela Cruz
- Department of Biological Sciences, College of Science, University of Santo Tomas (UST), España Blvd., Manila 1015, Philippines
| | - Jan Helge Behr
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Landscape Development and Ecotrophology, Anhalt University of Applied Sciences (AUAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Rita Grosch
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Katja Witzel
- Department of Plant-Microbes Systems, Leibniz Institute of Vegetables and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
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10
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Hernandez S, Das P, Holliday EB, Shen L, Lu W, Johnson B, Messick CA, Taniguchi CM, Skibber J, Ludmir EB, You YN, Smith GL, Bednarski B, Kostousov L, Koay EJ, Minsky BD, Tillman M, Portier S, Eng C, Koong AC, Chang GJ, Foo WC, Wang J, Soto LS, Morris VK. Differential Spatial Gene and Protein Expression Associated with Recurrence Following Chemoradiation for Localized Anal Squamous Cell Cancer. Cancers (Basel) 2023; 15:1701. [PMID: 36980587 PMCID: PMC10046657 DOI: 10.3390/cancers15061701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/12/2023] Open
Abstract
The identification of transcriptomic and protein biomarkers prognosticating recurrence risk after chemoradiation of localized squamous cell carcinoma of the anus (SCCA) has been limited by a lack of available fresh tissue at initial presentation. We analyzed archival FFPE SCCA specimens from pretreatment biopsies prior to chemoradiation for protein and RNA biomarkers from patients with localized SCCA who recurred (N = 23) and who did not recur (N = 25). Tumor cells and the tumor microenvironment (TME) were analyzed separately to identify biomarkers with significantly different expression between the recurrent and non-recurrent groups. Recurrent patients had higher mean protein expression of FoxP3, MAPK-activation markers (BRAF, p38-MAPK) and PI3K/Akt activation (phospho-Akt) within the tumor regions. The TME was characterized by the higher protein expression of immune checkpoint biomarkers such as PD-1, OX40L and LAG3. For patients with recurrent SCCA, the higher mean protein expression of fibronectin was observed in the tumor and TME compartments. No significant differences in RNA expression were observed. The higher baseline expression of immune checkpoint biomarkers, together with markers of MAPK and PI3K/Akt signaling, are associated with recurrence following chemoradiation for patients with localized SCCA. These data provide a rationale towards the application of immune-based therapeutic strategies to improve curative-intent outcomes beyond conventional therapies for patients with SCCA.
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Affiliation(s)
- Sharia Hernandez
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Prajnan Das
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emma B. Holliday
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Shen
- Bioinformatics, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Lu
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Benny Johnson
- Gastrointestinal Medical Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Craig A. Messick
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cullen M. Taniguchi
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John Skibber
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ethan B. Ludmir
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Y. Nancy You
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Grace Li Smith
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brian Bednarski
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Larisa Kostousov
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Eugene J. Koay
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bruce D. Minsky
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Tillman
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shaelynn Portier
- Gastrointestinal Medical Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cathy Eng
- Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Albert C. Koong
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George J. Chang
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wai Chin Foo
- Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Bioinformatics, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa Solis Soto
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Van K. Morris
- Gastrointestinal Medical Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
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11
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Pu K, Qiu J, Tong Y, Liu B, Cheng Z, Chen S, Ni WX, Lin Y, Ng KM. Integration of Non-targeted Proteomics Mass Spectrometry with Machine Learning for Screening Cooked Beef Adulterated Samples. J Agric Food Chem 2023; 71:2173-2182. [PMID: 36584280 DOI: 10.1021/acs.jafc.2c06266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The degradation of ingredients in heat-processed meat products makes their authentication challenging. In this study, protein profiles of raw beef, chicken, duck, pork, and binary simulated adulterated beef samples (chicken-beef, duck-beef, and pork-beef) and their heat-processed samples were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Heat-stable characteristic proteins were found by screening the overlapping characteristic protein ion peaks of the raw and corresponding heat-processed samples, which were discovered by partial least-squares discriminant analysis. Based on the 36 heat-stable characteristic proteins, qualitative classification for the raw and heat-processed meats was achieved by extreme gradient boosting. Moreover, quantitative analysis via partial least squares regression was applied to determine the adulteration ratio of the simulated adulterated beef samples. The validity of the approach was confirmed by a blind test with the mean accuracy of 97.4%. The limit of detection and limit of quantification of this method were determined to be 5 and 8%, respectively, showing its practical aspect for the beef authentication.
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Affiliation(s)
- Keyuan Pu
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Shantou, Guangdong Province 515063, P. R. China
| | - Jiamin Qiu
- Department of Biology, Shantou University, Shantou, Guangdong Province 515063, P. R. China
| | - Yongqi Tong
- Department of Biology, Shantou University, Shantou, Guangdong Province 515063, P. R. China
| | - Bolin Liu
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Shantou, Guangdong Province 515063, P. R. China
| | - Zibin Cheng
- Department of Biology, Shantou University, Shantou, Guangdong Province 515063, P. R. China
| | - Siyu Chen
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Shantou, Guangdong Province 515063, P. R. China
| | - Wen-Xiu Ni
- Department of Medicinal Chemistry, Shantou University Medical College, Shantou, Guangdong Province 515041, P. R. China
| | - Yan Lin
- The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong Province 515041, P. R. China
| | - Kwan-Ming Ng
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Shantou, Guangdong Province 515063, P. R. China
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12
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Li L, Konigsberg IR, Bhargava M, Liu S, MacPhail K, Mayer A, Davidson EJ, Liao SY, Lei Z, Mroz PM, Fingerlin TE, Yang IV, Maier LA. Multiomic Signatures of Chronic Beryllium Disease Bronchoalveolar Lavage Cells Relate to T-Cell Function and Innate Immunity. Am J Respir Cell Mol Biol 2022; 67:632-640. [PMID: 35972918 PMCID: PMC9743181 DOI: 10.1165/rcmb.2022-0077oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/16/2022] [Indexed: 12/15/2022] Open
Abstract
Chronic beryllium disease (CBD) is a Th1 granulomatous lung disease preceded by sensitization to beryllium (BeS). We profiled the methylome, transcriptome, and selected proteins in the lung to identify molecular signatures and networks associated with BeS and CBD. BAL cell DNA and RNA were profiled using microarrays from CBD (n = 30), BeS (n = 30), and control subjects (n = 12). BAL fluid proteins were measured using Olink Immune Response Panel proteins from CBD (n = 22) and BeS (n = 22) subjects. Linear models identified features associated with CBD, adjusting for covariation and batch effects. Multiomic integration methods identified correlated features between datasets. We identified 1,546 differentially expressed genes in CBD versus control subjects and 204 in CBD versus BeS. Of the 101 shared transcripts, 24 have significant cis relationships between gene expression and DNA methylation, assessed using expression quantitative trait methylation analysis, including genes not previously identified in CBD. A multiomic model of top DNA methylation and gene expression features demonstrated that the first component separated CBD from other samples and the second component separated control subjects from remaining samples. The top features on component one were enriched for T-lymphocyte function, and the top features on component two were enriched for innate immune signaling. We identified six differentially abundant proteins in CBD versus BeS, with two (SIT1 and SH2D1A) selected as important RNA features in the multiomic model. Our integrated analysis of DNA methylation, gene expression, and proteins in the lung identified multiomic signatures of CBD that differentiated it from BeS and control subjects.
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Affiliation(s)
- Li Li
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
- Division of Pulmonary and Critical Care Sciences
| | - Iain R. Konigsberg
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, School of Medicine
| | - Maneesh Bhargava
- Pulmonary, Allergy, Critical Care and Sleep, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Sucai Liu
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
| | - Kristyn MacPhail
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
| | - Annyce Mayer
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
- Department of Environmental and Occupational Health
| | - Elizabeth J. Davidson
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, School of Medicine
| | - Shu-Yi Liao
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
- Division of Pulmonary and Critical Care Sciences
- Department of Environmental and Occupational Health
| | - Zhe Lei
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
| | - Peggy M. Mroz
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
- Department of Biostatistics and Bioinformatics, and
| | - Ivana V. Yang
- Division of Pulmonary and Critical Care Sciences
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, School of Medicine
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado; and
| | - Lisa A. Maier
- Division of Environmental and Occupational Health Sciences, Department of Medicine, and
- Division of Pulmonary and Critical Care Sciences
- Department of Environmental and Occupational Health
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Nardone D, Ciaramella A, Cerreta M, Pulcrano S, Bellenchi GC, Leone L, Manco G, Febbraio F. Selymatra: A web application for protein-profiling analysis of mass spectra. Biotechnol Appl Biochem 2022; 69:1821-1829. [PMID: 34487563 PMCID: PMC9912196 DOI: 10.1002/bab.2249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/23/2021] [Indexed: 11/06/2022]
Abstract
Surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry is a variant of the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. It is used in many cases especially for the analysis of protein profiling and for preliminary screening of biomarkers in complex samples. Unfortunately, these analyses are time consuming and protein identification is generally strictly limited. SELDI-TOF analysis of mass spectra (SELYMATRA) is a web application (WA) developed to reduce these limitations by (i) automating the identification processes and (ii) introducing the possibility to predict proteins in complex mixtures from cells and tissues. The WA architectural pattern is the model-view-controller, commonly used in software development. The WA compares the mass value between two mass spectra (sample vs. control) to extract differences, and, according to the set parameters, it queries a local database to predict most likely proteins based on their masses and different expression amplification. The WA was validated in a cellular model overexpressing a tagged NURR1 receptor, being able to recognize the tagged protein in the profiling of transformed cells. A help page, including a description of parameters for WA use, is available on the website.
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Affiliation(s)
- Davide Nardone
- Department of Science and TechnologyUniversity of Naples ParthenopeNaplesItaly
| | - Angelo Ciaramella
- Department of Science and TechnologyUniversity of Naples ParthenopeNaplesItaly
| | - Mariangela Cerreta
- Institute of Biochemistry and Cellular BiologyNational Research CouncilNaples80131Italy
| | - Salvatore Pulcrano
- Institute of Genetic and Biophysics “A. Buzzati Traverso”National Research CouncilNaplesItaly
| | - Gian C. Bellenchi
- Institute of Genetic and Biophysics “A. Buzzati Traverso”National Research CouncilNaplesItaly
| | - Linda Leone
- Department of Chemical SciencesUniversity of Naples “Federico II”Naples80126Italy
| | - Giuseppe Manco
- Institute of Biochemistry and Cellular BiologyNational Research CouncilNaples80131Italy
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cellular BiologyNational Research CouncilNaples80131Italy
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Mo W, Xu W, Hong M, Yang T, Shi Y, Jiao Y, Nie J, Cui F, Cao J, Zhang S. Proteomic and miRNA profiling of radon-induced skin damage in mice: FASN regulated by miRNAs. J Radiat Res 2022; 63:706-718. [PMID: 35791446 PMCID: PMC9494515 DOI: 10.1093/jrr/rrac037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/21/2021] [Indexed: 06/15/2023]
Abstract
Radon is a naturally occurring radioactive gas and considered as a serious carcinogen to humans. Continuous radioactive decay of this gas emits high-energy alpha particles. Long-term radon exposure induces oxidative stress and inflammatory response, which results in chronic lung diseases. However, biological effects after radon exposure in other organs have been rarely reported. As the outermost organ of the human body, the skin suffers from environmental damage to agents such as air pollution. Epidemiological studies indicated that areas with high level of radon had a high incidence of skin cancer. However, whether radon exposure induces skin damage has not been reported yet. In this study, we established a radon-exposed mouse model and found that radon exposure affected the structure of skin tissues, which was manifested by inflammatory cell infiltration and skin atrophy. Using proteomic approach, we found 45 preferentially expressed proteins in 60 Working Level Months (WLM) group and 314 preferentially expressed proteins in 120 WLM group from radon-exposed skin tissues. Through microRNA (miRNA) sequencing profiling analysis, 57 dysregulated miRNAs were screened between the control and radon-treated mouse skin. By integrating the dysregulated proteins and miRNAs, radon-induced fatty acid synthase (FASN) was investigated in greater detail. Results showed that FASN was regulated by miR-206-3p and miR-378a-3p and involved in the pathogenesis of radon-induced skin damage. Overexpression of FASN inhibited the proliferation, and induced in WS1 cells. Our present findings illustrate the molecular change during radon-induced skin damage and the potential role of FASN during this process.
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Affiliation(s)
| | | | - Min Hong
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Tingyi Yang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yuhong Shi
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China
| | - Yang Jiao
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Jihua Nie
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Fengmei Cui
- School of Radiation Medicine and Protection, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China
| | - Jianping Cao
- Corresponding authors. Zhang S, Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China. Tel./Fax: +8628-85502429; E-mail: ; Cao J, No. 199 Ren’ai Rd, Medical College of Soochow University, Suzhou 215123, China. Tel./Fax:+86-512-65880037; E-mail:
| | - Shuyu Zhang
- Corresponding authors. Zhang S, Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu 610051, China. Tel./Fax: +8628-85502429; E-mail: ; Cao J, No. 199 Ren’ai Rd, Medical College of Soochow University, Suzhou 215123, China. Tel./Fax:+86-512-65880037; E-mail:
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15
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Malik AM, Riar CS. Difference in the nutritional, in vitro, and functional characteristics of protein and fat isolates of two Indian chia (Salvia hispanica L) seed genotypes with variation in seed coat color. J Food Sci 2022; 87:3872-3887. [PMID: 35982647 DOI: 10.1111/1750-3841.16276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/02/2022] [Accepted: 07/14/2022] [Indexed: 11/27/2022]
Abstract
This study aimed to determine the association between the seed coat color of two chia seed genotypes for their composition, protein content, amino acid, and fatty acid profiles. The optimal pH for protein isolation for both genotypes (BCPI and WCPI) was 10, based on protein purity and solubility. Fatty acid profiling indicated, overall, 18 different fatty acids higher in BCPI10 with linolenic acid domination (∼66%) followed by linoleic acid (∼19%) and oleic acid (∼6%), contributing PUFAs (∼86%). Optimized protein isolates, black (BCPI10) and white (WCPI10) chia, had shown purity, L*-value, solubility, and yields of 90.65%, 75.86%, 77.75%, 11.30%, and 90.00%, 77.83%, 76.07%, 10.69%, respectively. BCPI10 depicted higher EAA (33.19 g/100 g N) and EEA indices (57.676%) compared to WCPI10 (32.14 g/100 g N) and 56.360%, respectively. Amino acid profiling indicated higher, PER, TAA, TEAA, TNEAA, TAAA, TBA, acidic AA values for BCPI10, and higher leucine/isoleucine ratio for WCPI10 having leucine and sulfur amino acids as limiting amino acids. BCPI10 had higher sulfur-containing amino acid contents, as the main contributor to the albumin a water-soluble fraction, leading to its higher in vitro digestibility (71.97%) than WCPI10 (67.70%). Both isolates exhibited good WHC and OHC of 3.18, 2.39 and 3.00, 2.20, respectively. Both protein isolates had similar ∆Td (°C) values with some variation in FTIR spectrum from 1000 cm-1 to 1651 cm-1 having more peak intensity for BCPI10. SDS-PAGE indicated bands at 150 kDa, representing globulin and mild bands at 25-33 kDa for glutelin and albumin. A significant (p < 0.05) variation reported in this study for protein and lipid profiles of both genotype attributes to genetic differences between the seeds. PRACTICAL APPLICATION: Based on the nutritional profile, both chia seed isolates (black and white) are suitable for consumption with an edge for black seed when supplemented with their limiting amino acids. The high values of the functional properties and structural characteristics combined with high nutritional values make the chia protein isolate an excellent source of raw material for various food formulations. Fatty acid profile of the oils from the genotypes showed the presence of high amounts of unsaturated fatty acids, especially the PUFAs with more number of fatty acids in black chia seed. The excellent lipid profile of chia seed oil indicates the benefit of using chia seed oil as a source of essential fatty acids in the human diet for optimal health.
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Affiliation(s)
- Amanda Manoj Malik
- Department of Food Engineering and Technology, Sant Longowal Institute of Engineering and Technology, Sangrur, Punjab, India.,Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Charanjit S Riar
- Department of Food Engineering and Technology, Sant Longowal Institute of Engineering and Technology, Sangrur, Punjab, India
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16
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Sauer T, Facchinetti G, Kohl M, Kowal JM, Rozanova S, Horn J, Schmal H, Kwee I, Schulz AP, Hartwig S, Kassem M, Habermann JK, Gemoll T. Protein Expression of AEBP1, MCM4, and FABP4 Differentiate Osteogenic, Adipogenic, and Mesenchymal Stromal Stem Cells. Int J Mol Sci 2022; 23:2568. [PMID: 35269711 DOI: 10.3390/ijms23052568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023] Open
Abstract
Mesenchymal stem cells (MSCs) gain an increasing focus in the field of regenerative medicine due to their differentiation abilities into chondrocytes, adipocytes, and osteoblastic cells. However, it is apparent that the transformation processes are extremely complex and cause cellular heterogeneity. The study aimed to characterize differences between MSCs and cells after adipogenic (AD) or osteoblastic (OB) differentiation at the proteome level. Comparative proteomic profiling was performed using tandem mass spectrometry in data-independent acquisition mode. Proteins were quantified by deep neural networks in library-free mode and correlated to the Molecular Signature Database (MSigDB) hallmark gene set collections for functional annotation. We analyzed 4108 proteins across all samples, which revealed a distinct clustering between MSCs and cell differentiation states. Protein expression profiling identified activation of the Peroxisome proliferator-activated receptors (PPARs) signaling pathway after AD. In addition, two distinct protein marker panels could be defined for osteoblastic and adipocytic cell lineages. Hereby, overexpression of AEBP1 and MCM4 for OB as well as of FABP4 for AD was detected as the most promising molecular markers. Combination of deep neural network and machine-learning algorithms with data-independent mass spectrometry distinguish MSCs and cell lineages after adipogenic or osteoblastic differentiation. We identified specific proteins as the molecular basis for bone formation, which could be used for regenerative medicine in the future.
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17
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Jiang N, Zhao S, Wang S, Lu Z. Proteomics of Streptococcus mutans to Reveal the Antibiofilm Formation Mechanism of Ag/ZnO Nanocomposites with Light-Emitting Diode Radiation. Int J Nanomedicine 2021; 16:7741-7757. [PMID: 34848957 PMCID: PMC8612293 DOI: 10.2147/ijn.s333432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/30/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction As a biofilm-associated disease, dental caries benefits from nanoparticle (NP)-based therapies. Streptococcus mutans (S. mutans) is a primary aetiologic agent for dental caries development. We successfully applied a synergistic therapy of Ag/ZnO nanocomposites combined with light-emitting diode (LED) radiation to inhibit S. mutans biofilms. However, the antibiofilm mechanism has not been fully elucidated, and little is known about the biofilm formation ability of bacteria that survive NP-based therapies. Methods This study explored the antibiofilm formation mechanism of this synergistic therapy by an integrated approach based upon proteomics. Results Synergistic therapy killed 99.8% of bacteria, while the biofilm formation ability of 0.2% surviving bacteria was inhibited. The proteomic responses of S. mutans to synergistic therapy were comprehensively characterized to unveil the mechanism of bacterial death and biofilm formation inhibition of the surviving bacteria. In total, 55 differentially expressed proteins (12 upregulated and 43 downregulated) were recorded. The bioinformatic analysis demonstrated that cellular integrity damage and regulated expression of structure-associated proteins were the main reasons for bacterial death. In addition, the proteomic study indicated the potential inhibition of metabolism in surviving bacteria and provided a biofilm-related network consisting of 17 differentially expressed proteins, explaining the multiantibiofilm formation actions. Finally, we reported and verified the inhibitory effects of synergistic therapy on sucrose metabolism and D-alanine metabolism, which disturbed the biofilm formation of surviving bacteria. Conclusion Our findings demonstrated that synergistic therapy killed most bacteria and inhibited the surviving bacteria from forming biofilms. Furthermore, the antibiofilm formation mechanism was revealed by proteomics analysis of S. mutans after synergistic therapy and subsequent metabolic studies. Our success may provide a showcase to explore the antibiofilm formation mechanism of NP-based therapies using proteomic studies.
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Affiliation(s)
- Nan Jiang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Shuaiwei Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Shilei Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Zhong Lu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
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Araújo MJ, Sousa ML, Felpeto AB, Turkina MV, Fonseca E, Martins JC, Vasconcelos V, Campos A. Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species. Proteomes 2021; 9:proteomes9040046. [PMID: 34842808 PMCID: PMC8628934 DOI: 10.3390/proteomes9040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/07/2023] Open
Abstract
Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC–MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).
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Affiliation(s)
- Mário Jorge Araújo
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria Lígia Sousa
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Aldo Barreiro Felpeto
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden;
| | - Elza Fonseca
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - José Carlos Martins
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Vítor Vasconcelos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Alexandre Campos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Correspondence:
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Fontana S, Mauceri R, Novara ME, Alessandro R, Campisi G. Protein Cargo of Salivary Small Extracellular Vesicles as Potential Functional Signature of Oral Squamous Cell Carcinoma. Int J Mol Sci 2021; 22:ijms222011160. [PMID: 34681822 PMCID: PMC8539015 DOI: 10.3390/ijms222011160] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023] Open
Abstract
The early diagnosis of oral squamous cell carcinoma (OSCC) is still an investigative challenge. Saliva has been proposed as an ideal diagnostic medium for biomarker detection by mean of liquid biopsy technique. The aim of this pilot study was to apply proteomic and bioinformatic strategies to determine the potential use of saliva small extracellular vesicles (S/SEVs) as a potential tumor biomarker source. Among the twenty-three enrolled patients, 5 were free from diseases (OSCC_FREE), 6 were with OSCC without lymph node metastasis (OSCC_NLNM), and 12 were with OSCC and lymph node metastasis (OSCC_LNM). The S/SEVs from patients of each group were pooled and properly characterized before performing their quantitative proteome comparison based on the SWATH_MS (Sequential Window Acquisition of all Theoretical Mass Spectra) method. The analysis resulted in quantitative information for 365 proteins differentially characterizing the S/SEVs of analyzed clinical conditions. Bioinformatic analysis of the proteomic data highlighted that each S/SEV group was associated with a specific cluster of enriched functional network terms. Our results highlighted that protein cargo of salivary small extracellular vesicles defines a functional signature, thus having potential value as novel predict biomarkers for OSCC.
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Affiliation(s)
- Simona Fontana
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90133 Palermo, Italy; (M.E.N.); (R.A.)
- Correspondence: ; Tel.: +39-09123865731
| | - Rodolfo Mauceri
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy; (R.M.); (G.C.)
- Department of Biomedical and Dental Sciences, Morphological and Functional Images, University of Messina, 98124 Messina, Italy
- Department of Dental Surgery, Faculty of Dental Surgery, University of Malta, 2090 Msida, Malta
| | - Maria Eugenia Novara
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90133 Palermo, Italy; (M.E.N.); (R.A.)
| | - Riccardo Alessandro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90133 Palermo, Italy; (M.E.N.); (R.A.)
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), 90146 Palermo, Italy
| | - Giuseppina Campisi
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy; (R.M.); (G.C.)
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20
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Grønningsæter IS, Reikvam H, Aasebø E, Bartaula-Brevik S, Hernandez-Valladares M, Selheim F, Berven FS, Tvedt TH, Bruserud Ø, Hatfield KJ. Effects of the Autophagy-Inhibiting Agent Chloroquine on Acute Myeloid Leukemia Cells; Characterization of Patient Heterogeneity. J Pers Med 2021; 11:jpm11080779. [PMID: 34442423 PMCID: PMC8399694 DOI: 10.3390/jpm11080779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a highly conserved cellular degradation process that prevents cell damage and promotes cell survival, and clinical efforts have exploited autophagy inhibition as a therapeutic strategy in cancer. Chloroquine is a well-known antimalarial agent that inhibits late-stage autophagy. We evaluated the effects of chloroquine on cell viability and proliferation of acute myeloid leukemia acute myeloid leukemia (AML) cells derived from 81 AML patients. Our results show that chloroquine decreased AML cell viability and proliferation for the majority of patients. Furthermore, a subgroup of AML patients showed a greater susceptibility to chloroquine, and using hierarchical cluster analysis, we identified 99 genes upregulated in this patient subgroup, including several genes related to leukemogenesis. The combination of chloroquine with low-dose cytarabine had an additive inhibitory effect on AML cell proliferation. Finally, a minority of patients showed increased extracellular constitutive mediator release in the presence of chloroquine, which was associated with strong antiproliferative effects of chloroquine as well as cytarabine. We conclude that chloroquine has antileukemic activity and should be further explored as a therapeutic drug against AML in combination with other cytotoxic or metabolic drugs; however, due to the patient heterogeneity, chloroquine therapy will probably be effective only for selected patients.
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Affiliation(s)
- Ida Sofie Grønningsæter
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Medicine, Akershus University Hospital, N-1478 Lørenskog, Norway
| | - Håkon Reikvam
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway;
| | - Elise Aasebø
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
| | - Maria Hernandez-Valladares
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
- The Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
- The Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Frode S. Berven
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; (M.H.-V.); (F.S.); (F.S.B.)
- The Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Tor Henrik Tvedt
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway;
- Department of Hematology, Oslo University Hospital—The National Hospital, N-0372 Oslo, Norway
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Medicine, Haukeland University Hospital, N-5021 Bergen, Norway;
- Correspondence: (Ø.B.); (K.J.H.)
| | - Kimberley Joanne Hatfield
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.)
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, N-5009 Bergen, Norway
- Correspondence: (Ø.B.); (K.J.H.)
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21
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Hellberg S, Raffetseder J, Rundquist O, Magnusson R, Papapavlou G, Jenmalm MC, Ernerudh J, Gustafsson M. Progesterone Dampens Immune Responses in In Vitro Activated CD4 + T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy. Front Immunol 2021; 12:672168. [PMID: 34054852 PMCID: PMC8149943 DOI: 10.3389/fimmu.2021.672168] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
The changes in progesterone (P4) levels during and after pregnancy coincide with the temporary improvement and worsening of several autoimmune diseases like multiple sclerosis (MS) and rheumatoid arthritis (RA). Most likely immune-endocrine interactions play a major role in these pregnancy-induced effects. In this study, we used next generation sequencing to investigate the direct effects of P4 on CD4+ T cell activation, key event in pregnancy and disease. We report profound dampening effects of P4 on T cell activation, altering the gene and protein expression profile and reversing many of the changes induced during the activation. The transcriptomic changes induced by P4 were significantly enriched for genes associated with diseases known to be modulated during pregnancy such as MS, RA and psoriasis. STAT1 and STAT3 were significantly downregulated by P4 and their downstream targets were significantly enriched among the disease-associated genes. Several of these genes included well-known and disease-relevant cytokines, such as IL-12β, CXCL10 and OSM, which were further validated also at the protein level using proximity extension assay. Our results extend the previous knowledge of P4 as an immune regulatory hormone and support its importance during pregnancy for regulating potentially detrimental immune responses towards the semi-allogenic fetus. Further, our results also point toward a potential role for P4 in the pregnancy-induced disease immunomodulation and highlight the need for further studies evaluating P4 as a future treatment option.
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Affiliation(s)
- Sandra Hellberg
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Johanna Raffetseder
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Olof Rundquist
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Rasmus Magnusson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Georgia Papapavlou
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Maria C Jenmalm
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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Abstract
Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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23
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Cavallaro S, Pevere F, Stridfeldt F, Görgens A, Paba C, Sahu SS, Mamand DR, Gupta D, El Andaloussi S, Linnros J, Dev A. Multiparametric Profiling of Single Nanoscale Extracellular Vesicles by Combined Atomic Force and Fluorescence Microscopy: Correlation and Heterogeneity in Their Molecular and Biophysical Features. Small 2021; 17:e2008155. [PMID: 33682363 DOI: 10.1002/smll.202008155] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 05/22/2023]
Abstract
Being a key player in intercellular communications, nanoscale extracellular vesicles (EVs) offer unique opportunities for both diagnostics and therapeutics. However, their cellular origin and functional identity remain elusive due to the high heterogeneity in their molecular and physical features. Here, for the first time, multiple EV parameters involving membrane protein composition, size and mechanical properties on single small EVs (sEVs) are simultaneously studied by combined fluorescence and atomic force microscopy. Furthermore, their correlation and heterogeneity in different cellular sources are investigated. The study, performed on sEVs derived from human embryonic kidney 293, cord blood mesenchymal stromal and human acute monocytic leukemia cell lines, identifies both common and cell line-specific sEV subpopulations bearing distinct distributions of the common tetraspanins (CD9, CD63, and CD81) and biophysical properties. Although the tetraspanin abundances of individual sEVs are independent of their sizes, the expression levels of CD9 and CD63 are strongly correlated. A sEV population co-expressing all the three tetraspanins in relatively high abundance, however, having average diameters of <100 nm and relatively low Young moduli, is also found in all cell lines. Such a multiparametric approach is expected to provide new insights regarding EV biology and functions, potentially deciphering unsolved questions in this field.
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Affiliation(s)
- Sara Cavallaro
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
| | - Federico Pevere
- Department of Electrical Engineering, The Ångström Laboratory, Uppsala University, Uppsala, 75121, Sweden
| | - Fredrik Stridfeldt
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
| | - André Görgens
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 17177, Sweden
- Evox Therapeutics Limited, Oxford Science Park, Oxford, OX4 4HG, UK
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, 45141, Essen, Germany
| | | | - Siddharth S Sahu
- Department of Electrical Engineering, The Ångström Laboratory, Uppsala University, Uppsala, 75121, Sweden
| | - Doste R Mamand
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Dhanu Gupta
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 17177, Sweden
- Evox Therapeutics Limited, Oxford Science Park, Oxford, OX4 4HG, UK
| | - Samir El Andaloussi
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 17177, Sweden
- Evox Therapeutics Limited, Oxford Science Park, Oxford, OX4 4HG, UK
| | - Jan Linnros
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
| | - Apurba Dev
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
- Department of Electrical Engineering, The Ångström Laboratory, Uppsala University, Uppsala, 75121, Sweden
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Kalia A, Kaur J, Tondey M, Manchanda P, Bindra P, Alghuthaymi MA, Shami A, Abd-Elsalam KA. Differential Antimycotic and Antioxidant Potentials of Chemically Synthesized Zinc-Based Nanoparticles Derived from Different Reducing/Complexing Agents against Pathogenic Fungi of Maize Crop. J Fungi (Basel) 2021; 7:223. [PMID: 33803825 PMCID: PMC8003151 DOI: 10.3390/jof7030223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
The present study aimed for the synthesis, characterization, and comparative evaluation of anti-oxidant and anti-fungal potentials of zinc-based nanoparticles (ZnNPs) by using different reducing or organic complexing-capping agents. The synthesized ZnNPs exhibited quasi-spherical to hexagonal shapes with average particle sizes ranging from 8 to 210 nm. The UV-Vis spectroscopy of the prepared ZnNPs showed variation in the appearance of characteristic absorption peak(s) for the various reducing/complexing agents i.e., 210 (NaOH and NaBH4), 220 (albumin, and thiourea), 260 and 330 (starch), and 351 nm (cellulose) for wavelengths spanning over 190-800 nm. The FT-IR spectroscopy of the synthesized ZnNPs depicted the functional chemical group diversity. On comparing the antioxidant potential of these ZnNPs, NaOH as reducing agent, (NaOH (RA)) derived ZnNPs presented significantly higher DPPH radical scavenging potential compared to other ZnNPs. The anti-mycotic potential of the ZnNPs as performed through an agar well diffusion assay exhibited variability in the extent of inhibition of the fungal mycelia with maximum inhibition at the highest concentration (40 mg L-1). The NaOH (RA)-derived ZnNPs showcased maximum mycelial inhibition compared to other ZnNPs. Further, incubation of the total genomic DNA with the most effective NaOH (RA)-derived ZnNPs led to intercalation or disintegration of the DNA of all the three fungal pathogens of maize with maximum DNA degrading effect on Macrophomina phaseolina genomic DNA. This study thus identified that differences in size and surface functionalization with the protein (albumin)/polysaccharides (starch, cellulose) diminishes the anti-oxidant and anti-mycotic potential of the generated ZnNPs. However, the NaOH emerged as the best reducing agent for the generation of uniform nano-scale ZnNPs which possessed comparably greater anti-oxidant and antimycotic activities against the three test maize pathogenic fungal cultures.
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Affiliation(s)
- Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Jashanpreet Kaur
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana 141004, Punjab, India; (J.K.); (M.T.)
| | - Manisha Tondey
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana 141004, Punjab, India; (J.K.); (M.T.)
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India;
| | - Pulkit Bindra
- Institute of Nanoscience and Technology, Habitat Centre, Phase-10, Sector-64, Mohali 160062, Punjab, India;
| | - Mousa A. Alghuthaymi
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11726, Saudi Arabia
| | - Ashwag Shami
- Biology Department, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Kamel A. Abd-Elsalam
- Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt;
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Röhl M, Tjernlund A, Lajoie J, Edfeldt G, Bradley F, Bergström S, Kaldhusdal V, Åhlberg A, Månberg A, Omollo K, Boily-Larouche G, Asghar M, Kwon DS, Oyugi J, Kimani J, Nilsson P, Fowke KR, Broliden K. HIV-Exposed Seronegative Sex Workers Express Low T-Cell Activation and an Intact Ectocervical Tissue Microenvironment. Vaccines (Basel) 2021; 9:217. [PMID: 33806390 DOI: 10.3390/vaccines9030217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Immunological correlates of natural resistance to HIV have been identified in HIV-exposed seronegative (HESN) individuals and include a low-inflammatory genital mucosal status. The cervicovaginal epithelium has not been studied for such correlates despite constituting an important barrier against sexual HIV transmission. To fill this gap in knowledge, we collected samples of blood, cervical mononuclear cells, cervicovaginal lavage, and ectocervical tissue from Kenyan HESN sex workers (n = 29) and controls (n = 33). The samples were analyzed by flow cytometry, protein profiling, 16S rRNA gene sequencing, in situ image analysis, and tissue-based RNA sequencing. A significantly higher relative proportion of regulatory T cells in blood (B7+CD25hiFoxP3+CD127loCD4+ and B7+Helios+FoxP3+CD4+), and a significantly lower proportion of activated cervical T cells (CCR5+CD69+CD4+ and CCR5+CD69+CD8+), were found in the HESN group compared with the controls. In contrast, there were no statistically significant differences between the study groups in cervicovaginal protein and microbiome compositions, ectocervical epithelial thickness, E-cadherin expression, HIV receptor expression, and tissue RNA transcriptional profiles. The identification of an intact ectocervical microenvironment in HESN individuals add new data to current knowledge about natural resistance to sexual transmission of HIV.
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Halvorsen AR, Haugen MH, Öjlert ÅK, Lund-Iversen M, Jørgensen L, Solberg S, Mælandsmo GM, Brustugun OT, Helland Å. Protein Kinase C Isozymes Associated With Relapse Free Survival in Non-Small Cell Lung Cancer Patients. Front Oncol 2020; 10:590755. [PMID: 33324562 PMCID: PMC7725872 DOI: 10.3389/fonc.2020.590755] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Protein expression is deregulated in cancer, and the proteomic changes observed in lung cancer may be a consequence of mutations in essential genes. The purpose of this study was to identify protein expression associated with prognosis in lung cancers stratified by smoking status, molecular subtypes, and EGFR-, TP53-, and KRAS-mutations. METHODS We performed profiling of 295 cancer-relevant phosphorylated and non-phosphorylated proteins, using reverse phase protein arrays. Biopsies from 80 patients with operable lung adenocarcinomas were analyzed for protein expression and association with relapse free survival (RFS) were studied. RESULTS Spearman's rank correlation analysis identified 46 proteins with significant association to RFS (p<0.05). High expression of protein kinase C (PKC)-α and the phosporylated state of PKC-α, PKC-β, and PKC-δ, showed the strongest positive correlation to RFS, especially in the wild type samples. This was confirmed in gene expression data from 172 samples. Based on protein expression, unsupervised hierarchical clustering separated the samples into four subclusters enriched with the molecular subtypes terminal respiratory unit (TRU), proximal proliferative (PP), and proximal inflammatory (PI) (p=0.0001). Subcluster 2 contained a smaller cluster (2a) enriched with samples of the subtype PP, low expression of the PKC isozymes, and associated with poor RFS (p=0.003) compared to the other samples. Low expression of the PKC isozymes in the subtype PP and a reduced relapse free survival was confirmed with The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LUAD) samples. CONCLUSION This study identified different proteins associated with RFS depending on molecular subtype, smoking- and mutational-status, with PKC-α, PKC-β, and PKC-δ showing the strongest correlation.
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Affiliation(s)
- Ann Rita Halvorsen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Department of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Mads Haugland Haugen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Åsa Kristina Öjlert
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Marius Lund-Iversen
- Department of Pathology, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Lars Jørgensen
- Department of Cardiothoracic Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Steinar Solberg
- Department of Cardiothoracic Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Gunhild M. Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Faculty of Health Sciences, Institute of Medical Biology, UiT-Arctic University of Norway, Tromso, Norway
| | - Odd Terje Brustugun
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Section of Oncology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Åslaug Helland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Department of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
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27
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Enot MM, Weiland F, Mittal P, Hoffmann P, Sillero-Mahinay M, Pukala T. Differential proteome analysis of the leaves of lead hyperaccumulator, Rhoeo discolor (L. Her.) Hance. J Mass Spectrom 2020; 56:e4689. [PMID: 33247490 DOI: 10.1002/jms.4689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The present study investigated Rhoeo discolor (L. Her.) Hance for its ability to accumulate Pb, which is of relevance to phytoremediation applications. Based on this analysis, plants were found to accumulate greater than 10 mg/g (0.1%) of dry weight Pb in the shoots, which classifies the plant a Pb hyperaccumulator. Further, changes in the leaf proteome profiles in response to Pb stress were investigated. Wild-type plants were subjected to a high concentration of Pb(NO3 )2 , and the levels of Pb that accumulated in different plant tissues were determined using atomic absorption spectrophotometry. Using 2D-difference gel electrophoresis, 181 protein spots were detected to be differentially abundant in response to Pb stress and selected spots exhibiting the strongest differential abundance suggested an impairment of the photosynthetic apparatus of the plant under Pb stress. Subsequently, a more extensive, proteome wide analysis utilizing label-free quantitation further identified a predominant decrease in protein levels and a significant effect on the nuclear proteome, as well as photosynthesis, carbon fixation and metabolism, providing insight into the Pb tolerance of this system in a potential phytoremediation context.
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Affiliation(s)
- Melania M Enot
- Department of Chemistry, Central Mindanao University, Bukidnon, Philippines
| | - Florian Weiland
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Laboratory of Enzyme, Fermentation and Brewing Technology (EFBT), Department of Microbial and Molecular Systems, Technology Campus Ghent, KU Leuven, Leuven, Belgium
| | - Parul Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, 5095, Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, 5095, Australia
| | - Myrna Sillero-Mahinay
- Department of Chemistry, MSU-Iligan Institute of Technology, Iligan City, Philippines
| | - Tara Pukala
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
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28
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Dehghani M, Montange RK, Olszowy MW, Pollard D. An Emerging Fluorescence-Based Technique for Quantification and Protein Profiling of Extracellular Vesicles. SLAS Technol 2020; 26:189-199. [PMID: 33185120 DOI: 10.1177/2472630320970458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Robust and well-established techniques for the quantification and characterization of extracellular vesicles (EVs) are a crucial need for the utilization of EVs as potential diagnostic and therapeutic tools. Current bulk analysis techniques such as proteomics and Western blot suffer from low resolution in the detection of small changes in target marker expression levels, exemplified by the heterogeneity of EVs. Microscopy-based techniques can provide valuable information from individual EVs; however, they are time-consuming and statistically less powerful than other techniques. Flow cytometry has been successfully employed for the quantification and characterization of individual EVs within larger populations. However, traditional flow cytometry is not highly suited for the examination of smaller, submicron particles. Here we demonstrate the accurate and precise quantification of nanoparticles such as EVs using the Virus Counter 3100 (VC3100) platform, a fluorescence-based technique that uses the principles of flow cytometry with critical enhancements to enable the effective detection of smaller particles. This approach can detect nanoparticles precisely with no evidence of inaccurate concentration measurement from masking effects associated with traditional nanoparticle tracking analysis (NTA). Fluorescently labeled EVs from different sources were successfully quantified using the VC3100 without a postlabeling washing step. Moreover, protein profiling and characterization of individual EVs were achieved and have been shown to determine the expression level of target protein markers.
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Affiliation(s)
- Mehdi Dehghani
- Sartorius Corporate Research, Sartorius (Smart Labs), Boston, MA, USA.,Sartorius Corporate Research, Sartorius (Smart Labs), Boston, MA, USA.,Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | | | | | - David Pollard
- Sartorius Corporate Research, Sartorius (Smart Labs), Boston, MA, USA
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Abu Bakar ZH, Damanhuri HA, Makpol S, Wan Kamaruddin WMA, Abdul Sani NF, Amir Hamzah AIZ, Nor Aripin KN, Mohd Rani MD, Noh NA, Razali R, Mazlan M, Abdul Hamid H, Mohamad M, Wan Ngah WZ. Effect of Age on the Protein Profile of Healthy Malay Adults and its Association with Cognitive Function Competency. J Alzheimers Dis 2020; 70:S43-S62. [PMID: 30594926 PMCID: PMC6706781 DOI: 10.3233/jad-180511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background: Many studies on biochemical and psychological variables have aimed to elucidate the association between aging and cognitive function. Demographic differences and protein expression have been reported to play a role in determining the cognitive capability of a population. Objective: This study aimed to determine the effect of age on the protein profile of Malay individuals and its association with cognitive competency. Methods: A total of 160 individuals were recruited and grouped accordingly. Cognitive competency of each subject was assessed with several neuropsychological tests. Plasma samples were collected and analyzed with Q Exactive HF Orbitrap. Proteins were identified and quantitated with MaxQuant and further analyzed with Perseus to determine differentially expressed proteins. PANTHER, Reactome, and STRING were applied for bioinformatics output. Results: Our data showed that the Malay individuals are vulnerable to the deterioration of cognitive function with aging, and most of the proteins were differentially expressed in concordance. Several physiological components and pathways were shown to be involved, giving a hint of a promising interpretation on the induction of aging toward the state of the Malays’ cognitive function. Nevertheless, some proteins have shown a considerable interaction with the generated protein network, which provides a direction of focus for further investigation. Conclusion: This study demonstrated notable changes in the expression of several proteins as age increased. These changes provide a promising platform for understanding the biochemical factors affecting cognitive function in the Malay population. The exhibited network of protein-protein interaction suggests the possibility of implementing regulatory intervention in ameliorating Malay cognitive function.
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Affiliation(s)
- Zulzikry Hafiz Abu Bakar
- Department of Biochemistry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Hanafi Ahmad Damanhuri
- Department of Biochemistry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Suzana Makpol
- Department of Biochemistry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | | | - Nur Fathiah Abdul Sani
- Department of Biochemistry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Ahmad Imran Zaydi Amir Hamzah
- Department of Biochemistry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Khairun Nain Nor Aripin
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Persiaran MPAJ, Jalan Pandan Utama, Pandan Indah, Kuala Lumpur, Malaysia
| | - Mohd Dzulkhairi Mohd Rani
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Persiaran MPAJ, Jalan Pandan Utama, Pandan Indah, Kuala Lumpur, Malaysia
| | - Nor Azila Noh
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Persiaran MPAJ, Jalan Pandan Utama, Pandan Indah, Kuala Lumpur, Malaysia
| | - Rosdinom Razali
- Department of Psychiatry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif Bandar Tun Razak, Kuala Lumpur, Malaysia
| | - Musalmah Mazlan
- Faculty of Medicine, Universiti Teknologi Mara, Jalan Hospital, Selangor Darul Ehsan, Malaysia
| | - Hamzaini Abdul Hamid
- Department of Radiology Hospital Chancellor Tuanku Mukhriz, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Mazlyfarina Mohamad
- Department Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
| | - Wan Zurinah Wan Ngah
- Department of Biochemistry, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
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30
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Di H, Mi Z, Sun Y, Liu X, Liu X, Li A, Jiang Y, Gao H, Rong P, Liu D. Nanozyme-assisted sensitive profiling of exosomal proteins for rapid cancer diagnosis. Am J Cancer Res 2020; 10:9303-9314. [PMID: 32802193 PMCID: PMC7415820 DOI: 10.7150/thno.46568] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/04/2020] [Indexed: 01/04/2023] Open
Abstract
The proteins expressed on exosomes have emerged as promising liquid-biopsy biomarkers for cancer diagnosis. However, molecular profiling of exosomal proteins remains technically challenging. Herein, we report a nanozyme-assisted immunosorbent assay (NAISA) that enables sensitive and rapid multiplex profiling of exosomal proteins. This NAISA system is based on the installation of peroxidase-like nanozymes onto the phospholipid membranes of exosomes, thus avoiding the need for post-labelling detection antibodies. The exosomal proteins are determined by a sensitive nanozyme-catalyzed colorimetric assay less than 3 h, without the need for multi-step incubation and washing operations. Using NAISA to profile exosomal proteins from different cell lines and clinical samples, we reveal that tumor-associated exosomal proteins can serve as promising biomarkers for accurate cancer diagnosis in a cooperative detection pattern. Methods: Exosomes were engineered with DSPE-PEG-SH through hydrophobic interaction, and then were assembled with gold nanoparticles (2 nm) to produce Exo@Au nanozyme. The proteins on Exo@Au could be selectively captured by their specific antibodies seeded into a 96-well plate. The immobilized Exo@Au shows peroxidase-like activity to perform colorimetric assays by reaction with 3,3',5,5'-tetramethylbenzidine (TMB) and H2O2. The protein levels of exosomes were recorded on a microplate reader. Results: The NAISA platform is capable of profiling multiple exosomal proteins from both cancer cell lines and clinical samples. The expression levels of exosomal proteins, such as CD63, CEA, GPC-3, PD-L1 and HER2, were used to classify different cancer cell lines. Moreover, the protein profiles have been applied to differentiate healthy donors, hepatitis B patients, and hepatic cell carcinoma (HCC) patients with high accuracy. Conclusion: The NAISA nanozyme was allowed to rapidly profile multiple exosomal proteins and could have great promise for early HCC diagnosis and identification of other cancer types.
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Krause JL, Schaepe SS, Fritz-Wallace K, Engelmann B, Rolle-Kampczyk U, Kleinsteuber S, Schattenberg F, Liu Z, Mueller S, Jehmlich N, Von Bergen M, Herberth G. Following the community development of SIHUMIx - a new intestinal in vitro model for bioreactor use. Gut Microbes 2020; 11:1116-1129. [PMID: 31918607 PMCID: PMC7524388 DOI: 10.1080/19490976.2019.1702431] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/21/2019] [Accepted: 12/03/2019] [Indexed: 02/03/2023] Open
Abstract
Diverse intestinal microbiota is frequently used in in vitro bioreactor models to study the effects of diet, chemical contaminations, or medication. However, the reproducible cultivation of fecal microbiota is challenging and the resultant communities behave highly dynamic. To approach the issue of reproducibility in in vitro models, we established an intestinal microbiota model community of reduced complexity, SIHUMIx, as a valuable model for in vitro use. The development of the SIHUMIx community was monitored over time with methods covering the cellular and the molecular level. We used microbial flow cytometry, intact protein profiling and terminal restriction fragment length polymorphism analysis to assess community structure. In parallel, we analyzed the functional level by targeted analysis of short-chain fatty acids and untargeted metabolomics. The stability properties constancy, resistance, and resilience were approached both on the structural and functional level of the community. We show that the SIHUMIx community is highly reproducible and constant since day 5 of cultivation. Furthermore, SIHUMIx has the ability to resist and recover from a pulsed perturbation, with changes in community structure recovered earlier than functional changes. Since community structure and function changed divergently, both levels need to be monitored at the same time to gain a full overview of the community development. All five methods are highly suitable to follow the community dynamics of SIHUMIx and indicated stability on day five. This makes SIHUMIx a suitable in vitro model to investigate the effects of e.g. medical, chemical, or dietary interventions.
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Affiliation(s)
- Jannike Lea Krause
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, German
| | - Stephanie Serena Schaepe
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Katarina Fritz-Wallace
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Florian Schattenberg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Zishu Liu
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Susann Mueller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin Von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, German
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32
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Altomare AA, Baron G, Aldini G, Carini M, D'Amato A. Silkworm pupae as source of high-value edible proteins and of bioactive peptides. Food Sci Nutr 2020; 8:2652-2661. [PMID: 32566182 PMCID: PMC7300080 DOI: 10.1002/fsn3.1546] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/07/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
To characterize the high-value protein content and to discover new bioactive peptides, present in edible organisms, as silkworm pupae, semiquantitative analytical approach has been applied. The combination of appropriate protein extraction methods, semiquantitative high-resolution mass spectrometry analyses of peptides, in silico bioactivity and gene ontology analyses, allowed protein profiling of silkworm pupae (778 gene products) and the characterization of bioactive peptides. The semiquantitative analysis, based on the measurement of the emPAI, revealed the presence of high-abundance class of proteins, such as larval storage protein (LSP) class. This class of proteins, beside its nutrient reservoir activity, is of great pharmaceutical interest for their efficacy in cardiovascular diseases. Potential allergens were also characterized and quantified, such as arginine kinase, thiol peroxiredoxin, and Bom m 9. This powerful bioanalytical approach proved the potential industrial applications of Bombyx mori pupae, as source of high-value proteins in a green and "circular" economy perspective.
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Affiliation(s)
| | - Giovanna Baron
- Department of Pharmaceutical SciencesUniversità degli Studi di MilanoMilanItaly
| | - Giancarlo Aldini
- Department of Pharmaceutical SciencesUniversità degli Studi di MilanoMilanItaly
| | - Marina Carini
- Department of Pharmaceutical SciencesUniversità degli Studi di MilanoMilanItaly
| | - Alfonsina D'Amato
- Department of Pharmaceutical SciencesUniversità degli Studi di MilanoMilanItaly
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33
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Dezfouli M, Bergström S, Skattum L, Abolhassani H, Neiman M, Torabi-Rahvar M, Franco Jarava C, Martin-Nalda A, Ferrer Balaguer JM, Slade CA, Roos A, Fernandez Pereira LM, López-Trascasa M, Gonzalez-Granado LI, Allende-Martinez LM, Mizuno Y, Yoshida Y, Friman V, Lundgren Å, Aghamohammadi A, Rezaei N, Hernández-Gonzalez M, von Döbeln U, Truedsson L, Hara T, Nonoyama S, Schwenk JM, Nilsson P, Hammarström L. Newborn Screening for Presymptomatic Diagnosis of Complement and Phagocyte Deficiencies. Front Immunol 2020; 11:455. [PMID: 32256498 PMCID: PMC7090021 DOI: 10.3389/fimmu.2020.00455] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022] Open
Abstract
The clinical outcomes of primary immunodeficiencies (PIDs) are greatly improved by accurate diagnosis early in life. However, it is not common to consider PIDs before the manifestation of severe clinical symptoms. Including PIDs in the nation-wide newborn screening programs will potentially improve survival and provide better disease management and preventive care in PID patients. This calls for the detection of disease biomarkers in blood and the use of dried blood spot samples, which is a part of routine newborn screening programs worldwide. Here, we developed a newborn screening method based on multiplex protein profiling for parallel diagnosis of 22 innate immunodeficiencies affecting the complement system and respiratory burst function in phagocytosis. The proposed method uses a small fraction of eluted blood from dried blood spots and is applicable for population-scale performance. The diagnosis method is validated through a retrospective screening of immunodeficient patient samples. This diagnostic approach can pave the way for an earlier, more comprehensive and accurate diagnosis of complement and phagocytic disorders, which ultimately lead to a healthy and active life for the PID patients.
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Affiliation(s)
- Mahya Dezfouli
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Lillemor Skattum
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Region Skåne, Lund, Sweden
| | - Hassan Abolhassani
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maja Neiman
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Monireh Torabi-Rahvar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Clara Franco Jarava
- Immunology Department, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrea Martin-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juana M Ferrer Balaguer
- Immunology, Hospital Universitari Son Espases/Institut d'Investigació Sanitària Illes Balears, Palma, Spain
| | - Charlotte A Slade
- Royal Melbourne Hospital, Melbourne, VIC, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Anja Roos
- Department of Microbiology and Immunology, Sint Antonius Hospital, Nieuwegein, Netherlands
| | | | - Margarita López-Trascasa
- Departamento de Medicina, Hospital La Paz Institute for Health Research (IdiPAZ), Universidad Autónoma de Madrid and Complement Research Group, Madrid, Spain
| | - Luis I Gonzalez-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, University Hospital 12 de Octubre, Research Institute Hospital 12 Octubre (I+12), Madrid, Spain
| | - Luis M Allende-Martinez
- Immunology Department, University Hospital 12 de Octubre, Research Institute Hospital 12 Octubre (I+12), Madrid, Spain
| | - Yumi Mizuno
- Fukuoka Children's Hospital, Kyushu University, Fukuoka, Japan
| | - Yusuke Yoshida
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Vanda Friman
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Åsa Lundgren
- Departments of Infectious Diseases, Central Hospital, Kristianstad, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Manuel Hernández-Gonzalez
- Immunology Department, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ulrika von Döbeln
- Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Lennart Truedsson
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Toshiro Hara
- Fukuoka Children's Hospital, Kyushu University, Fukuoka, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Jochen M Schwenk
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
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Plazyo O, Hao W, Jin JP. The Absence of Calponin 2 in Rabbits Suggests Caution in Choosing Animal Models. Front Bioeng Biotechnol 2020; 8:42. [PMID: 32185166 PMCID: PMC7058930 DOI: 10.3389/fbioe.2020.00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/21/2020] [Indexed: 12/17/2022] Open
Abstract
While the rapid development of CRISPR/CAS9 technology has allowed for readily performing site-specific genomic editing in non-rodent species, an emerging challenge is to select the most suitable species to generate animal models for the study of human biology and diseases. Improving CRISPR/CAS9 methodology for more effective and precise editing in the rabbit genome to replicate human disease is an active area of biomedical research. Although rabbits are more closely related to humans than mice (based on DNA sequence analysis), our whole-genome protein database search revealed that rabbits have more missing human protein sequences than mice. Hence, precisely replicating human diseases in rabbits requires further consideration, especially in studies involving essential functions of the missing proteins. For example, rabbits lack calponin 2, an actin-associated cytoskeletal protein that is important in the pathogenesis of inflammatory arthritis, atherosclerosis, and calcific aortic valve disease. The justification of using rabbits as models for human biomedical research is based on their larger size and their closer phylogenetic distance to humans (based on sequence similarity of conserved genes), but this may be misleading. Our findings, which consider whole-genome protein profiling together with actual protein expressions, serve as a warning to the scientific community to consider overall conservation as well as the conservation of specific proteins when choosing an animal model to study a particular aspect of human biology prior to investing in genetic engineering.
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Affiliation(s)
- Olesya Plazyo
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI, United States
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Jian-Ping Jin
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI, United States
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35
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Ahmad A, Akram W, Shahzadi I, Wang R, Hu D, Bashir Z, Jaleel W, Ahmed S, Tariq W, Li G, Wu T, Ahmad Yasin N, Shafique S. Benzenedicarboxylic acid upregulates O48814 and Q9FJQ8 for improved nutritional contents of tomato and low risk of fungal attack. J Sci Food Agric 2019; 99:6139-6154. [PMID: 31152450 DOI: 10.1002/jsfa.9836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/05/2019] [Accepted: 05/27/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Tomato is an important food item and a cocktail of phytonutrients. In the current study, metabolites from a non-pathogenic fungal species Penicillium oxalicum have been exploited to obtain nutritionally augmented tomato fruits from the plants to better withstand against Alternaria alternata infection. RESULTS Initially, bioactivity-guided assay and chromatographic analyses identified the bioactive metabolites of P. oxalicum [benzenedicarboxylic acid (BDA) and benzimidazole]. Then, ≥3 times elevated quantities of vitamins and other nutritional elements (protein, fat, fibers, and carbohydrates) were achieved by the foliar application of BDA. The maximum increase (625.81%) was recorded in riboflavin contents; however, thiamine showed the second highest enhancement (542.86%). Plant metabolites analysis revealed that jasmonic acid contents were boosted 121.53% to significantly enhance guaiacyl lignin defenses along with the reduction in coumarin contents. The protein profile analysis explored three most actively responding protein species toward BDA applications, (i) palmitoyltransferase protein Q9FLM3; (ii) serine/threonine-protein kinase O48814; and (iii) E3 ubiquitin-protein ligase Q9FJQ8. The O48814 improved plant defenses; whereas, Q9FJQ8 protein was negatively regulating cysteine-type endopeptidase activity and assisted plant to resist schedule alterations. Tomato cultivar with more active innate metabolism was found to be more responsive toward BDA. Furthermore, the bioactive compounds were enriched by using the two-step extraction method of ethyl acetate and chloroform, respectively. CONCLUSION Penicillium oxalicum a non-pathogenic fungal species, produced BDA, induced nutritional contents in tomato and protected it against Alternaria alternata. The current study is the first report on the bioactivity of BDA and benzimidazole concerning the nutritional enhancement and plant defense improvement. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Aqeel Ahmad
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Waheed Akram
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Iqra Shahzadi
- School of Resource and Environmental Science, Wuhan University, Wuchang, China
| | - Rui Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Du Hu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Zoobia Bashir
- National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, Nanjing, China
| | - Waqar Jaleel
- Plant Protection Research Institute Guangdong Academy Agricultural Sciences, Guangzhou, China
| | - Shakeel Ahmed
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile
| | - Wajeeha Tariq
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
- Technical and Further Education, Brisbane, Australia
| | - Guihua Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Tingquan Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Nasim Ahmad Yasin
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Shazia Shafique
- Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
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36
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Khoo XH, Paterson IC, Goh BH, Lee WL. Cisplatin-Resistance in Oral Squamous Cell Carcinoma: Regulation by Tumor Cell-Derived Extracellular Vesicles. Cancers (Basel) 2019; 11:cancers11081166. [PMID: 31416147 PMCID: PMC6721547 DOI: 10.3390/cancers11081166] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
Drug resistance remains a severe problem in most chemotherapy regimes. Recently, it has been suggested that cancer cell-derived extracellular vesicles (EVs) could mediate drug resistance. In this study, the role of EVs in mediating the response of oral squamous cell carcinoma (OSCC) cells to cisplatin was investigated. We isolated and characterized EVs from OSCC cell lines showing differential sensitivities to cisplatin. Increased EV production was observed in both de novo (H314) and adaptive (H103/cisD2) resistant lines compared to sensitive H103 cells. The protein profiles of these EVs were then analyzed. Differences in the proteome of EVs secreted by H103 and H103/cisD2 indicated that adaptation to cisplatin treatment caused significant changes in the secreted nanovesicles. Intriguingly, both resistant H103/cisD2 and H314 cells shared a highly similar EV protein profile including downregulation of the metal ion transporter, ATP1B3, in the EVs implicating altered drug delivery. ICP-MS analysis revealed that less cisplatin accumulated in the resistant cells, but higher levels were detected in their EVs. Therefore, we inhibited EV secretion from the cells using a proton pump inhibitor and observed an increased drug sensitivity in cisplatin-resistant H314 cells. This finding suggests that control of EV secretion could be a potential strategy to enhance the efficacy of cancer treatment.
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Affiliation(s)
- Xin-Hui Khoo
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ian C Paterson
- Department of Oral and Craniofacial Sciences, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Health and Well-being Cluster, Global Asia in the 21st Century (GA21) Platform, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Wai-Leng Lee
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia.
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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38
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Cavallaro S, Horak J, Hååg P, Gupta D, Stiller C, Sahu SS, Görgens A, Gatty HK, Viktorsson K, El Andaloussi S, Lewensohn R, Karlström AE, Linnros J, Dev A. Label-Free Surface Protein Profiling of Extracellular Vesicles by an Electrokinetic Sensor. ACS Sens 2019; 4:1399-1408. [PMID: 31020844 DOI: 10.1021/acssensors.9b00418] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Small extracellular vesicles (sEVs) generated from the endolysosomal system, often referred to as exosomes, have attracted interest as a suitable biomarker for cancer diagnostics, as they carry valuable biological information and reflect their cells of origin. Herein, we propose a simple and inexpensive electrical method for label-free detection and profiling of sEVs in the size range of exosomes. The detection method is based on the electrokinetic principle, where the change in the streaming current is monitored as the surface markers of the sEVs interact with the affinity reagents immobilized on the inner surface of a silica microcapillary. As a proof-of-concept, we detected sEVs derived from the non-small-cell lung cancer (NSCLC) cell line H1975 for a set of representative surface markers, such as epidermal growth factor receptor (EGFR), CD9, and CD63. The detection sensitivity was estimated to be ∼175000 sEVs, which represents a sensor surface coverage of only 0.04%. We further validated the ability of the sensor to measure the expression level of a membrane protein by using sEVs displaying artificially altered expressions of EGFR and CD63, which were derived from NSCLC and human embryonic kidney (HEK) 293T cells, respectively. The analysis revealed that the changes in EGFR and CD63 expressions in sEVs can be detected with a sensitivity in the order of 10% and 3%, respectively, of their parental cell expressions. The method can be easily parallelized and combined with existing microfluidic-based EV isolation technologies, allowing for rapid detection and monitoring of sEVs for cancer diagnosis.
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Affiliation(s)
- Sara Cavallaro
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, 16440 Kista, Sweden
| | - Josef Horak
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Petra Hååg
- Department of Oncology/Pathology, Karolinska Institutet, Karolinska University Hospital (Theme, Cancer; Patient Area, Pelvis), Akademiska stråket 1, 171 64 Solna, Stockholm, Sweden
| | - Dhanu Gupta
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Evox Therapeutics Limited, Oxford OX4 4HG, United Kingdom
| | - Christiane Stiller
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Siddharth S. Sahu
- Department of Solid State Electronics, The Ångström Laboratory, Uppsala University, Box 534, Uppsala SE-751-21, Sweden
| | - André Görgens
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Evox Therapeutics Limited, Oxford OX4 4HG, United Kingdom
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Hithesh K. Gatty
- Department of Solid State Electronics, The Ångström Laboratory, Uppsala University, Box 534, Uppsala SE-751-21, Sweden
| | - Kristina Viktorsson
- Department of Oncology/Pathology, Karolinska Institutet, Karolinska University Hospital (Theme, Cancer; Patient Area, Head and Neck, Lung, and Skin), Akademiska stråket 1, 171 64 Solna, Stockholm, Sweden
| | - Samir El Andaloussi
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Evox Therapeutics Limited, Oxford OX4 4HG, United Kingdom
| | - Rolf Lewensohn
- Department of Oncology/Pathology, Karolinska Institutet, Karolinska University Hospital (Theme, Cancer; Patient Area, Head and Neck, Lung, and Skin), Akademiska stråket 1, 171 64 Solna, Stockholm, Sweden
| | - Amelie E. Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Jan Linnros
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, 16440 Kista, Sweden
| | - Apurba Dev
- Department of Solid State Electronics, The Ångström Laboratory, Uppsala University, Box 534, Uppsala SE-751-21, Sweden
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Vandemoortele G, Eyckerman S, Gevaert K. Pick a Tag and Explore the Functions of Your Pet Protein. Trends Biotechnol 2019; 37:1078-90. [PMID: 31036349 DOI: 10.1016/j.tibtech.2019.03.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Abstract
Protein tags have been essential for advancing our knowledge of the function of proteins, their localization, and the mapping of their interaction partners. Expressing epitope-tagged proteins has become a standard practice in every life science laboratory and, thus, continues to enable new studies. In recent years, several new tagging moieties have entered the limelight, many of them bringing new functionalities, such as targeted protein degradation, accurate quantification, and proximity labeling. Other novel tags aim at tackling research questions in challenging niches. In this review, we elaborate on recently introduced tags and the opportunities they provide for future research endeavors. In addition, we highlight how the genome-engineering revolution may boost the field of protein tags.
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40
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Vagner T, Chin A, Mariscal J, Bannykh S, Engman DM, Di Vizio D. Protein Composition Reflects Extracellular Vesicle Heterogeneity. Proteomics 2019; 19:e1800167. [PMID: 30793499 PMCID: PMC7521840 DOI: 10.1002/pmic.201800167] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/11/2019] [Indexed: 12/23/2022]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed particles that are released by virtually all cells from all living organisms. EVs shuttle biologically active cargo including protein, RNA, and DNA between cells. When shed by cancer cells, they function as potent intercellular messangers with important functional consequences. Cells produce a diverse spectrum of EVs, spanning from small vesicles of 40-150 nm in diameter, to large vesicles up to 10 μm in diameter. While this diversity was initially considered to be purely based on size, it is becoming evident that different classes of EVs, and different populations within one EV class may harbor distinct molecular cargo and play specific functions. Furthermore, there are considerable cell type-dependent differences in the cargo and function of shed EVs. This review focuses on the most recent proteomic studies that have attempted to capture the EV heterogeneity by directly comparing the protein composition of different EV classes and EV populations derived from the same cell source. Recent studies comparing protein composition of the same EV class(es) derived from different cell types are also summarized. Emerging approaches to study EV heterogeneity and their important implications for future studies are also discussed.
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Affiliation(s)
- Tatyana Vagner
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Andrew Chin
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Javier Mariscal
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Serguei Bannykh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - David M Engman
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Medicine, University of California, Los Angeles, CA, 90095, USA
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41
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Chen L, Keller LJ, Cordasco E, Bogyo M, Lentz CS. Fluorescent Triazole Urea Activity-Based Probes for the Single-Cell Phenotypic Characterization of Staphylococcus aureus. Angew Chem Int Ed Engl 2019; 58:5643-5647. [PMID: 30768830 DOI: 10.1002/anie.201900511] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/01/2019] [Indexed: 11/05/2022]
Abstract
Phenotypically distinct cellular (sub)populations are clinically relevant for the virulence and antibiotic resistance of a bacterial pathogen, but functionally different cells are usually indistinguishable from each other. Herein, we introduce fluorescent activity-based probes as chemical tools for the single-cell phenotypic characterization of enzyme activity levels in Staphylococcus aureus. We screened a 1,2,3-triazole urea library to identify selective inhibitors of fluorophosphonate-binding serine hydrolases and lipases in S. aureus and synthesized target-selective activity-based probes. Molecular imaging and activity-based protein profiling studies with these probes revealed a dynamic network within this enzyme family involving compensatory regulation of specific family members and exposed single-cell phenotypic heterogeneity. We propose the labeling of enzymatic activities by chemical probes as a generalizable method for the phenotyping of bacterial cells at the population and single-cell level.
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Affiliation(s)
- Linhai Chen
- Stanford University School of Medicine, Department of Pathology, 300 Pasteur Drive, Stanford, CA, 94305, USA.,National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guoshoujing Road, Shanghai, 201203, China
| | - Laura J Keller
- Stanford University School of Medicine, Department of Chemical & Systems Biology, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Edward Cordasco
- Stanford University School of Medicine, Department of Pathology, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Matthew Bogyo
- Stanford University School of Medicine, Department of Pathology, 300 Pasteur Drive, Stanford, CA, 94305, USA.,Stanford University School of Medicine, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Christian S Lentz
- Stanford University School of Medicine, Department of Pathology, 300 Pasteur Drive, Stanford, CA, 94305, USA.,Department of Chemical Biology, Helmholtz-Centre for Infection Research (HZI), Braunschweig, Germany
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42
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Abstract
This manuscript describes protocols for separation of complex protein samples using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Electrophoresis in a single dimension, e.g., 1D SDS polyacrylamide gels, has the potential to rapidly separate hundreds of proteins. When two orthogonal high-resolution electrophoretic methods are efficiently combined in perpendicular dimensions, complex protein mixtures can be separated into thousands of discrete spots. The most common 2D gel separation for intact proteins involves a first-dimensional separation using isoelectric focusing (IEF) followed by separation based on protein size (SDS-PAGE). Currently, most 2D gel studies rely on the use of commercially available immobilized pH gradient (IPG) gels, which provide improved ease of use and reproducibility compared with older methods. IPG gels are available in a range of sizes and different pH ranges. Resolution typically increases as the 2D gel size increases; however, difficulty of use increases sharply and throughput decreases as gel size increases. © 2019 by John Wiley & Sons, Inc.
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43
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Abstract
The elucidation of substrate-protein interactions is an important component of the drug development process. Due to the complexity of native cellular environments, elucidating these fundamental biochemical interactions remains challenging. Photoaffinity labeling (PAL) is a versatile technique that can provide insight into ligand-target interactions. By judicious modification of substrates with a photoreactive group, PAL creates a covalent crosslink between a substrate and its biological target following UV-irradiation. Among the commonly employed photoreactive groups, diazirines have emerged as the gold standard. In this Minireview, recent developments in the field of diazirine-based photoaffinity labeling will be discussed, with emphasis being placed on their applications in chemical proteomic studies.
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Affiliation(s)
- Matthew W Halloran
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Jean-Philip Lumb
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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44
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Ludwig S, Sharma P, Theodoraki MN, Pietrowska M, Yerneni SS, Lang S, Ferrone S, Whiteside TL. Molecular and Functional Profiles of Exosomes From HPV(+) and HPV(-) Head and Neck Cancer Cell Lines. Front Oncol 2018; 8:445. [PMID: 30370252 PMCID: PMC6194188 DOI: 10.3389/fonc.2018.00445] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
Exosomes produced by tumor cells have been shown to reprogram functions of human immune cells. Molecular cargos of exosomes isolated from supernatants of HPV(+) and HPV(−) head and neck cancer (HNC) cell lines or from HNC patients' plasma were compared. The exosome protein profiles resembled those of respective parent tumor cells. Only HPV(+) exosomes carried E6/E7, p16, and survivin. HPV(−) exosomes were negative for cyclin D1 and carried low p53 levels. Immunomodulatory molecules (TGF-β, FasL, OX40, OX40L, and HSP70) were carried by HPV(+) and HPV(−) exosomes. These exosomes co-incubated with human T cells induced apoptosis and suppressed T cell activation and proliferation. HPV(−) exosomes suppressed DC maturation and expression of antigen processing machinery (APM) components. In contrast, HPV(+) exosomes promoted DC maturation and did not suppress expression of APM components in mature DCs. While DCs readily internalized exosomes, T lymphocytes resisted their uptake during the initial 12 h co-culture. Thus, HPV(+) exosomes capable of sustaining DC functions may play a key role in promoting anti-tumor immune responses thereby improving outcome in patients with HPV(+) cancers.
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Affiliation(s)
- Sonja Ludwig
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Duisburg-Essen, Essen, Germany.,UPMC Hillman Cancer Center, Pittsburgh, PA, United States
| | | | - Marie-Nicole Theodoraki
- UPMC Hillman Cancer Center, Pittsburgh, PA, United States.,Department of Otorhinolaryngology, Head and Neck Surgery, University of Ulm, Ulm, Germany
| | - Monika Pietrowska
- Gliwice Branch, Maria Sklodowska-Curie Institute - Oncology Center, Gliwice, Poland
| | - Saigopalakrishna S Yerneni
- Department of Biomedical Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Stephan Lang
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Duisburg-Essen, Essen, Germany
| | - Soldano Ferrone
- Massachussets General Hospital, Harvard Medical School, Boston, MA, United States
| | - Theresa L Whiteside
- UPMC Hillman Cancer Center, Pittsburgh, PA, United States.,Departments of Pathology, Immunology and Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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45
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Lawrence AL, Batovska J, Webb CE, Lynch SE, Blacket MJ, Šlapeta J, Parola P, Laroche M. Accurate identification of Australian mosquitoes using protein profiling. Parasitology 2019; 146:462-71. [PMID: 30269696 DOI: 10.1017/S0031182018001658] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Australian mosquito species significantly impact human health through nuisance biting and the transmission of endemic and exotic pathogens. Surveillance programmes designed to provide an early warning of mosquito-borne disease risk require reliable identification of mosquitoes. This study aimed to investigate the viability of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a rapid and inexpensive approach to the identification of Australian mosquitoes and was validated using a three-step taxonomic approach. A total of 300 mosquitoes representing 21 species were collected from south-eastern New South Wales and morphologically identified. The legs from the mosquitoes were removed and subjected to MALDI-TOF MS analysis. Fifty-eight mosquitoes were sequenced at the cytochrome c oxidase subunit I (cox1) gene region and genetic relationships were analysed. We create the first MALDI-TOF MS spectra database of Australian mosquito species including 19 species. We clearly demonstrate the accuracy of MALDI-TOF MS for identification of Australian mosquitoes. It is especially useful for assessing gaps in the effectiveness of DNA barcoding by differentiating closely related taxa. Indeed, cox1 DNA barcoding was not able to differentiate members of the Culex pipiens group, Cx. quinquefasciatus and Cx. pipiens molestus, but these specimens were correctly identified using MALDI-TOF MS.
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46
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Backert S, Tegtmeyer N, Oyarzabal OA, Osman D, Rohde M, Grützmann R, Vieth M. Unusual Manifestation of Live Staphylococcus saprophyticus, Corynebacterium urinapleomorphum, and Helicobacter pylori in the Gallbladder with Cholecystitis. Int J Mol Sci 2018; 19:E1826. [PMID: 29933576 DOI: 10.3390/ijms19071826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/08/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
Culture-independent studies have identified DNA of bacterial pathogens in the gallbladder under pathological conditions, yet reports on the isolation of corresponding live bacteria are rare. Thus, it is unclear which pathogens, or pathogen communities, can colonize the gallbladder and cause disease. Using light microscopy, scanning electron microscopy, culture techniques, phylogenetic analysis, urease assays and Western blotting, we investigated the presence of live bacterial communities in the gallbladder of a cholecystitis patient after cholecystectomy. 16S rRNA gene sequencing of isolated bacterial colonies revealed the presence of pathogens most closely resembling Corynebacterium urinapleomorphum nov. sp., Staphylococcus saprophyticus and Helicobacter pylori. The latter colonies were confirmed as H. pylori by immunohistochemistry and biochemical methods. H. pylori cultured from the gallbladder exhibited both the same DNA fingerprinting and Western cagA gene sequence with ABC-type EPIYA (Glu-Pro-Ile-Tyr-Ala) phosphorylation motifs as isolates recovered from the gastric mucus of the same patient, suggesting that gastric H. pylori can also colonize other organs in the human body. Taken together, here we report, for the first time, the identification and characterization of a community consisting of live S. saprophyticus; C. urinapleomorphum, and H. pylori in the gallbladder of a patient with acute cholecystitis. Their potential infection routes and roles in pathogenesis are discussed.
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47
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Segura V, Valero ML, Cantero L, Muñoz J, Zarzuela E, García F, Aloria K, Beaskoetxea J, Arizmendi JM, Navajas R, Paradela A, Díez P, Dégano RM, Fuentes M, Orfao A, Montero AG, Garin-Muga A, Corrales FJ, Pino MMSD. In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets. Proteomes 2018; 6:proteomes6010008. [PMID: 29401756 PMCID: PMC5874767 DOI: 10.3390/proteomes6010008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/24/2018] [Accepted: 02/01/2018] [Indexed: 01/02/2023] Open
Abstract
Monocytes are bone marrow-derived leukocytes that are part of the innate immune system. Monocytes are divided into three subsets: classical, intermediate and non-classical, which can be differentiated by their expression of some surface antigens, mainly CD14 and CD16. These cells are key players in the inflammation process underlying the mechanism of many diseases. Thus, the molecular characterization of these cells may provide very useful information for understanding their biology in health and disease. We performed a multicentric proteomic study with pure classical and non-classical populations derived from 12 healthy donors. The robust workflow used provided reproducible results among the five participating laboratories. Over 5000 proteins were identified, and about half of them were quantified using a spectral counting approach. The results represent the protein abundance catalogue of pure classical and enriched non-classical blood peripheral monocytes, and could serve as a reference dataset of the healthy population. The functional analysis of the differences between cell subsets supports the consensus roles assigned to human monocytes.
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Affiliation(s)
- Víctor Segura
- Proteomics, Genomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona 31008, Spain.
| | - M Luz Valero
- Proteomics Unit; Central Service for Experimental Research (SCSIE), University of Valencia. Dr Moliner 50, 46100 Burjassot, Spain.
| | - Laura Cantero
- Proteomics Unit; Central Service for Experimental Research (SCSIE), University of Valencia. Dr Moliner 50, 46100 Burjassot, Spain.
| | - Javier Muñoz
- Spanish National Cancer Research Centre (CNIO), Melchor Férnandez Almagro, 3, 28029 Madrid. Spain.
| | - Eduardo Zarzuela
- Spanish National Cancer Research Centre (CNIO), Melchor Férnandez Almagro, 3, 28029 Madrid. Spain.
| | - Fernando García
- Spanish National Cancer Research Centre (CNIO), Melchor Férnandez Almagro, 3, 28029 Madrid. Spain.
| | - Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.
| | - Javier Beaskoetxea
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.
| | - Jesús M Arizmendi
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain.
| | - Rosana Navajas
- Proteomics Unit, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain.
| | - Alberto Paradela
- Proteomics Unit, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain.
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
- Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Rosa Mª Dégano
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
- Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
- Proteomics Unit. Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Alberto Orfao
- Cancer Research Center. University of Salamanca-CSIC, IBSAL, 37007 Salamanca, Spain.
| | - Andrés García Montero
- Spanish National DNA Bank Carlos III, University of Salamanca, 37007 Salamanca, Spain.
| | - Alba Garin-Muga
- Proteomics, Genomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona 31008, Spain.
| | - Fernando J Corrales
- Proteomics Unit, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain.
| | - Manuel M Sánchez Del Pino
- Department of Biochemistry and Molecular Biology, University of Valencia. Dr Moliner 50, 46100 Burjassot, Spain.
- Biotechnology and Biomedicine Interdisciplinary Research Unit (ERI BIOTECMED), University of Valencia. Dr Moliner 50, 46100 Burjassot, Spain.
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48
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Tian Y, Ma L, Gong M, Su G, Zhu S, Zhang W, Wang S, Li Z, Chen C, Li L, Wu L, Yan X. Protein Profiling and Sizing of Extracellular Vesicles from Colorectal Cancer Patients via Flow Cytometry. ACS Nano 2018; 12:671-680. [PMID: 29300458 DOI: 10.1021/acsnano.7b07782] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Extracellular vesicles (EVs) have stimulated considerable scientific and clinical interest, yet protein profiling and sizing of individual EVs remains challenging due to their small particle size, low abundance of proteins, and overall heterogeneity. Building upon a laboratory-built high-sensitivity flow cytometer (HSFCM), we report here a rapid approach for quantitative multiparameter analysis of single EVs down to 40 nm with an analysis rate up to 10 000 particles per minute. Statistically robust particle size distribution was acquired in minutes with a resolution and profile well matched with those of cryo-TEM measurements. Subpopulations of EVs expressing CD9, CD63, and/or CD81 were quantified upon immunofluorescent staining. When HSFCM was used to analyze blood samples, a significantly elevated level of CD147-positive EVs was identified in colorectal cancer patients compared to healthy controls (P < 0.001). HSFCM provides a sensitive and rapid platform for surface protein profiling and sizing of individual EVs, which could greatly aid the understanding of EV-mediated intercellular communication and the development of advanced diagnostic and therapeutic strategies.
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Affiliation(s)
- Ye Tian
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Ling Ma
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Manfei Gong
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Guoqiang Su
- Department of General Surgery, The First Affiliated Hospital of Xiamen University , Xiamen, Fujian 361003, People's Republic of China
| | - Shaobin Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Wenqiang Zhang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Shuo Wang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Zhibin Li
- Epidemiology Research Unit, The First Affiliated Hospital of Xiamen University , Xiamen, Fujian 361003, People's Republic of China
| | - Chaoxiang Chen
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Lihong Li
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Lina Wu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
| | - Xiaomei Yan
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, People's Republic of China
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Wang S, Chen G, Lin X, Xing X, Cai Z, Liu X, Liu J. Role of exosomes in hepatocellular carcinoma cell mobility alteration. Oncol Lett 2017; 14:8122-8131. [PMID: 29250190 PMCID: PMC5727617 DOI: 10.3892/ol.2017.7257] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/23/2017] [Indexed: 02/07/2023] Open
Abstract
Exosomes have gained increased research focus due to their key roles as messengers. The components of exosomes include proteins and RNAs that may be horizontally transferred between adjacent or distant cells. Hepatocellular carcinoma (HCC) is among the most malignant types of cancer worldwide, with exosomes implicated to play a crucial role in its regulation; however, the possible function of exosomes in modulating the motile ability of tumor cells and key molecules in HCC remain largely unknown. To investigate the regulatory effect of exosomes on the motile ability of HCC cells, exosomes from the culture medium of different HCC origins (high metastatic MHCC97-H and low metastatic MHCC97-L cells) were isolated for in vitro migration and invasion assays. The results indicated that the motile ability of MHCC97-L cells was significantly increased by pretreatment with MHCC97-H-derived exosomes when compared with MHCC97-L-exosome pretreatment (P<0.05). To further characterize the function of exosomes at the molecular level, protein profiling of exosomes from different cell origins was performed, which identified 129 proteins. Among these, adenylyl cyclase-associated protein 1, a protein implicated in HCC metastasis, was significantly enriched in exosomes from cells with high motile ability (P<0.05). The results of the present study validated the regulatory effect of exosomes on the motile ability of HCC cells. Furthermore, systematic analysis of the protein profiles of exosomes from different origins identified potential factors correlated with HCC metastasis, which may provide a basis for future functional analysis of exosomes regarding their involvement in cancer metastasis and recurrence.
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Affiliation(s)
- Sen Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
| | - Xiao Lin
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350007, P.R. China
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
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50
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Jiang Y, Shi M, Liu Y, Wan S, Cui C, Zhang L, Tan W. Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins. Angew Chem Int Ed Engl 2017; 56:11916-11920. [PMID: 28834063 PMCID: PMC5912341 DOI: 10.1002/anie.201703807] [Citation(s) in RCA: 324] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/30/2022]
Abstract
Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high-salt solution. In the presence of exosomes, the non-specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.
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Affiliation(s)
- Ying Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Muling Shi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Yuan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Cheng Cui
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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