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Abyadeh M, Gupta V, Paulo JA, Mahmoudabad AG, Shadfar S, Mirshahvaladi S, Gupta V, Nguyen CTO, Finkelstein DI, You Y, Haynes PA, Salekdeh GH, Graham SL, Mirzaei M. Amyloid-beta and tau protein beyond Alzheimer's disease. Neural Regen Res 2024; 19:1262-1276. [PMID: 37905874 DOI: 10.4103/1673-5374.386406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 11/02/2023] Open
Abstract
ABSTRACT The aggregation of amyloid-beta peptide and tau protein dysregulation are implicated to play key roles in Alzheimer's disease pathogenesis and are considered the main pathological hallmarks of this devastating disease. Physiologically, these two proteins are produced and expressed within the normal human body. However, under pathological conditions, abnormal expression, post-translational modifications, conformational changes, and truncation can make these proteins prone to aggregation, triggering specific disease-related cascades. Recent studies have indicated associations between aberrant behavior of amyloid-beta and tau proteins and various neurological diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, as well as retinal neurodegenerative diseases like Glaucoma and age-related macular degeneration. Additionally, these proteins have been linked to cardiovascular disease, cancer, traumatic brain injury, and diabetes, which are all leading causes of morbidity and mortality. In this comprehensive review, we provide an overview of the connections between amyloid-beta and tau proteins and a spectrum of disorders.
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Affiliation(s)
| | - Vivek Gupta
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Sina Shadfar
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Shahab Mirshahvaladi
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Christine T O Nguyen
- Department of Optometry and Vision Sciences, School of Health Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - David I Finkelstein
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Yuyi You
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Ghasem H Salekdeh
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW, Australia
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Masoomi-Aladizgeh F, Jabbari L, Khayam Nekouei R, Aalami A, Atwell BJ, Haynes PA. A universal protocol for high-quality DNA and RNA isolation from diverse plant species. PLoS One 2023; 18:e0295852. [PMID: 38096235 PMCID: PMC10721051 DOI: 10.1371/journal.pone.0295852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Next-generation sequencing demands high-quality nucleic acid, yet isolating DNA and RNA is often challenging, particularly from plant tissues. Despite advances in developing various kits and reagents, these products are tailored to isolation of nucleic acid from model plant tissues. Here we introduce a universal lysis buffer to separate nucleic acid from various plant species, including recalcitrant plants, to facilitate molecular analyses, such as quantitative PCR (qPCR), transcriptomics, and whole-genome sequencing (WGS). The protocol is a modification of the original CTAB methods, which leads to nucleic acid isolation from many plant species, including monocots and eudicots. The lysis buffer consists of hexadecyltrimethylammonium bromide (CTAB), sodium chloride (NaCl), Tris base, ethylenediaminetetraacetic acid (EDTA) and β-mercaptoethanol (βME). The modified CTAB method enables the isolation of nucleic acid from small amounts of plant tissues (e.g., 15-100 mg) in a timely manner, which is well-suited for a large number of samples and also when adequate sample collection is a limiting factor. The protocol isolates not only DNA from various plant species but also RNA. This makes it highly effective for molecular analyses compared to previously described CTAB methods optimised for DNA isolation. The appropriate concentration of the components enables high-quality DNA and RNA isolation from plant tissues simultaneously. Additionally, this protocol is compatible with commercially available columns. For DNA and RNA to be qualified for next-generation sequencing platforms, the protocol is supplemented with columns to purify either DNA or RNA from the same tissue to meet high standards for sequencing analyses. This protocol provides an ideal approach to overcome potential obstacles in isolating high-quality DNA or RNA from a wide range of plant species for downstream molecular analysis.
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Affiliation(s)
| | - Leila Jabbari
- Department of Tissue Culture and Gene Transformation, Agricultural Biotechnology Research Institute of Iran (ABRII), AREEO, Karaj, Iran
| | - Reza Khayam Nekouei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Ali Aalami
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Brian J. Atwell
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
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Abyadeh M, Gupta V, Liu X, Rossio V, Mirzaei M, Cornish J, Paulo JA, Haynes PA. Proteome-Wide Profiling Using Sample Multiplexing of a Human Cell Line Treated with Cannabidiol (CBD) and Tetrahydrocannabinol (THC). Proteomes 2023; 11:36. [PMID: 37987316 PMCID: PMC10661330 DOI: 10.3390/proteomes11040036] [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: 08/29/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Cannabis has been used historically for both medicinal and recreational purposes, with the most notable cannabinoids being cannabidiol (CBD) and tetrahydrocannabinol (THC). Although their therapeutic effects have been well studied and their recreational use is highly debated, the underlying mechanisms of their biological effects remain poorly defined. In this study, we use isobaric tag-based sample multiplexed proteome profiling to investigate protein abundance differences in the human neuroblastoma SH-SY5Y cell line treated with CBD and THC. We identified significantly regulated proteins by each treatment and performed a pathway classification and associated protein-protein interaction analysis. Our findings suggest that these treatments may lead to mitochondrial dysfunction and induce endoplasmic reticulum stress. These data can potentially be interrogated further to investigate the potential role of CBD and THC in various biological and disease contexts, providing a foundation for future studies.
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Affiliation(s)
- Morteza Abyadeh
- ProGene Technologies Pty Ltd., Macquarie Park, NSW 2113, Australia;
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (V.G.); (M.M.)
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; (X.L.); (V.R.); (J.A.P.)
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; (X.L.); (V.R.); (J.A.P.)
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (V.G.); (M.M.)
| | - Jennifer Cornish
- School of Psychological Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia;
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; (X.L.); (V.R.); (J.A.P.)
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Habibpourmehraban F, Masoomi-Aladizgeh F, Haynes PA. Effect of ABA Pre-Treatment on Rice Plant Transcriptome Response to Multiple Abiotic Stress. Biomolecules 2023; 13:1554. [PMID: 37892236 PMCID: PMC10604926 DOI: 10.3390/biom13101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Half of the world's population depends on rice plant cultivation, yet environmental stresses continue to substantially impact the production of one of our most valuable staple foods. The aim of this study was to investigate the changes in the transcriptome of the IAC1131 rice genotype when exposed to a suite of multiple abiotic stresses, either with or without pre-treatment with the plant hormone ABA (Abscisic acid). Four groups of IAC1131 rice plants were grown including control plants incubated with ABA, non-ABA-incubated control plants, stressed plants incubated with ABA, and non-ABA-incubated stressed plants, with leaf samples harvested after 0 days (control) and 4 days (stressed). We found that high concentrations of ABA applied exogenously to the control plants under normal conditions did not alter the IAC1131 transcriptome profile significantly. The observed changes in the transcriptome of the IAC1131 plants in response to multiple abiotic stress were made even more pronounced by ABA pre-treatment, which induced the upregulation of a significant number of additional genes. Although ABA application impacted the plant transcriptome, multiple abiotic stress was the dominant factor in modifying gene expression in the IAC1131 plants. Exogenous ABA application may mitigate the effects of stress through ABA-dependent signalling pathways related to biological photosynthesis functions. Pre-treatment with ABA alters the photosynthesis function negatively by reducing stomatal conductance, therefore helping plants to conserve the energy required for survival under unfavourable environmental conditions.
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Affiliation(s)
- Fatemeh Habibpourmehraban
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.H.); (F.M.-A.)
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.H.); (F.M.-A.)
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.H.); (F.M.-A.)
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
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Grey AC, Lin Q, Low TY, Wu W, Haynes PA, Chung MCM, Chen YJ, Cordwell SJ, Ishihama Y, Xu P, Hoffmann P, Kwon HJ, Poon TCW. 11th Asia Oceania Human Proteome Organization Congress Report. Mol Cell Proteomics 2023; 22:100627. [PMID: 37532177 PMCID: PMC10472285 DOI: 10.1016/j.mcpro.2023.100627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023] Open
Abstract
As the first in-person Asia Oceania Human Proteomics Organization (AOHUPO) congress since 2018, the 11th AOHUPO congress was an opportune time for the research community to reconnect and to renew friendships after the long period of restricted travel due to the global pandemic. Moreover, this congress was a great opportunity for the many AO regional proteomics and mass spectrometry scientists to meet in Singapore to exchange ideas and to present their latest findings. Cohosted by the Singapore Society for Mass Spectrometry and the Malaysian Proteomics Society and held in conjunction with the seventh Asia Oceania Agricultural Proteomics Organization Congress and Singapore Society for Mass Spectrometry 2023, the meeting featured both human and agricultural proteomics. Over five hundred scientists from the AO region converged on the MAX Atria @ Singapore EXPO, Changi, Singapore from May 8 to 10 for the main congress. The diverse program was made up of 64 invited speakers and panellists for seven plenary lectures, 27 concurrent symposia, precongress and postcongress workshops, and 174 poster presentations. The AOHUPO society were able to celebrate not only their 20th anniversary but also the outstanding academic research from biological and agricultural proteomics and related 'omics fields being conducted across the Asia-Oceania region.
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Affiliation(s)
- Angus C Grey
- Department of Physiology, University of Auckland, Auckland, New Zealand.
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), and Department of Pharmacy, National University of Singapore, Singapore
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, Nova Scotia, Australia
| | - Maxey C M Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Stuart J Cordwell
- School of Life and Environmental Sciences and Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Peter Hoffmann
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Initiative, Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Terence C W Poon
- Pilot Laboratory, Proteomics Core, Institute of Translational Medicine, Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
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Abyadeh M, Gupta V, Paulo JA, Sheriff S, Shadfar S, Fitzhenry M, Amirkhani A, Gupta V, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. Apolipoprotein ε in Brain and Retinal Neurodegenerative Diseases. Aging Dis 2023; 14:1311-1330. [PMID: 37199411 PMCID: PMC10389820 DOI: 10.14336/ad.2023.0312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/12/2023] [Indexed: 05/19/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia that remains incurable and has become a major medical, social, and economic challenge worldwide. AD is characterized by pathological hallmarks of senile plaques (SP) and neurofibrillary tangles (NFTs) that damage the brain up to twenty years before a clinical diagnosis is made. Interestingly these pathological features have also been observed in retinal neurodegenerative diseases including age related macular degeneration (ARMD), glaucoma and diabetic retinopathy (DR). An association of AD with these diseases has been suggested in epidemiological studies and several common pathological events and risk factors have been identified between these diseases. The E4 allele of Apolipoprotein E (APOE) is a well-established genetic risk factor for late onset AD. The ApoE ε4 allele is also associated with retinal neurodegenerative diseases however in contrast to AD, it is considered protective in AMD, likewise ApoE E2 allele, which is a protective factor for AD, has been implicated as a risk factor for AMD and glaucoma. This review summarizes the evidence on the effects of ApoE in retinal neurodegenerative diseases and discusses the overlapping molecular pathways in AD. The involvement of ApoE in regulating amyloid beta (Aβ) and tau pathology, inflammation, vascular integrity, glucose metabolism and vascular endothelial growth factor (VEGF) signaling is also discussed.
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Affiliation(s)
| | - Vivek Gupta
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Samran Sheriff
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Sina Shadfar
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Matthew Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2113, Australia.
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2113, Australia.
| | - Veer Gupta
- School of Medicine, Deakin University, VIC, Australia.
| | - Ghasem H Salekdeh
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia.
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia.
| | - Stuart L Graham
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie Medical School, Macquarie University, Macquarie Park, North Ryde, Sydney, NSW 2109, Australia.
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Habibpourmehraban F, Wu Y, Masoomi-Aladizgeh F, Amirkhani A, Atwell BJ, Haynes PA. Pre-Treatment of Rice Plants with ABA Makes Them More Tolerant to Multiple Abiotic Stress. Int J Mol Sci 2023; 24:ijms24119628. [PMID: 37298579 DOI: 10.3390/ijms24119628] [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] [Received: 04/27/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Multiple abiotic stress is known as a type of environmental unfavourable condition maximizing the yield and growth gap of crops compared with the optimal condition in both natural and cultivated environments. Rice is the world's most important staple food, and its production is limited the most by environmental unfavourable conditions. In this study, we investigated the pre-treatment of abscisic acid (ABA) on the tolerance of the IAC1131 rice genotype to multiple abiotic stress after a 4-day exposure to combined drought, salt and extreme temperature treatments. A total of 3285 proteins were identified and quantified across the four treatment groups, consisting of control and stressed plants with and without pre-treatment with ABA, with 1633 of those proteins found to be differentially abundant between groups. Compared with the control condition, pre-treatment with the ABA hormone significantly mitigated the leaf damage against combined abiotic stress at the proteome level. Furthermore, the application of exogenous ABA did not affect the proteome profile of the control plants remarkably, while the results were different in stress-exposed plants by a greater number of proteins changed in abundance, especially those which were increased. Taken together, these results suggest that exogenous ABA has a potential priming effect for enhancing the rice seedlings' tolerance against combined abiotic stress, mainly by affecting stress-responsive mechanisms dependent on ABA signalling pathways in plants.
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Affiliation(s)
- Fatemeh Habibpourmehraban
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Yunqi Wu
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Ardeshir Amirkhani
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW 2109, Australia
| | - Brian J Atwell
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
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Deng L, Gupta V, Abyadeh M, Chitranshi N, Pushpitha K, Wu Y, Gupta V, You Y, Paulo JA, Graham SL, Mirzaei M, Haynes PA. Oxidative Stress Induced Dysfunction of Protein Synthesis in 661W Mice Photoreceptor Cells. Proteomes 2023; 11:12. [PMID: 37092453 PMCID: PMC10123756 DOI: 10.3390/proteomes11020012] [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: 12/05/2022] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Photoreceptor cells are highly susceptible to oxidative-stress-induced damage due to their high metabolic rate. Oxidative stress plays a key role in driving pathological events in several different ocular diseases, which lead to retinal degeneration and ultimately blindness. A growing number of studies have been performed to understand downstream events caused by ROS induced oxidative stress in photoreceptor cells; however, the underlying mechanisms of ROS toxicity are not fully understood. To shed light on ROS induced downstream pathological events, we employed a tandem mass tag (TMT) labelling-based quantitative mass-spectrometric approach to determine proteome changes in 661W photoreceptor cells following oxidative stress induction via the application of different concentrations of H2O2 at different time points. Overall, 5920 proteins were identified and quantified, and 450 differentially expressed proteins (DEPs) were identified, which were altered in a dose and time dependent manner in all treatment groups compared to the control group. These proteins were involved in several biological pathways, including spliceosome and ribosome response, activated glutathione metabolism, decreased ECM-receptor interaction, oxidative phosphorylation, abnormally regulated lysosome, apoptosis, and ribosome biogenesis. Our results highlighted ECM receptor interaction, oxidative phosphorylation and spliceosome pathways as the major targets of oxidative stress that might mediate vascular dysfunction and cellular senescence.
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Affiliation(s)
- Liting Deng
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | | | - Nitin Chitranshi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Kanishka Pushpitha
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Yuyi You
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart L. Graham
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Macquarie Park, NSW 2109, Australia
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9
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Multari DH, Ravishankar P, Sullivan GJ, Power RK, Lord C, Fraser JA, Haynes PA. Proteomics dataset from 26th Dynasty Egyptian mummified remains sampled using minimally invasive skin sampling tape strips. Data Brief 2022; 45:108562. [PMID: 36118295 PMCID: PMC9478331 DOI: 10.1016/j.dib.2022.108562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/30/2022] Open
Abstract
Paleoproteomics typically involves the destructive sampling of precious bioarchaeological materials. This analysis aims to investigate the proteins identifiable via nanoLC-MS/MS from highly degraded 26th Dynasty Egyptian mummified human remains (NMR.29.1-8) after non-destructive sampling with commercially available dermatology-grade skin sampling tape strips. A collection of cranial and other bone fragments were sampled with the tape strips then subsequently analysed using a shotgun proteomics approach. The number of proteins identified using this method ranged from 18 to 437 at a peptide FDR of <1%. Deamidation ratios were assessed using an in-house R script, with asparagine deamidation averaging ∼20–30% and glutamine deamidation averaging ∼15–25%.
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Affiliation(s)
- Dylan H. Multari
- School of Natural Sciences, Macquarie University1, North Ryde, NSW 2109, Australia
| | - Prathiba Ravishankar
- School of Natural Sciences, Macquarie University1, North Ryde, NSW 2109, Australia
| | | | - Ronika K. Power
- Department of History and Archaeology, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
- Centre for Ancient Cultural Heritage and Environment, Macquarie University, North Ryde, NSW 2109, Australia
| | - Constance Lord
- Chau Chak Wing Museum, University of Sydney, Camperdown, NSW 2006, Australia
| | | | - Paul A. Haynes
- School of Natural Sciences, Macquarie University1, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
- Centre for Ancient Cultural Heritage and Environment, Macquarie University, North Ryde, NSW 2109, Australia
- Corresponding author at: School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia. @HaynesLabMQ
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Abdirad S, Wu Y, Ghorbanzadeh Z, Tazangi SE, Amirkhani A, Fitzhenry MJ, Kazemi M, Ghaffari MR, Koobaz P, Zeinalabedini M, Habibpourmehraban F, Masoomi-Aladizgeh F, Atwell BJ, Mirzaei M, Salekdeh GH, Haynes PA. Proteomic analysis of the meristematic root zone in contrasting genotypes reveals new insights in drought tolerance in rice. Proteomics 2022; 22:e2200100. [PMID: 35920597 DOI: 10.1002/pmic.202200100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 12/29/2022]
Abstract
Drought is responsible for major losses in rice production. Root tips contain meristematic and elongation zones that play major roles in determination of root traits and adaptive strategies to drought. In this study we analysed two contrasting genotypes of rice: IR64, a lowland, drought-susceptible, and shallow-rooting genotype; and Azucena, an upland, drought-tolerant, and deep-rooting genotype. Samples were collected of root tips of plants grown under control and water deficit stress conditions. Quantitative proteomics analysis resulted in the identification of 7294 proteins from the root tips of IR64 and 6307 proteins from Azucena. Data are available via ProteomeXchange with identifier PXD033343. Using a Partial Least Square Discriminant Analysis on 4170 differentially abundant proteins, 1138 statistically significant proteins across genotypes and conditions were detected. Twenty two enriched biological processes showing contrasting patterns between two genotypes in response to stress were detected through gene ontology enrichment analysis. This included identification of novel proteins involved in root elongation with specific expression patterns in Azucena, including four Expansins and seven Class III Peroxidases. We also detected an antioxidant network and a metallo-sulfur cluster assembly machinery in Azucena, with roles in reactive oxygen species and iron homeostasis, and positive effects on root cell cycle, growth and elongation.
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Affiliation(s)
- Somayeh Abdirad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Esmaeili Tazangi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Matthew J Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Mehrbano Kazemi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Parisa Koobaz
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | | | | | - Brian J Atwell
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia.,School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.,School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, New South Wales, Australia
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11
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Mirzaei M, Abyadeh M, Turner AJ, Wall RV, Chick JM, Paulo JA, Gupta VK, Basavarajappa D, Chitranshi N, Mirshahvaladi SSO, You Y, Fitzhenry MJ, Amirkhani A, Haynes PA, Klistorner A, Gupta V, Graham SL. Fingolimod effects on the brain are mediated through biochemical modulation of bioenergetics, autophagy, and neuroinflammatory networks. Proteomics 2022; 22:e2100247. [PMID: 35866514 PMCID: PMC9786555 DOI: 10.1002/pmic.202100247] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022]
Abstract
Fingolimod (FTY720) is an oral drug approved by the Food and Drug Administration (FDA) for management of multiple sclerosis (MS) symptoms, which has also shown beneficial effects against Alzheimer's (AD) and Parkinson's (PD) diseases pathologies. Although an extensive effort has been made to identify mechanisms underpinning its therapeutic effects, much remains unknown. Here, we investigated Fingolimod induced proteome changes in the cerebellum (CB) and frontal cortex (FC) regions of the brain which are known to be severely affected in MS, using a tandem mass tag (TMT) isobaric labeling-based quantitative mass-spectrometric approach to investigate the mechanism of action of Fingolimod. This study identified 6749 and 6319 proteins in CB and FC, respectively, and returned 2609 and 3086 differentially expressed proteins in mouse CB and FC, respectively, between Fingolimod treated and control groups. Subsequent bioinformatics analyses indicated a metabolic reprogramming in both brain regions of the Fingolimod treated group, where oxidative phosphorylation was upregulated while glycolysis and pentose phosphate pathway were downregulated. In addition, modulation of neuroinflammation in the Fingolimod treated group was indicated by upregulation of retrograde endocannabinoid signaling and autophagy pathways, and downregulation of neuroinflammation related pathways including neutrophil degranulation and the IL-12 mediated signaling pathway. Our findings suggest that Fingolimod may exert its protective effects on the brain by inducing metabolic reprogramming and neuroinflammation pathway modulation.
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Affiliation(s)
- Mehdi Mirzaei
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | | | - Anita J. Turner
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Roshana Vander Wall
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Joel M. Chick
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Joao A. Paulo
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Veer K. Gupta
- School of MedicineDeakin UniversityGeelongVICAustralia
| | - Devaraj Basavarajappa
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Nitin Chitranshi
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Seyed Shahab Oddin Mirshahvaladi
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Yuyi You
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | | | - Ardeshir Amirkhani
- Australian Proteome Analysis FacilityMacquarie UniversitySydneyNSWAustralia
| | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityMacquarie ParkNSWAustralia
- Biomolecular Discovery Research CentreMacquarie UniversitySydneyNSWAustralia
| | - Alexander Klistorner
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Vivek Gupta
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
| | - Stuart L. Graham
- Department of Clinical MedicineFaculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie Park, North RydeSydneyNSWAustralia
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12
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Masoomi‐Aladizgeh F, Kamath KS, Haynes PA, Atwell BJ. Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat. Plant Cell Environ 2022; 45:1242-1256. [PMID: 35092006 PMCID: PMC9415111 DOI: 10.1111/pce.14268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
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Affiliation(s)
| | | | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Brian J. Atwell
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
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13
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Abdirad S, Ghaffari MR, Majd A, Irian S, Soleymaniniya A, Daryani P, Koobaz P, Shobbar ZS, Farsad LK, Yazdanpanah P, Sadri A, Mirzaei M, Ghorbanzadeh Z, Kazemi M, Hadidi N, Haynes PA, Salekdeh GH. Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation. Front Plant Sci 2022; 13:792079. [PMID: 35265092 PMCID: PMC8899714 DOI: 10.3389/fpls.2022.792079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/05/2022] [Indexed: 06/02/2023]
Abstract
Root system architecture (RSA) is an important agronomic trait with vital roles in plant productivity under water stress conditions. A deep and branched root system may help plants to avoid water stress by enabling them to acquire more water and nutrient resources. Nevertheless, our knowledge of the genetics and molecular control mechanisms of RSA is still relatively limited. In this study, we analyzed the transcriptome response of root tips to water stress in two well-known genotypes of rice: IR64, a high-yielding lowland genotype, which represents a drought-susceptible and shallow-rooting genotype; and Azucena, a traditional, upland, drought-tolerant and deep-rooting genotype. We collected samples from three zones (Z) of root tip: two consecutive 5 mm sections (Z1 and Z2) and the following next 10 mm section (Z3), which mainly includes meristematic and maturation regions. Our results showed that Z1 of Azucena was enriched for genes involved in cell cycle and division and root growth and development whereas in IR64 root, responses to oxidative stress were strongly enriched. While the expansion of the lateral root system was used as a strategy by both genotypes when facing water shortage, it was more pronounced in Azucena. Our results also suggested that by enhancing meristematic cell wall thickening for insulation purposes as a means of confronting stress, the sensitive IR64 genotype may have reduced its capacity for root elongation to extract water from deeper layers of the soil. Furthermore, several members of gene families such as NAC, AP2/ERF, AUX/IAA, EXPANSIN, WRKY, and MYB emerged as main players in RSA and drought adaptation. We also found that HSP and HSF gene families participated in oxidative stress inhibition in IR64 root tip. Meta-quantitative trait loci (QTL) analysis revealed that 288 differentially expressed genes were colocalized with RSA QTLs previously reported under drought and normal conditions. This finding warrants further research into their possible roles in drought adaptation. Overall, our analyses presented several major molecular differences between Azucena and IR64, which may partly explain their differential root growth responses to water stress. It appears that Azucena avoided water stress through enhancing growth and root exploration to access water, whereas IR64 might mainly rely on cell insulation to maintain water and antioxidant system to withstand stress. We identified a large number of novel RSA and drought associated candidate genes, which should encourage further exploration of their potential to enhance drought adaptation in rice.
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Affiliation(s)
- Somayeh Abdirad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
- Department of Plant Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Ahmad Majd
- Department of Plant Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Saeed Irian
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Parisa Daryani
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Parisa Koobaz
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Zahra-Sadat Shobbar
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Laleh Karimi Farsad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Parisa Yazdanpanah
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
- Department of Plant Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Amirhossein Sadri
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Mehdi Mirzaei
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Zahra Ghorbanzadeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Mehrbano Kazemi
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Naghmeh Hadidi
- Department of Clinical Research and Electronic Microscope, Pasteur Institute of Iran, Tehran, Iran
| | - Paul A. Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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14
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Masoomi-Aladizgeh F, McKay MJ, Asar Y, Haynes PA, Atwell BJ. Patterns of gene expression in pollen of cotton (Gossypium hirsutum) indicate downregulation as a feature of thermotolerance. Plant J 2022; 109:965-979. [PMID: 34837283 DOI: 10.1111/tpj.15608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/10/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Reproductive performance in plants is impaired as maximum temperatures consistently approach 40°C. However, the timing of heatwaves critically affects their impact. We studied the molecular responses during pollen maturation in cotton to investigate the vulnerability to high temperature. Tetrads (TEs), uninucleate and binucleate microspores, and mature pollen were subjected to SWATH-MS and RNA-seq analyses after exposure to 38/28°C (day/night) for 5 days. The results indicated that molecular signatures were downregulated progressively in response to heat during pollen development. This was even more evident in leaves, where three-quarters of differentially changed proteins decreased in abundance during heat. Functional analysis showed that translation of genes increased in TEs after exposure to heat; however, the reverse pattern was observed in mature pollen and leaves. For example, proteins involved in transport were highly abundant in TEs whereas in later stages of pollen formation and leaves, heat suppressed synthesis of proteins involved in cell-to-cell communication. Moreover, a large number of heat shock proteins were identified in heat-affected TEs, but these proteins were less abundant in mature pollen and leaves. We speculate that the sensitivity of TE cells to heat is related to high rates of translation targeted to pathways that might not be essential for thermotolerance. Molecular signatures during stages of pollen development after heatwaves could provide markers for future genetic improvement.
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Affiliation(s)
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, NSW, Australia
| | - Yasmin Asar
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, NSW, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, NSW, Australia
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15
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Hezavehei M, Mirzaei M, Sharafi M, Wu Y, Gupta V, Fitzhenry M, Kouchesfahani HM, Eftekhari-Yazdi P, Baharvand H, Dalman A, Haynes PA, Shahverdi A, Salekdeh GH. Proteomics study reveals the molecular mechanisms underlying cryotolerance induced by mild sublethal stress in human sperm. Cell Tissue Res 2021; 387:143-157. [PMID: 34729646 DOI: 10.1007/s00441-021-03537-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 10/05/2021] [Indexed: 10/19/2022]
Abstract
The preconditioning of human sperm with sublethal nitrosative stress before cryopreservation can potentially improve the thawed sperm quality. However, the underlying mechanisms behind this protective strategy are not entirely understood. We compared the cryosurvival of human sperm exposed to 0.01 μM nitric oxide (NO) throughout the cryopreservation and used multiplexed quantitative proteomics approach to identify changes in the proteome profile of preconditioned sperm cells. Semen samples were obtained from 30 normospermia donors and then each sample was divided into three equal parts: fresh (F), frozen-control (C), and frozen exposed to nitric oxide (NO). The sperm undergoing mild sublethal stress showed higher values for motility and viability compared to the frozen control sperm. Moreover, out of 2912 identified proteins, 248 proteins were detected as differentially abundant proteins (DAPs) between cryopreserved groups and fresh group (F) (p < 0.05). Gene ontology (GO) analysis of differentially abundant proteins indicated that the abundance of proteins associated with glycolysis, gluconeogenesis, and fertilization processes was reduced while oxidative phosphorylation pathway was increased in abundance in cryopreserved sperm compared to the fresh sperm. Moreover, redox protein such as thioredoxin 17 was increased in abundance in the NO group compared to the control freezing group. Therefore, the pre-conditioning of sperm prior to cryopreservation may play an important role in maintaining the redox balance in mitochondria of sperm after freezing. Overall, our results indicate that arylsulfatase A (ARSA), serine protease 37 (PRSS37), and sperm surface protein (SP17) may potentially serve as protein biomarkers associated with screening the fertilization potential of the thawed sperm.
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Affiliation(s)
- Maryam Hezavehei
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Animal Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Mohsen Sharafi
- Department of Animal Science, College of Agriculture, Tarbiat Modarres University, Tehran, Iran
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Matthew Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | | | - Poopak Eftekhari-Yazdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Azam Dalman
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Abdolhossein Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW, Australia. .,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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16
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Abyadeh M, Gupta V, Paulo JA, Gupta V, Chitranshi N, Godinez A, Saks D, Hasan M, Amirkhani A, McKay M, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. A Proteomic View of Cellular and Molecular Effects of Cannabis. Biomolecules 2021; 11:1411. [PMID: 34680044 PMCID: PMC8533448 DOI: 10.3390/biom11101411] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
Cannabis (Cannabis sativa), popularly known as marijuana, is the most commonly used psychoactive substance and is considered illicit in most countries worldwide. However, a growing body of research has provided evidence of the therapeutic properties of chemical components of cannabis known as cannabinoids against several diseases including Alzheimer's disease (AD), multiple sclerosis (MS), Parkinson's disease, schizophrenia and glaucoma; these have prompted changes in medicinal cannabis legislation. The relaxation of legal restrictions and increased socio-cultural acceptance has led to its increase in both medicinal and recreational usage. Several biochemically active components of cannabis have a range of effects on the biological system. There is an urgent need for more research to better understand the molecular and biochemical effects of cannabis at a cellular level, to understand fully its implications as a pharmaceutical drug. Proteomics technology is an efficient tool to rigorously elucidate the mechanistic effects of cannabis on the human body in a cell and tissue-specific manner, drawing conclusions associated with its toxicity as well as therapeutic benefits, safety and efficacy profiles. This review provides a comprehensive overview of both in vitro and in vivo proteomic studies involving the cellular and molecular effects of cannabis and cannabis-derived compounds.
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Affiliation(s)
- Morteza Abyadeh
- ProGene Technologies Pty Ltd., Macquarie Park, Sydney, NSW 2113, Australia;
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia; (N.C.); (A.G.); (D.S.); (S.L.G.)
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
| | - Veer Gupta
- School of Medicine, Deakin University, Geelong, VIC 2600, Australia;
| | - Nitin Chitranshi
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia; (N.C.); (A.G.); (D.S.); (S.L.G.)
| | - Angela Godinez
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia; (N.C.); (A.G.); (D.S.); (S.L.G.)
| | - Danit Saks
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia; (N.C.); (A.G.); (D.S.); (S.L.G.)
| | - Mafruha Hasan
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia;
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia;
| | - Matthew McKay
- Bowel Cancer and Biomarker Laboratory, Kolling Institute, Northern Clinical School, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Ghasem H. Salekdeh
- Department of Molecular Sciences, Macquarie University, Macquarie Park, Sydney, NSW 2109, Australia; (G.H.S.); (P.A.H.)
| | - Paul A. Haynes
- Department of Molecular Sciences, Macquarie University, Macquarie Park, Sydney, NSW 2109, Australia; (G.H.S.); (P.A.H.)
| | - Stuart L. Graham
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia; (N.C.); (A.G.); (D.S.); (S.L.G.)
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia; (N.C.); (A.G.); (D.S.); (S.L.G.)
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17
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Hamzelou S, Melino VJ, Plett DC, Kamath KS, Nawrocki A, Larsen MR, Atwell BJ, Haynes PA. The phosphoproteome of rice leaves responds to water and nitrogen supply. Mol Omics 2021; 17:706-718. [PMID: 34291261 DOI: 10.1039/d1mo00137j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or excess nitrogen supply, plants employ complex systems for signalling and regulation of metabolic processes. There is limited information on the involvement of one of the most important post-translational modifications (PTMs), protein phosphorylation, in plant adaptation to long-term changes in resource supply. Oryza sativa cv. Nipponbare was grown under two regimes of nitrogen from the time of germination to final harvest. Twenty-five days after germination, water was withheld from half the pots in each nitrogen treatment and low water supply continued for an additional 26 days, while the remaining pots were well watered. Leaves from all four groups of plants were harvested after 51 days in order to test whether phosphorylation of leaf proteins responded to prior abiotic stress events. The dominant impact of these resources is exerted in leaves, where PTMs have been predicted to occur. Proteins were extracted and phosphopeptides were analysed by nanoLC-MS/MS analysis, coupled with label-free quantitation. Water and nitrogen regimes triggered extensive changes in phosphorylation of proteins involved in membrane transport, such as the aquaporin OsPIP2-6, a water channel protein. Our study reveals phosphorylation of several peptides belonging to proteins involved in RNA-processing and carbohydrate metabolism, suggesting that phosphorylation events regulate the signalling cascades that are required to optimize plant response to resource supply.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Vanessa J Melino
- King Abdullah University for Science and Technology, 2955-6990, Kingdom of Saudi Arabia
| | - Darren C Plett
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia. and Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Arkadiusz Nawrocki
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
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18
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Handler DCL, Haynes PA. Correction to "Statistics in Proteomics: A Meta-analysis of 100 Proteomics Papers Published in 2019". J Am Soc Mass Spectrom 2021; 32:1846. [PMID: 32697095 DOI: 10.1021/jasms.0c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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19
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Masoomi-Aladizgeh F, Najeeb U, Hamzelou S, Pascovici D, Amirkhani A, Tan DKY, Mirzaei M, Haynes PA, Atwell BJ. Pollen development in cotton (Gossypium hirsutum) is highly sensitive to heat exposure during the tetrad stage. Plant Cell Environ 2021; 44:2150-2166. [PMID: 33047317 DOI: 10.1111/pce.13908] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 05/22/2023]
Abstract
The development of gametes in plants is acutely susceptible to heatwaves as brief as a few days, adversely affecting pollen maturation and reproductive success. Pollen in cotton (Gossypium hirsutum) was differentially affected when tetrad and binucleate stages were exposed to heat, revealing new insights into the interaction between heat and pollen development. Squares were tagged and exposed to 36/25°C (day/night, moderate heat) or 40/30°C (day/night, extreme heat) for 5 days. Mature pollen grains and leaves were collected for physiological and proteomic responses. While photosynthetic competence was not compromised even at 40°C, leaf tissues became leakier. In contrast, pollen grains were markedly smaller after the tetrad stage was exposed to 40°C and boll production was reduced by 65%. Sugar levels in pollen grains were elevated after exposure to heat, eliminating carbohydrate deficits as a likely cause of poor reproductive capacity. Proteomic analysis of pure pollen samples revealed a particularly high abundance of 70-kDa heat shock (Hsp70s) and cytoskeletal proteins. While short-term bursts of heat had a minor impact on leaves, male gametophyte development was profoundly damaged. Cotton acclimates to maxima of 36°C at both the vegetative and reproductive stages but 5-days exposure to 40°C significantly impairs reproductive development.
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Affiliation(s)
| | - Ullah Najeeb
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Toowoomba, Australia
| | - Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Daniel K Y Tan
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Plant Breeding Institute, Sydney Institute of Agriculture, Sydney, New South Wales, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
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20
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Abyadeh M, Gupta V, Chitranshi N, Gupta V, Wu Y, Saks D, Wander Wall R, Fitzhenry MJ, Basavarajappa D, You Y, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. Mitochondrial dysfunction in Alzheimer's disease - a proteomics perspective. Expert Rev Proteomics 2021; 18:295-304. [PMID: 33874826 DOI: 10.1080/14789450.2021.1918550] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is involved in Alzheimer's disease (AD) pathogenesis. Mitochondria have their own genetic material; however, most of their proteins (∼99%) are synthesized as precursors on cytosolic ribosomes, and then imported into the mitochondria. Therefore, exploring proteome changes in these organelles can yield valuable information and shed light on the molecular mechanisms underlying mitochondrial dysfunction in AD. Here, we review AD-associated mitochondrial changes including the effects of amyloid beta and tau protein accumulation on the mitochondrial proteome. We also discuss the relationship of ApoE genetic polymorphism with mitochondrial changes, and present a meta-analysis of various differentially expressed proteins in the mitochondria in AD.Area covered: Proteomics studies and their contribution to our understanding of mitochondrial dysfunction in AD pathogenesis.Expert opinion: Proteomics has proven to be an efficient tool to uncover various aspects of this complex organelle, which will broaden our understanding of mitochondrial dysfunction in AD. Evidently, mitochondrial dysfunction is an early biochemical event that might play a central role in driving AD pathogenesis.
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Affiliation(s)
- Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran Iran
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Nitin Chitranshi
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, VIC, Australia
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW Australia
| | - Danit Saks
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Roshana Wander Wall
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Matthew J Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW Australia
| | - Devaraj Basavarajappa
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Yuyi You
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Ghasem H Salekdeh
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
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21
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Deng L, Gupta VK, Wu Y, Pushpitha K, Chitranshi N, Gupta VB, Fitzhenry MJ, Moghaddam MZ, Karl T, Salekdeh GH, Graham SL, Haynes PA, Mirzaei M. Mouse model of Alzheimer's disease demonstrates differential effects of early disease pathology on various brain regions. Proteomics 2021; 21:e2000213. [PMID: 33559908 DOI: 10.1002/pmic.202000213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 12/17/2022]
Abstract
Different parts of the brain are affected distinctively in various stages of the Alzheimer's disease (AD) pathogenesis. Identifying the biochemical changes in specific brain regions is key to comprehend the neuropathological mechanisms in early pre-symptomatic phases of AD. Quantitative proteomics profiling of four distinct areas of the brain of young APP/PS1 mouse model of AD was performed followed by biochemical pathway enrichment analysis. Findings revealed fundamental compositional and functional shifts even in the early stages of the disease. This novel study highlights unique proteome and biochemical pathway alterations in specific regions of the brain that underlie the early stages of AD pathology and will provide a framework for future longitudinal studies. The proteomics data were deposited into the ProteomeXchange Consortium via PRIDE with the identifier PXD019192.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Vivek K Gupta
- Faculty of Medicine and Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Yunqi Wu
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Kanishka Pushpitha
- Faculty of Medicine and Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Nitin Chitranshi
- Faculty of Medicine and Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Veer B Gupta
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Matthew J Fitzhenry
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, New South Wales, Australia
| | | | - Tim Karl
- School of Medicine, Western Sydney University, Penrith, New South Wales, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Stuart L Graham
- Faculty of Medicine and Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Mehdi Mirzaei
- Faculty of Medicine and Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
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22
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Ghazizadeh Z, Fattahi F, Mirzaei M, Bayersaikhan D, Lee J, Chae S, Hwang D, Byun K, Tabar MS, Taleahmad S, Mirshahvaladi S, Shabani P, Fonoudi H, Haynes PA, Baharvand H, Aghdami N, Evans T, Lee B, Salekdeh GH. Prospective Isolation of ISL1 + Cardiac Progenitors from Human ESCs for Myocardial Infarction Therapy. Stem Cell Reports 2021; 16:666-668. [PMID: 33691147 PMCID: PMC7940248 DOI: 10.1016/j.stemcr.2021.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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23
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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24
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Mirzaei M, Gupta VK, Chitranshi N, Deng L, Pushpitha K, Abbasi M, Chick JM, Rajput R, Wu Y, McKay MJ, Salekdeh GH, Gupta VB, Haynes PA, Graham SL. Retinal proteomics of experimental glaucoma model reveal intraocular pressure-induced mediators of neurodegenerative changes. J Cell Biochem 2020; 121:4931-4944. [PMID: 32692886 DOI: 10.1002/jcb.29822] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 12/07/2019] [Revised: 02/27/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Current evidence suggests that exposure to chronically induced intraocular pressure (IOP) leads to neurodegenerative changes in the inner retina. This study aimed to determine retinal proteomic alterations in a rat model of glaucoma and compared findings with human retinal proteomics changes in glaucoma reported previously. We developed an experimental glaucoma rat model by subjecting the rats to increased IOP (9.3 ± 0.1 vs 20.8 ± 1.6 mm Hg) by weekly microbead injections into the eye (8 weeks). The retinal tissues were harvested from control and glaucomatous eyes and protein expression changes analysed using a multiplexed quantitative proteomics approach (TMT-MS3). Immunofluorescence was performed for selected protein markers for data validation. Our study identified 4304 proteins in the rat retinas. Out of these, 139 proteins were downregulated (≤0.83) while the expression of 109 proteins was upregulated (≥1.2-fold change) under glaucoma conditions (P ≤ .05). Computational analysis revealed reduced expression of proteins associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, cytoskeleton, and actin filament organisation, along with increased expression of proteins in coagulation cascade, apoptosis, oxidative stress, and RNA processing. Further functional network analysis highlighted the differential modulation of nuclear receptor signalling, cellular survival, protein synthesis, transport, and cellular assembly pathways. Alterations in crystallin family, glutathione metabolism, and mitochondrial dysfunction associated proteins shared similarities between the animal model of glaucoma and the human disease condition. In contrast, the activation of the classical complement pathway and upregulation of cholesterol transport proteins were exclusive to human glaucoma. These findings provide insights into the neurodegenerative mechanisms that are specifically affected in the retina in response to chronically elevated IOP.
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Affiliation(s)
- Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Vivek K Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
| | - Nitin Chitranshi
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
| | | | - Kanishka Pushpitha
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
| | - Mojdeh Abbasi
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Rashi Rajput
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Ghasem H Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Veer B Gupta
- School of Medicine, Deakin University, Melbourne, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Macquarie University, Sydney, Australia
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25
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Hamzelou S, Kamath KS, Masoomi-Aladizgeh F, Johnsen MM, Atwell BJ, Haynes PA. Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought. Int J Mol Sci 2020; 21:ijms21175980. [PMID: 32825202 PMCID: PMC7504292 DOI: 10.3390/ijms21175980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 06/26/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Matthew M. Johnsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Paul A. Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Correspondence:
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26
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Muralidharan S, Poon YY, Wright GC, Haynes PA, Lee NA. Quantitative proteomics analysis of high and low polyphenol expressing recombinant inbred lines (RILs) of peanut (Arachis hypogaea L.). Food Chem 2020; 334:127517. [PMID: 32711266 DOI: 10.1016/j.foodchem.2020.127517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 06/22/2020] [Accepted: 07/05/2020] [Indexed: 11/28/2022]
Abstract
To facilitate selective breeding of polyphenol-rich peanuts, we looked for mass spectrometry-based proteomic evidence, investigating a subset of recombinant inbred lines (RILs) developed by the Australian peanut breeding program. To do this, we used label-free shotgun proteomics for protein and peptide quantitation, statistically analyzed normalized spectral abundance factors using R-package, as well as assayed important antioxidants. Results revealed statistically significant protein expression changes in 82 proteins classified between high or low polyphenols expressing RILs. Metabolic changes in polyphenol-rich RIL p27-362 point towards increased enzymatic breakdown of sugars and phenylalanine biosynthesis. The study revealed phenylpropanoid pathway overexpression resulting in increased polyphenols biosynthesis. Overexpression of antioxidant enzymes such as catalase, by 73.4 fold was also observed. A strong metabolic correlation exists with the observed phenotypic traits. Peanut RIL p27-362 presents a superior nutritional composition with antioxidant-rich peanut phenotype and could yield commercial profits. Data are available via ProteomeXchange with identifierPXD015493.
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Affiliation(s)
- Sridevi Muralidharan
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Yan Yee Poon
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Graeme C Wright
- Peanut Company of Australia, Kingaroy, Queensland, Australia
| | - Paul A Haynes
- ARC Training Centre for Molecular Technology in the Food Industry, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nanju A Lee
- ARC Training Centre for Advanced Technologies in Food Manufacture, School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia.
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27
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Abstract
We randomly selected 100 journal articles published in five proteomics journals in 2019 and manually examined each of them against a set of 13 criteria concerning the statistical analyses used, all of which were based on items mentioned in the journals' instructions to authors. This included questions such as whether a pilot study was conducted and whether false discovery rate calculation was employed at either the quantitation or identification stage. These data were then transformed to binary inputs, analyzed via machine learning algorithms, and classified accordingly, with the aim of determining if clusters of data existed for specific journals or if certain statistical measures correlated with each other. We applied a variety of classification methods including principal component analysis decomposition, agglomerative clustering, and multinomial and Bernoulli naïve Bayes classification and found that none of these could readily determine journal identity given extracted statistical features. Logistic regression was useful in determining high correlative potential between statistical features such as false discovery rate criteria and multiple testing corrections methods, but was similarly ineffective at determining correlations between statistical features and specific journals. This meta-analysis highlights that there is a very wide variety of approaches being used in statistical analysis of proteomics data, many of which do not conform to published journal guidelines, and that contrary to implicit assumptions in the field there are no clear correlations between statistical methods and specific journals.
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Affiliation(s)
- David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
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28
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2020; 19:e1800105. [PMID: 31218790 DOI: 10.1002/pmic.201800105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
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Affiliation(s)
- Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, P. R. China
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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29
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Deng L, Haynes PA, Wu Y, Amirkhani A, Kamath KS, Wu JX, Pushpitha K, Gupta V, Graham S, Gupta VK, Mirzaei M. Amyloid-beta peptide neurotoxicity in human neuronal cells is associated with modulation of insulin-like growth factor transport, lysosomal machinery and extracellular matrix receptor interactions. Neural Regen Res 2020; 15:2131-2142. [PMID: 32394972 PMCID: PMC7716038 DOI: 10.4103/1673-5374.282261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Indexed: 12/16/2022] Open
Abstract
Extracellular deposits of the amyloid-beta peptide (Aβ) are known as the main pathological hallmark of Alzheimer’s disease. In Alzheimer’s disease, neurons are injured and die throughout the brain, a process in which Aβ neurotoxicity is considered to play an important role. However, the molecular mechanisms underlying Aβ toxicity that lead to neurodegeneration are not clearly established. Here we have elucidated the molecular pathways and networks which are impacted by Aβ in neurons using SH-SY5Y human neuroblastoma cells as a model. These cells were treated with Aβ1–42 peptides to study changes in biochemical networks using tandem mass tag labeled quantitative proteomic technique followed by computational analysis of the data. The molecular impacts of Aβ on cells were evident in a time- and dose-dependent manner, albeit the duration of treatment induced greater differential changes in cellular proteome compared to the effects of concentration. Aβ induced early changes in proteins associated with lysosomes, collagen chain trimerization and extracellular matrix receptor interaction, complement and coagulation cascade, oxidative stress induced senescence, ribosome biogenesis, regulation of insulin-like growth factor transport and uptake by insulin-like growth factor-binding protein. These novel findings provide molecular insights on the effects of Aβ on neurons, with implications for better understanding the impacts of Aβ on early neurodegeneration in Alzheimer’s disease pathology.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Yunqi Wu
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | | | - Jemma X Wu
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | - Kanishka Pushpitha
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Stuart Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Vivek K Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Faculty of Science and Engineering; Australian Proteome Analysis Facility (APAF); Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Front Cover: Plant–Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2019. [DOI: 10.1002/pmic.201970141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Wu Y, Mirzaei M, Pascovici D, Haynes PA, Atwell BJ. Front Cover: Proteomes of Leaf‐Growing Zones in Rice Genotypes with Contrasting Drought Tolerance. Proteomics 2019. [DOI: 10.1002/pmic.201970071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wu Y, Mirzaei M, Pascovici D, Haynes PA, Atwell BJ. Proteomes of Leaf-Growing Zones in Rice Genotypes with Contrasting Drought Tolerance. Proteomics 2019; 19:e1800310. [PMID: 30891909 DOI: 10.1002/pmic.201800310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 02/25/2019] [Indexed: 11/10/2022]
Abstract
Plants require a distinctive cohort of enzymes to coordinate cell division and expansion. Proteomic analysis now enables interrogation of immature leaf bases where these processes occur. Hence, proteins in tissues sampled from leaves of a drought-tolerant rice (IAC1131) are investigated to provide insights into the effect of soil drying on gene expression relative to the drought-sensitive genotype Nipponbare. Shoot growth zones are dissected to estimate the proportion of dividing cells and extract protein for subsequent tandem mass tags quantitative proteomic analysis. Gene ontology annotations of differentially expressed proteins provide insights into responses of Nipponbare and IAC1131 to drought. Soil drying does not affect the percentage of mitotic cells in IAC1131. More than 800 proteins across most functional categories increase in drought (and decrease on rewatering) in IAC1131, including proteins involved in "organizing the meristem" and "new cell formation". On the other hand, the percentage of dividing cells in Nipponbare is severely impaired during drought and fewer than 200 proteins respond in abundance when growing zones undergo a drying cycle. Remarkably, the proteomes of the growing zones of each genotype respond in a highly distinctive manner, reflecting their contrasting drought tolerance even at the earliest stages of leaf development.
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Affiliation(s)
- Yunqi Wu
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
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Deng L, Pushpitha K, Joseph C, Gupta V, Rajput R, Chitranshi N, Dheer Y, Amirkhani A, Kamath K, Pascovici D, Wu JX, Salekdeh GH, Haynes PA, Graham SL, Gupta VK, Mirzaei M. Amyloid β Induces Early Changes in the Ribosomal Machinery, Cytoskeletal Organization and Oxidative Phosphorylation in Retinal Photoreceptor Cells. Front Mol Neurosci 2019; 12:24. [PMID: 30853886 PMCID: PMC6395395 DOI: 10.3389/fnmol.2019.00024] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 01/21/2019] [Indexed: 01/20/2023] Open
Abstract
Amyloid β (Aβ) accumulation and its aggregation is characteristic molecular feature of the development of Alzheimer's disease (AD). More recently, Aβ has been suggested to be associated with retinal pathology associated with AD, glaucoma and drusen deposits in age related macular degeneration (AMD). In this study, we investigated the proteins and biochemical networks that are affected by Aβ in the 661 W photoreceptor cells in culture. Time and dose dependent effects of Aβ on the photoreceptor cells were determined utilizing tandem mass tag (TMT) labeling-based quantitative mass-spectrometric approach. Bioinformatic analysis of the data revealed concentration and time dependent effects of the Aβ peptide stimulation on various key biochemical pathways that might be involved in mediating the toxicity effects of the peptide. We identified increased Tau phosphorylation, GSK3β dysregulation and reduced cell viability in cells treated with Aβ in a dose and time dependent manner. This study has delineated for the first-time molecular networks in photoreceptor cells that are impacted early upon Aβ treatment and contrasted the findings with a longer-term treatment effect. Proteins associated with ribosomal machinery homeostasis, mitochondrial function and cytoskeletal organization were affected in the initial stages of Aβ exposure, which may provide key insights into AD effects on the photoreceptors and specific molecular changes induced by Aβ peptide.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Kanishka Pushpitha
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Chitra Joseph
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Waurn Ponds, VIC, Australia
| | - Rashi Rajput
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nitin Chitranshi
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Yogita Dheer
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ardeshir Amirkhani
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | - Karthik Kamath
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | - Dana Pascovici
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | - Jemma X. Wu
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Paul A. Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Stuart L. Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Vivek K. Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, NSW, Australia
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Mirzaei M, Pushpitha K, Deng L, Chitranshi N, Gupta V, Rajput R, Mangani AB, Dheer Y, Godinez A, McKay MJ, Kamath K, Pascovici D, Wu JX, Salekdeh GH, Karl T, Haynes PA, Graham SL, Gupta VK. Upregulation of Proteolytic Pathways and Altered Protein Biosynthesis Underlie Retinal Pathology in a Mouse Model of Alzheimer's Disease. Mol Neurobiol 2019; 56:6017-6034. [PMID: 30707393 DOI: 10.1007/s12035-019-1479-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022]
Abstract
Increased amyloid β (Aβ) aggregation is a hallmark feature of Alzheimer's disease (AD) pathology. The APP/PS1 mouse model of AD exhibits accumulation of Aβ in the retina and demonstrates reduced retinal function and other degenerative changes. The overall molecular effects of AD pathology on the retina remain undetermined. Using a proteomics approach, this study assessed the molecular effects of Aβ accumulation and progression of AD pathology on the retina. Retinal tissues from younger (2.5 months) and older 8-month APP/PS1 mice were analysed for protein expression changes. A multiplexed proteomics approach using chemical isobaric tandem mass tags was applied followed by functional and protein-protein interaction analyses using Ingenuity pathway (IPA) and STRING computational tools. We identified approximately 2000 proteins each in the younger (upregulated 50; downregulated 36) and older set of APP/PS1 (upregulated 85; downregulated 79) mice retinas. Amyloid precursor protein (APP) was consistently upregulated two to threefold in both younger and older retinas (p < 0.0001). Mass spectrometry data further revealed that older APP/PS1 mice retinas had elevated levels of proteolytic enzymes cathepsin D, presenilin 2 and nicastrin that are associated with APP processing. Increased levels of proteasomal proteins Psma5, Psmd3 and Psmb2 were also observed in the older AD retinas. In contrast to the younger animals, significant downregulation of protein synthesis and elongation associated proteins such as Eef1a1, Rpl35a, Mrpl2 and Eef1e1 (p < 0.04) was identified in the older mice retinas. This study reports for the first time that not only old but also young APP/PS1 animals demonstrate increased amyloid protein levels in their retinas. Quantitative proteomics reveals new molecular insights which may represent a cellular response to clear amyloid build-up. Further, downregulation of ribosomal proteins involved in protein biosynthesis was observed which might be considered a toxicity effect.
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Affiliation(s)
- Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia. .,Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia.
| | - Kanishka Pushpitha
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Liting Deng
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nitin Chitranshi
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, Melbourne, VIC, Australia
| | - Rashi Rajput
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Abu Bakr Mangani
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Yogita Dheer
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Angela Godinez
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Department of Molecular Systems Biology, Cell Science Research Center, Royan, Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Tim Karl
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Stuart L Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Vivek K Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.
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Maher T, Mirzaei M, Pascovici D, Wright IJ, Haynes PA, Gallagher RV. Evidence from the proteome for local adaptation to extreme heat in a widespread tree species. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Timothy Maher
- Department of Biological Sciences Macquarie University North Ryde New South Wales Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences Macquarie University North Ryde New South Wales Australia
- Australian Proteome Analysis Facility Macquarie University North Ryde New South Wales Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility Macquarie University North Ryde New South Wales Australia
| | - Ian J. Wright
- Department of Biological Sciences Macquarie University North Ryde New South Wales Australia
| | - Paul A. Haynes
- Department of Molecular Sciences Macquarie University North Ryde New South Wales Australia
| | - Rachael V. Gallagher
- Department of Biological Sciences Macquarie University North Ryde New South Wales Australia
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36
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Wu Y, Mirzaei M, Atwell BJ, Haynes PA. Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery. Data Brief 2019; 22:697-702. [PMID: 30656201 PMCID: PMC6329202 DOI: 10.1016/j.dib.2018.12.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 11/28/2018] [Accepted: 12/12/2018] [Indexed: 12/03/2022] Open
Abstract
Two rice cultivars, IAC1131 (drought tolerant) and Nipponbare (drought sensitive), with contrasting genetic backgrounds and levels of tolerance to drought, were analysed using both label-free and tandem mass tags (TMTs) quantitative proteomics approaches, aiming to elucidate the mechanisms of drought tolerance. Four-week-old seedlings of both cultivars were grown in large soil volumes in the glasshouse under controlled conditions and then exposed to moderate and extreme drought for 7 days, followed by 3 days of re-watering period. Mature leaves were harvested from plants of each treatment for protein extraction and subsequent complementary shotgun proteomic analyses. The data from this study are related to the research article “Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease” (Wu et al., 2016) [1].
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Affiliation(s)
- Yunqi Wu
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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37
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Rahiminejad M, Ledari MT, Mirzaei M, Ghorbanzadeh Z, Kavousi K, Ghaffari MR, Haynes PA, Komatsu S, Salekdeh GH. The Quest for Missing Proteins in Rice. Mol Plant 2019; 12:4-6. [PMID: 30543994 DOI: 10.1016/j.molp.2018.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Mohsen Rahiminejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREO), Karaj, Iran; Department of Biotechnology, University of Tehran, Tehran, Iran
| | | | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREO), Karaj, Iran
| | - Kaveh Kavousi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREO), Karaj, Iran
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Setsuko Komatsu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREO), Karaj, Iran; Department of Molecular Sciences, Macquarie University, Sydney, Australia.
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38
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Emery SJ, Baker L, Ansell BRE, Mirzaei M, Haynes PA, McConville MJ, Svärd SG, Jex AR. Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis. Gigascience 2018; 7:4931738. [PMID: 29688452 PMCID: PMC5913674 DOI: 10.1093/gigascience/giy024] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/06/2018] [Indexed: 01/20/2023] Open
Abstract
Background Metronidazole (Mtz) is the frontline drug treatment for multiple anaerobic pathogens, including the gastrointestinal protist, Giardia duodenalis. However, treatment failure is common and linked to in vivo drug resistance. In Giardia, in vitro drug-resistant lines allow controlled experimental interrogation of resistance mechanisms in isogenic cultures. However, resistance-associated changes are inconsistent between lines, phenotypic data are incomplete, and resistance is rarely genetically fixed, highlighted by reversion to sensitivity after drug selection ceases or via passage through the life cycle. Comprehensive quantitative approaches are required to resolve isolate variability, fully define Mtz resistance phenotypes, and explore the role of post-translational modifications therein. Findings We performed quantitative proteomics to describe differentially expressed proteins in 3 seminal Mtz-resistant lines compared to their isogenic, Mtz-susceptible, parental line. We also probed changes in post-translational modifications including protein acetylation, methylation, ubiquitination, and phosphorylation via immunoblotting. We quantified more than 1,000 proteins in each genotype, recording substantial genotypic variation in differentially expressed proteins between isotypes. Our data confirm substantial changes in the antioxidant network, glycolysis, and electron transport and indicate links between protein acetylation and Mtz resistance, including cross-resistance to deacetylase inhibitor trichostatin A in Mtz-resistant lines. Finally, we performed the first controlled, longitudinal study of Mtz resistance stability, monitoring lines after cessation of drug selection, revealing isolate-dependent phenotypic plasticity. Conclusions Our data demonstrate understanding that Mtz resistance must be broadened to post-transcriptional and post-translational responses and that Mtz resistance is polygenic, driven by isolate-dependent variation, and is correlated with changes in protein acetylation networks.
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Affiliation(s)
- Samantha J Emery
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Louise Baker
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Mehdi Mirzaei
- Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW, Australia
| | - Paul A Haynes
- Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Malcom J McConville
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Aaron R Jex
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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Handler DC, Pascovici D, Mirzaei M, Gupta V, Salekdeh GH, Haynes PA. The Art of Validating Quantitative Proteomics Data. Proteomics 2018; 18:e1800222. [DOI: 10.1002/pmic.201800222] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/28/2018] [Indexed: 12/13/2022]
Affiliation(s)
- David C. Handler
- Department of Molecular Sciences; Macquarie University; Sydney NSW 2109 Australia
| | - Dana Pascovici
- Department of Molecular Sciences; Macquarie University; Sydney NSW 2109 Australia
- Australian Proteome Analysis Facility; Macquarie University; Sydney NSW 2109 Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences; Macquarie University; Sydney NSW 2109 Australia
- Australian Proteome Analysis Facility; Macquarie University; Sydney NSW 2109 Australia
| | - Vivek Gupta
- Faculty of Medicine and Health Sciences; Macquarie University; Sydney NSW 2109 Australia
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences; Macquarie University; Sydney NSW 2109 Australia
- Department of Molecular Systems Biology; Cell Science Research Center Royan Institute for Stem Cell Biology and Technology; ACECR; Tehran Iran
| | - Paul A. Haynes
- Department of Molecular Sciences; Macquarie University; Sydney NSW 2109 Australia
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40
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Shekari F, Han CL, Lee J, Mirzaei M, Gupta V, Haynes PA, Lee B, Baharvand H, Chen YJ, Hosseini Salekdeh G. Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reports. Expert Rev Proteomics 2018; 15:911-922. [PMID: 30358457 DOI: 10.1080/14789450.2018.1539669] [Citation(s) in RCA: 6] [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] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Human embryonic stem cells (hESCs) have unique biological features and attributes that make them attractive in various areas of biomedical research. With heightened applications, there is an ever increasing need for advancement of proteome analysis. Membrane proteins are one of the most important subset of hESC proteins as they can be used as surface markers. Areas covered: This review discusses commonly used surface markers of hESCs, and provides in-depth analysis of available hESC membrane proteome reports and the existence of these markers in many other cell types, especially cancer cells. Appreciating, existing ambiguity in the definition of a membrane protein, we have attempted a meta analysis of the published membrane protein reports of hESCs by using a combination of protein databases and prediction tools to find the most confident plasma membrane proteins in hESCs. Furthermore, responsiveness of plasma membrane proteins to differentiation has been discussed based on available transcriptome profiling data bank. Expert commentary: Combined transcriptome and membrane proteome analysis highlighted additional proteins that may eventually find utility as new cell surface markers.
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Affiliation(s)
- Faezeh Shekari
- a Department of Molecular Systems Biology at Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran , Iran.,b Department of Developmental Biology , University of Science and Culture, ACECR , Tehran , Iran
| | - Chia-Li Han
- c Chemical Biology and Molecular Biophysics Program , Institute of Chemistry , Taipei , Taiwan , Republic of China
| | - Jaesuk Lee
- d Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute , Gachon University , Incheon , Republic of Korea
| | - Mehdi Mirzaei
- e Department of Molecular Sciences , Macquarie University , Sydney , NSW , Australia.,f Australian Proteome Analysis Facility , Macquarie University , Sydney , NSW , Australia.,g Department of Clinical Medicine , Macquarie University , Sydney , NSW , Australia
| | - Vivek Gupta
- g Department of Clinical Medicine , Macquarie University , Sydney , NSW , Australia
| | - Paul A Haynes
- e Department of Molecular Sciences , Macquarie University , Sydney , NSW , Australia
| | - Bonghee Lee
- d Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute , Gachon University , Incheon , Republic of Korea
| | - Hossein Baharvand
- b Department of Developmental Biology , University of Science and Culture, ACECR , Tehran , Iran.,h Department of Stem Cells and Developmental Biology at Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran , Iran
| | - Yu-Ju Chen
- c Chemical Biology and Molecular Biophysics Program , Institute of Chemistry , Taipei , Taiwan , Republic of China
| | - Ghasem Hosseini Salekdeh
- a Department of Molecular Systems Biology at Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran , Iran.,e Department of Molecular Sciences , Macquarie University , Sydney , NSW , Australia.,i Department of Systems and Synthetic biology , Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization , Karaj , Iran
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41
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Fathi A, Mirzaei M, Dolatyar B, Sharifitabar M, Bayat M, Shahbazi E, Lee J, Javan M, Zhang SC, Gupta V, Lee B, Haynes PA, Baharvand H, Salekdeh GH. Discovery of Novel Cell Surface Markers for Purification of Embryonic Dopamine Progenitors for Transplantation in Parkinson's Disease Animal Models. Mol Cell Proteomics 2018; 17:1670-1684. [PMID: 29848781 PMCID: PMC6126395 DOI: 10.1074/mcp.ra118.000809] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 04/21/2018] [Revised: 05/20/2018] [Indexed: 12/30/2022] Open
Abstract
Despite the progress in safety and efficacy of cell replacement therapy with pluripotent stem cells (PSCs), the presence of residual undifferentiated stem cells or proliferating neural progenitor cells with rostral identity remains a major challenge. Here we report the generation of a LIM homeobox transcription factor 1 alpha (LMX1A) knock-in GFP reporter human embryonic stem cell (hESC) line that marks the early dopaminergic progenitors during neural differentiation to find reliable membrane protein markers for isolation of midbrain dopaminergic neurons. Purified GFP positive cells in vitro exhibited expression of mRNA and proteins that characterized and matched the midbrain dopaminergic identity. Further quantitative proteomics analysis of enriched LMX1A+ cells identified several membrane-associated proteins including a polysialylated embryonic form of neural cell adhesion molecule (PSA-NCAM) and contactin 2 (CNTN2), enabling prospective isolation of LMX1A+ progenitor cells. Transplantation of human-PSC-derived purified CNTN2+ progenitors enhanced dopamine release from transplanted cells in the host brain and alleviated Parkinson's disease-related phenotypes in animal models. This study establishes an efficient approach for purification of large numbers of human-PSC-derived dopaminergic progenitors for therapeutic applications.
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Affiliation(s)
- Ali Fathi
- From the ‡Department of Molecular Systems Biology
- ¶Department of Developmental Biology, University of Science and Culture, Tehran, Iran
- ‖Waisman Center
| | - Mehdi Mirzaei
- ‡‡Department of Molecular Sciences
- §§Australian Proteome Analysis Facility
- ¶¶Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Banafsheh Dolatyar
- ¶Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | | | - Mahnaz Bayat
- ‖‖Center for Regenerative Medicine, Gachon University Medical School, Incheon, Korea
| | - Ebrahim Shahbazi
- From the ‡Department of Molecular Systems Biology
- ¶Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Jaesuk Lee
- ‖‖Center for Regenerative Medicine, Gachon University Medical School, Incheon, Korea
| | - Mohammad Javan
- §Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- ***Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Su-Chun Zhang
- ‖Waisman Center
- **Departments of Neuroscience and Neurology, University of Wisconsin, 1500 Highland Avenue, Madison, WI 53705
| | - Vivek Gupta
- ¶¶Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Bonghee Lee
- ‖‖Center for Regenerative Medicine, Gachon University Medical School, Incheon, Korea
| | | | - Hossein Baharvand
- ¶Department of Developmental Biology, University of Science and Culture, Tehran, Iran;
- §Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- From the ‡Department of Molecular Systems Biology,
- ‡‡Department of Molecular Sciences
- ‡‡‡Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization, Karaj, Iran
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42
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Ghazizadeh Z, Fattahi F, Mirzaei M, Bayersaikhan D, Lee J, Chae S, Hwang D, Byun K, Tabar MS, Taleahmad S, Mirshahvaladi S, Shabani P, Fonoudi H, Haynes PA, Baharvand H, Aghdami N, Evans T, Lee B, Salekdeh GH. Prospective Isolation of ISL1 + Cardiac Progenitors from Human ESCs for Myocardial Infarction Therapy. Stem Cell Reports 2018; 10:848-859. [PMID: 29503094 PMCID: PMC5918615 DOI: 10.1016/j.stemcr.2018.01.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 01/28/2023] Open
Abstract
The LIM-homeodomain transcription factor ISL1 marks multipotent cardiac progenitors that give rise to cardiac muscle, endothelium, and smooth muscle cells. ISL1+ progenitors can be derived from human pluripotent stem cells, but the inability to efficiently isolate pure populations has limited their characterization. Using a genetic selection strategy, we were able to highly enrich ISL1+ cells derived from human embryonic stem cells. Comparative quantitative proteomic analysis of enriched ISL1+ cells identified ALCAM (CD166) as a surface marker that enabled the isolation of ISL1+ progenitor cells. ALCAM+/ISL1+ progenitors are multipotent and differentiate into cardiomyocytes, endothelial cells, and smooth muscle cells. Transplantation of ALCAM+ progenitors enhances tissue recovery, restores cardiac function, and improves angiogenesis through activation of AKT-MAPK signaling in a rat model of myocardial infarction, based on cardiac MRI and histology. Our study establishes an efficient method for scalable purification of human ISL1+ cardiac precursor cells for therapeutic applications.
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Affiliation(s)
- Zaniar Ghazizadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Faranak Fattahi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia; Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Delger Bayersaikhan
- Center for Regenerative Medicine, Gachon University, Incheon City, Republic of Korea
| | - Jaesuk Lee
- Center for Regenerative Medicine, Gachon University, Incheon City, Republic of Korea
| | - Sehyun Chae
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Daehee Hwang
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Kyunghee Byun
- Center for Regenerative Medicine, Gachon University, Incheon City, Republic of Korea
| | - Mehdi Sharifi Tabar
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran, Iran
| | - Sara Taleahmad
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran, Iran
| | - Shahab Mirshahvaladi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran, Iran
| | - Parisa Shabani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hananeh Fonoudi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Regenerative Biomedicine at Cell Science Research, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Bonghee Lee
- Center for Regenerative Medicine, Gachon University, Incheon City, Republic of Korea.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran, Iran; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
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43
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Mirzaei M, Gupta VB, Chick JM, Greco TM, Wu Y, Chitranshi N, Wall RV, Hone E, Deng L, Dheer Y, Abbasi M, Rezaeian M, Braidy N, You Y, Salekdeh GH, Haynes PA, Molloy MP, Martins R, Cristea IM, Gygi SP, Graham SL, Gupta VK. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Sci Rep 2017; 7:12685. [PMID: 28978942 PMCID: PMC5627288 DOI: 10.1038/s41598-017-12858-7] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/14/2017] [Indexed: 12/05/2022] Open
Abstract
Glaucoma is a chronic disease that shares many similarities with other neurodegenerative disorders of the central nervous system. This study was designed to evaluate the association between glaucoma and other neurodegenerative disorders by investigating glaucoma-associated protein changes in the retina and vitreous humour. The multiplexed Tandem Mass Tag based proteomics (TMT-MS3) was carried out on retinal tissue and vitreous humour fluid collected from glaucoma patients and age-matched controls followed by functional pathway and protein network interaction analysis. About 5000 proteins were quantified from retinal tissue and vitreous fluid of glaucoma and control eyes. Of the differentially regulated proteins, 122 were found linked with pathophysiology of Alzheimer’s disease (AD). Pathway analyses of differentially regulated proteins indicate defects in mitochondrial oxidative phosphorylation machinery. The classical complement pathway associated proteins were activated in the glaucoma samples suggesting an innate inflammatory response. The majority of common differentially regulated proteins in both tissues were members of functional protein networks associated brain changes in AD and other chronic degenerative conditions. Identification of previously reported and novel pathways in glaucoma that overlap with other CNS neurodegenerative disorders promises to provide renewed understanding of the aetiology and pathogenesis of age related neurodegenerative diseases.
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Affiliation(s)
- Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia. .,Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia.
| | - Veer B Gupta
- School of Medical Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Yunqi Wu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nitin Chitranshi
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Roshana Vander Wall
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Eugene Hone
- School of Medical Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Liting Deng
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Yogita Dheer
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mojdeh Abbasi
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mahdie Rezaeian
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Yuyi You
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Save Sight Institute, Sydney University, Sydney, NSW, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan, Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark P Molloy
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Ralph Martins
- School of Medical Sciences, Edith Cowan University, Joondalup, WA, Australia.,Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart L Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Save Sight Institute, Sydney University, Sydney, NSW, Australia
| | - Vivek K Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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44
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Pascovici D, Handler DCL, Wu JX, Haynes PA. Multiple testing corrections in quantitative proteomics: A useful but blunt tool. Proteomics 2017; 16:2448-53. [PMID: 27461997 DOI: 10.1002/pmic.201600044] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [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: 01/28/2016] [Revised: 07/12/2016] [Accepted: 07/21/2016] [Indexed: 11/08/2022]
Abstract
Multiple testing corrections are a useful tool for restricting the FDR, but can be blunt in the context of low power, as we demonstrate by a series of simple simulations. Unfortunately, in proteomics experiments low power can be common, driven by proteomics-specific issues like small effects due to ratio compression, and few replicates due to reagent high cost, instrument time availability and other issues; in such situations, most multiple testing corrections methods, if used with conventional thresholds, will fail to detect any true positives even when many exist. In this low power, medium scale situation, other methods such as effect size considerations or peptide-level calculations may be a more effective option, even if they do not offer the same theoretical guarantee of a low FDR. Thus, we aim to highlight in this article that proteomics presents some specific challenges to the standard multiple testing corrections methods, which should be employed as a useful tool but not be regarded as a required rubber stamp.
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Affiliation(s)
- Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - David C L Handler
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Jemma X Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
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45
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Taleahmad S, Mirzaei M, Samadian A, Hassani SN, Haynes PA, Salekdeh GH, Baharvand H. Low Focal Adhesion Signaling Promotes Ground State Pluripotency of Mouse Embryonic Stem Cells. J Proteome Res 2017; 16:3585-3595. [DOI: 10.1021/acs.jproteome.7b00322] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | | | | | | | - Ghasem Hosseini Salekdeh
- Department
of Systems Biology, Agricultural Biotechnology, Research Institute of Iran, Karaj, Iran
| | - Hossein Baharvand
- Department
of Developmental Biology, University of Science and Culture, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
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46
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Alikhani M, Mirzaei M, Sabbaghian M, Parsamatin P, Karamzadeh R, Adib S, Sodeifi N, Gilani MAS, Zabet-Moghaddam M, Parker L, Wu Y, Gupta V, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia. J Proteomics 2017; 162:141-154. [DOI: 10.1016/j.jprot.2017.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 01/22/2017] [Accepted: 02/13/2017] [Indexed: 12/17/2022]
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47
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Tacchi JL, Raymond BBA, Haynes PA, Berry IJ, Widjaja M, Bogema DR, Woolley LK, Jenkins C, Minion FC, Padula MP, Djordjevic SP. Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae. Open Biol 2016; 6:150210. [PMID: 26865024 PMCID: PMC4772806 DOI: 10.1098/rsob.150210] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [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: 11/20/2022] Open
Abstract
Mycoplasma hyopneumoniae is a genome-reduced, cell wall-less, bacterial pathogen with a predicted coding capacity of less than 700 proteins and is one of the smallest self-replicating pathogens. The cell surface of M. hyopneumoniae is extensively modified by processing events that target the P97 and P102 adhesin families. Here, we present analyses of the proteome of M. hyopneumoniae-type strain J using protein-centric approaches (one- and two-dimensional GeLC–MS/MS) that enabled us to focus on global processing events in this species. While these approaches only identified 52% of the predicted proteome (347 proteins), our analyses identified 35 surface-associated proteins with widely divergent functions that were targets of unusual endoproteolytic processing events, including cell adhesins, lipoproteins and proteins with canonical functions in the cytosol that moonlight on the cell surface. Affinity chromatography assays that separately used heparin, fibronectin, actin and host epithelial cell surface proteins as bait recovered cleavage products derived from these processed proteins, suggesting these fragments interact directly with the bait proteins and display previously unrecognized adhesive functions. We hypothesize that protein processing is underestimated as a post-translational modification in genome-reduced bacteria and prokaryotes more broadly, and represents an important mechanism for creating cell surface protein diversity.
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Affiliation(s)
- Jessica L Tacchi
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | - Benjamin B A Raymond
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, New South Wales 2109, Australia
| | - Iain J Berry
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | - Michael Widjaja
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | - Daniel R Bogema
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Lauren K Woolley
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - F Chris Minion
- Department of Veterinary Microbiology and Preventative Medicine, Iowa State University, Ames, IA 50011, USA
| | - Matthew P Padula
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
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48
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Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim DS, Shin DH, Bianucci R, Haynes PA. Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response. Philos Trans A Math Phys Eng Sci 2016; 374:rsta.2015.0373. [PMID: 27644972 PMCID: PMC5031639 DOI: 10.1098/rsta.2015.0373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 05/18/2023]
Abstract
We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jana Jones
- Department of Ancient History, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Prathiba Ravishankar
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Dylan Xavier
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Do Seon Lim
- Department of Dental Hygiene, College of Health Sciences, Eulji University, Sungnam, South Korea
| | - Dong Hoon Shin
- Department of Anatomy, Seoul National University, College of Medicine, Seoul, South Korea
| | - Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Legal Medicine Section, University of Turin, 10126 Turin, Italy UMR 7268, Laboratoire d'Anthropologie bio-culturelle, Droit, Étique and Santé (ADÉS), Faculté de Médecine de Marseille, 13344 Marseille, France
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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49
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Raftos DA, Melwani AR, Haynes PA, Muralidharan S, Birch GF, Amaral V, Thompson EL, Taylor DA. Correction: The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata). Environ Sci Process Impacts 2016; 18:1359. [PMID: 27711878 DOI: 10.1039/c6em90036d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Correction for 'The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata)' by D. A. Raftos et al., Environ. Sci.: Processes Impacts, 2016, 18, 1129-1139.
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Affiliation(s)
- D A Raftos
- Department of Biological Sciences, Macquarie University, Sydney Institute of Marine Science, North Ryde, 2109, NSW, Australia.
| | - A R Melwani
- Department of Biological Sciences, Macquarie University, Sydney Institute of Marine Science, North Ryde, 2109, NSW, Australia.
| | - P A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, 2109, NSW, Australia
| | - S Muralidharan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, 2109, NSW, Australia
| | - G F Birch
- School of Geosciences, University of Sydney, NSW 2006, Australia
| | - V Amaral
- Department of Biological Sciences, Macquarie University, Sydney Institute of Marine Science, North Ryde, 2109, NSW, Australia. and MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, PT-1749-016 Lisboa, Portugal
| | - E L Thompson
- Department of Biological Sciences, Macquarie University, Sydney Institute of Marine Science, North Ryde, 2109, NSW, Australia.
| | - D A Taylor
- Department of Biological Sciences, Macquarie University, Sydney Institute of Marine Science, North Ryde, 2109, NSW, Australia.
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50
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