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Riaz, Tahira
(2023).
Comparative proteomics explain the mechanism of action of mycobacterial tolerance inhibitors.
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Riaz, Tahira
(2022).
Fighting Antimicrobial Resistance – Education, Surveillance, Innovative therapeutics, Basic and Clinical research.
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Riaz, Tahira
(2022).
Genome Dynamics in Infection Biology and Precision Medicine - The AMR paradigm: TB as a model example.
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Riaz, Tahira
(2022).
Development of novel Mycobacterial Tolerance Inhibitors (MTIs) against MDR/XDR tuberculosis.
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Riaz, Tahira
(2021).
JPIAMR Capacity Building Ideathon - Rapporteur.
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Riaz, Tahira
(2021).
Development of novel Mycobacterial Tolerance Inhibitors (MTIs) against MDR/XDR tuberculosis.
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Kaniusaite, Milda; Riaz, Tahira; Lillenes, Meryl Sønderby; Detlie, Trond Espen; Alfredo, Rabano & Tonjum, Tone
(2020).
On the Brain-Gut axis: The gut microbiome affects the differential expression of DNA repair pathways in the human brain and mucosal gut tissue.
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Riaz, Tahira
(2020).
Novel Mycobacterial Tolerance Inhibitors (MTIs) Against Multidrug-Resistant Tuberculosis.
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Riaz, Tahira & Muñoz, Marta Gómez
(2020).
Genome dynamics in health and disease: Focus on AMR, TB and COVID-19.
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Riaz, Tahira & Tonjum, Tone
(2020).
Resistance mechanisms and novel drug targets.
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Riaz, Tahira
(2019).
Proteomics studies to combat Tuberculosis.
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Riaz, Tahira
(2019).
Proteome characterization of Mycobacterium tuberculosis.
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Lillenes, Meryl Sønderby; Riaz, Tahira; Støen, Mari; Kalayou, Shewit; Rabano, Alberto & Tonjum, Tone
(2019).
Proteomic Analysis of Brain Tissue from Patients with Alzheimer’s disease and Healthy Controls Reveals Differential Expression of Proteins Involved in Mitochondrial Dysfunction between Brain Domains.
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Tonjum, Tone; Birhanu, Alemayehu Godana; Riaz, Tahira & Yimer, Solomon Abebe
(2019).
Abundance of post-translational modifications in Mycobacterium tuberculosis.
Show summary
Background
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide and the leading cause of death from infectious disease. Despite the discovery of a multitude of Mtb strains with a high degree of genetic conservation, only a few sub-groups cause extensive outbreaks and antimicrobial drug resistance (AMR), with different clinical presentations in terms of transmissibility, virulence and elicited immune responses.
Various regulatory mechanisms contribute to the complexity of the simpler genomes and proteomes of Mtb, and post-translational modifications (PTMs) play a significant role in this variability. PTMs allow bacteria to rapidly alter protein activity in response to host factors and have been implicated in Mtb virulence and AMR. Our aim is to characterize the global acetylome and glycoproteomic profile of different Mtb lineages, to unveil the role of these PTMs in mycobacterial adaptation, survival and AMR.
Materials/methods
The global acetylome and glycoproteomic patterns in five Mtb strains, four clinical isolates including the slow-growing lineage 7 and the reference strain H37Rv, were analyzed. Mtb cell lysates were subjected to in-gel trypsin digestion and injected into a Nano LC-MS/MS mass spectrometer (Thermo Scientific). The MaxQuant and Perseus softwares were used peptide search and PTM site identification. Poteins were searched for 57 different glycan residues. The findings on N-linked protein glycosylation were verified by manual inspection. The Cytoscape plug-in MCODE was used to develop protein-protein interaction networks.
Results
Our analysis resulted in the identification of 2944 glycosylation sites on 1325 proteins and 2490 acetylation sites on 953 proteins. Notably, we report 489 sites that were N-glycosylated at N residues (17% of the total glycosylation events). The study identified strain-specific qualitative and quantitative differences in PTM abundances on proteins involved in virulence, pathogenesis and AMR.
Conclusions
Notably, this study reports a vast abundance of PTMs in clinical Mtb strains and is the first report on N-linked glycosylation and O-acetylation in Mtb. These novel PTM data also explain the role of protein acetylation and glycosylation in creating phenotypic variability and fitness for survival among the genetically conserved lineages of Mtb.
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Riaz, Tahira
(2018).
Proteomics of selected microbes and man.
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Yimer, Solomon Abebe; Birhanu, Alemayehu Godana; Shewit, Kalayou; Riaz, Tahira; Zegeye, Ephrem Debebe & Beyene, Getachew Tesfaye
[Show all 11 contributors for this article]
(2016).
First proteomic analysis of Mycobacterium tuberculosis lineage 7 differentially expressed proteins involved for growth.
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Tonjum, Tone; Riaz, Tahira; Lillenes, Meryl Sønderby; Detlie, Trond Espen & Jensen, Helge Leander B.
(2016).
The Brain-Gut axis:
Differential expression of DNA repair in human brain and mucosal gut tissue
.
Show summary
The biology of the neurological and gastrointestinal systems are tightly interconnected, interacting with and influencing each other through multiple bidirectional signaling pathways. The human microbiome strongly influences the physiology of all organs including the central nervous system (CNS), and the CNS in turn modulates gut function, beyond the effects of the vagal nerve. Therefore, imbalance in the brain-gut axis could correlate with incipient pathology in the CNS and/or the gastrointestinal tract. We asked if and how the gut microbiome modulates susceptibility to progressive neurodegenerative Alzheimer’s disease (AD). The primary hypothesis we are testing is that imbalance in the brain-gut axis promotes neurodegeneration or gastrointestinal dysfunction, or both.
The proteomic expression profile was tested in post-mortem human brain tissue and gut mucosal biopsies. In terms of DNA repair, predominant base excision repair (BER) was expressed in brain tissue, while nucleotide excision repair (NER) was more highly expressed in the gut mucosa. This differential expression pattern reflects local stress and organ environments, both the nature of non-replicating versus replicating cells as well as the state of a sterile organ versus that of an organ with a rich microbiome. Different DNA repair responses were evident in the prodromal versus late stages of AD and in IBD. We have previously shown that signature reactions in BER patterns in brain appear before AD pathology is evident and may represent a response to increased oxidative stress. These studies extend our findings on DNA repair and bioenergetics in AD and IBD, and will also address the contribution of the gut microbiome.
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Birhanu, Alemayehu Godana; Yimer, Solomon Abebe; Riaz, Tahira & Tonjum, Tone
(2016).
Proteomic Analysis of Mycobacterium tuberculosis Membrane Vesicles.
Show summary
Secreted membrane vesicles (MVs) are abundant in Mycobacterium tuberculosis (Mtb) and are suggested to have important roles in mycobacterial physiology and pathogenesis. MVs may contain varied cargo, including nucleic acids, toxins, lipoproteins and enzymes. In particular, MVs have been shown to serve as a vehicle for the selective packaging and release of virulence factors, such as toxins and immunomodulatory molecules. However, how and why MVs escape the thick cell walls of mycobacteria is still unknown.
The aim of this project is characterize the proteomic profile of MVs from selected Mtb lineages and to unveil the role of MVs in mycobacterial adaptation to environmental factors.
Mtb cells were cultured with and without oxidative and nitrosative stress. The Mtb cell free culture supernatant was used as a source to isolate enriched MVs by density gradient ultra-centrifugation. The purified membrane vesicles were investigated by mass spectrometry. The MaxQuant and Perseus softwares were used for peptide search, data analysis and quality control, respectively. The functional categories of the proteins identified were grouped using the KEGG pathway database.
The mass spectrometry proteomic data revealed that MVs contain enriched packaging of virulence associated mycobacterial proteins. A total of 83 proteins were identified in Mtb MVs, out of which 69 were shared with the cellular proteome and 14 were found exclusively in MVs. The majority of the MV-specific components detected were secreted proteins which are reported to be major virulence factors (antigen-85 complexes, ESAT-6 and PE/PPE, etc). Based on the KEGG pathway functional analysis, the identified proteins were found to be involved in two-component systems, ABC transporters, amino acid and fatty acid metabolism, as well as catalytic and hydrolase activity and hypothetical proteins.
Thereby, this study generated new knowledge on the proteomic profile of Mtb MVs. We have characterized Mtb membrane vesicles, which are enriched with surface/secreted antigenic proteins and virulence factors. Further in silico and in vitro/in-vivo studies are required to investigate the adaptive and clinical relevance of the MV proteins identified, including the newly discovered un-characterized proteins.
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Birhanu, Alemayehu Godana; Yimer, Solomon Abebe; Riaz, Tahira & Tonjum, Tone
(2016).
Proteomic Analysis of Mycobacterium tuberculosis Membrane Vesicles.
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Birhanu, Alemayehu Godana; Yimer, Solomon Abebe; Riaz, Tahira & Tonjum, Tone
(2016).
Proteomic Analysis of Mycobacterium tuberculosis Membrane Vesicles.
Show summary
Studies in the last decades have demonstrated the importance of secreted proteins in bacterial pathogenesis. Secreted membrane vesicles (MVs), in particular, have been suggested to serve as a vehicle for the selective packaging and release of virulence factors, such as toxins and immunomodulatory molecules (1-2). Previous studies on Mycobacterium tuberculosis (Mtb) pathogenesis have shown that phagocytosed dead bacilli with no secreted proteins lose their ability to hinder phagosome-lysosome fusion (3). Therefore, understanding the contents and mechanism of action of MV proteins will lead to deeper understanding of TB disease. The aim of this project is characterise the proteomic profile of Mtb MVs to unveil their role in host-pathogen interaction.
Mtb H37Rv cells were cultured in minimal media (MM) at 37 °C to mid-log phase (OD600 = 0.8) and the filtered cell free supernatant was used as a source to isolate MVs by density gradient ultra-centrifugation (4). The purified membrane vesicles and cellular pellets were loaded on Bis-Tris Protein Gels (4-12%) for in-gel digestion and cleaned up using c-18 zip-tip columns (5) before injection into the Q-Exactive mass spectrometer (Thermo Scientific, Germany) in triplicates. MaxQuant software was used to define the amounts of the various peptides present and the data was analyzed using Perseus software. The functional categories for the differentially expressed proteins identified were grouped using the KEGG database.
The concentration and size distribution of membrane vesicles isolated were measured using NanoSight and the size ranges from 70-400 nm in diameter. Next-generation mass spectrometry revealed that there is enriched packaging of virulence associated mycobacterial proteins in MVs. A total of 83 proteins were identified in Mtb MVs out of which 69 are shared with the cellular proteome and 14 found exclusively in MVs. The majority of the MV components detected were secreted proteins which are reported to be major virulence factors (antigen 85 complex, ESAT-6 and PE/PPE). Furthermore, 71 proteins have never been reported in Mtb membrane vesicles before (2, 4), and some of the proteins were uncharacterized. KEGG pathway enrichment analysis showed proteins involved in two-component systems, ABC transporters, amino acid and fatty acid metabolism, and catalytic and hydrolase activity.
This study generated new knowledge on the proteomic profile of Mtb MVs and their surface-exposed antigens. We have characterized Mtb membrane vesicles, which are enriched with surface/secreted antigenic proteins and virulence factors. Further in-silico and in-vitro/in-vivo study is needed to investigate the clinical relevance of the MV proteins identified, including the newly discovered un-characterized proteins.
References:
1. Kuehn MJ, Kesty NC. Bacterial outer membrane vesicles and the host–pathogen interaction. Genes & development. 2005 Nov 15;19(22):2645-55.
2. Lee J, Kim SH, Choi DS, Lee JS, Kim DK, Go G, Park SM, Kim SH, Shin JH, Chang CL, Gho YS. Proteomic analysis of extracellular vesicles derived from Mycobacterium tuberculosis. Proteomics. 2015 Oct 1;15(19):3331-7.
3. Russell DG, Purdy GE, Owens RM, Rohde KH, Yates RM. Mycobacterium tuberculosis and the four minute phagosome. ASM News. 2005;71:459–463.
4. Prados-Rosales R, Brown L, Casadevall A, Montalvo-Quirós S, Luque-Garcia JL. Isolation and identification of membrane vesicle-associated proteins in Gram-positive bacteria and mycobacteria. MethodsX. 2014 Dec 31;1:124-9
5. Wiśniewski JR, Zougman A, Mann M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 8(12):5674-8, 2009.
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Lillenes, Meryl Sønderby; Riaz, Tahira; Rabano, Alberto; Fladby, Tormod & Tonjum, Tone
(2016).
Altered DNA base excision repair profile in brain tissue and blood in Alzheimer's disease.
Show summary
Alzheimer’s disease (AD) is the major contributor to cognitive decline and dementia worldwide. Considering the expanding numbers of elderly in our society, studies of health and disease in the aging population is increasingly important. In order to understand AD, one must understand normal aging. AD is preceded by mild cognitive impairment (MCI), and once MCI occurs, early diagnostics and therapies are urgently needed. MCI/AD is associated with increased oxidative stress, resulting from imbalance in production and clearance of reactive oxygen species (ROS). ROS can damage DNA and other macromolecules, leading to genome instability and disrupted cellular functions. To counteract the harmful effects of oxidative DNA damage, cells use the base excision repair (BER) pathway. We have monitored the expression of the DNA repair profile in human blood and post-mortem brain biopsies from AD and MCI patients and healthy aged individuals by transcriptional profiling and mass spectrometry. In this context, we have a particular a focus on selected BER components, to define if the expression profile varies between AD patients as compared to healthy controls. Notably, BER expression was significantly higher in brain tissue compared to blood. BER mRNA levels were correlated to clinical signs and cerebrospinal fluid biomarkers for AD. Blood mRNA levels of OGG1 was low and PARP1 high in MCI and AD. These findings suggest that alteration in BER gene expression is an event preceding AD and reflect the oxidative stress-generating energy-consumption in the brain and the importance of BER in repairing these damage events. Collectively, these studies provide new keys to understanding early events in the progression of AD and also expand the pool of potential biomarkers for pre-clinical AD
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Riaz, Tahira
(2016).
Th1 og Th1/Th17-cellekloner i tarmbiopsier fra pasienter med Crohns sykdom.
BestPractice Gastroenterologi.
ISSN 1903-6590.
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Yimer, Solomon Abebe; Namouchi, Amine; Riaz, Tahira; Zegeye, Ephrem Debebe; Godana, Alemayehu & Holm-Hansen, Carol J C
[Show all 9 contributors for this article]
(2015).
Genomic and proteomic analysis of Mycobacterium tuberculosis lineage 7 strains from Ethiopia. Oral presentation at the 46th Union World Conference on Lung Health Cape Town, South Africa: 2 December - 6 December 2015.
Show summary
Background:
Understanding the various factors driving the tuberculosis (TB) pandemic is essential to achieve the Global Plan for TB control and elimination. Recently, a new phylogenetic M. tuberculosis (Mtb) lineage (lineage 7) has been identified in Ethiopia, which is associated with prolonged delay among patients and grows slowly in vitro compared to other lineages. Given the potential implications for pathogenesis and virulence of the bacteria, genomic and proteomic studies on Mtb are warranted. The aim of this study was to delineate the molecular characteristics of Mtb lineage 7 strains by analysing genomic and proteomic profiles.
Methods:
The BACTEC MGIT 960 culture system was used to cultivate 30 Mtb lineage 7 isolates. DNA was extracted and whole genome sequencing was performed using the Illumina Hiseq2000. Overall, after aligning the generated reads for each strain to the genome sequence of the Mtb H37Rv strain, the coverage rate was above 300 times. High resolution Q-Exactive mass spectrometer was used to achieve proteome characterization. MaxQuant software was used to define the amounts of the various proteins present, while post-translational modifications (PTMs) were identified by Proteome Discoverer and manual inspection.
Results:
More than 800 mutations or single nucleotide polymorphisms (SNPs) specific to Mtb lineage 7 strains were identified. Compared to other lineages, Mtb lineage 7 strains exhibited a high number of mutations in genes involved in carbohydrate transport and metabolism, transcription, energy production and conversion. Notably, low frequencies of mutations were observed in genes involved in amino acid, lipid and coenzyme transport and metabolism, post translational modification, protein turnover and chaperone. Several interesting proteins, such as transcription factors, membrane proteins and proteins involved in pathogenesis of the bacteria were identified in lineage 7 strains. We also identified novel site-specific PTMs.
Conclusions:
This study generated novel knowledge regarding the genomic and proteomic profile of Mtb lineage 7 strains. Further research is essential to understand the consequences of the differential frequencies of mutations observed in the main gene groups of lineage 7 strains. Taken together, these studies have generated significant novel knowledge on a new lineage of Mtb, which can elucidate how these strains can have fitness for survival despite their relatively slow growth.
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Mathiesen, Geir; Riaz, Tahira; Bøhle, Liv Anette; Skaugen, Morten; Busk, Øyvind & Jacobsen, Wolfgang Mathias
[Show all 7 contributors for this article]
(2011).
Identification of surface proteins in Enterococcus faecalis V583.
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Bøhle, Liv Anette; Riaz, Tahira; Egge-Jacobsen, Wolfgang; Skaugen, Morten; Busk, Øyvind & Eijsink, Vincent
(2010).
Direct LC-MS/MS-based identification of surface-associated proteins in Enterococcus faecalis V583.
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Riaz, Tahira; Mathiesen, Geir; Busk, Øyvind; Skaugen, Morten; Bøhle, Liv Anette & Egge-Jacobsen, Wolfgang
[Show all 7 contributors for this article]
(2009).
Identification of Enterococcus faecalisV583 surface-associated proteins.
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Riaz, Tahira; Tønjum, Tone; Støen, Mari; Berge, Tone; Sukenthirarasa, Pravina & Ka Wai Kai, Celina
(2021).
New Drugs to Combat AMR.
OsloMet - storbyuniversitetet.
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Riaz, Tahira; Tonjum, Tone & Olsen, Ingrid
(2019).
Proteomic approaches to study CD4+ T cells and meningococci:
New insight into life science and infection biology.
Universitetet i Oslo.
ISSN 978-82-8377-448-1.
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Riaz, Tahira
(2008).
Proteome analysis of microtubule-associated proteins and S-trityl-L-cysteine-induced mitotic arrest and apoptosis.
UMB.