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  1. Article: Identification of protein profile in metacyclic and amastigote-like stages of Leishmania tropica: a proteomic approach.

    Ashrafmansouri, Marzieh / Amiri-Dashatan, Nasrin / Ahmadi, Nayebali

    AMB Express

    2022  Volume 12, Issue 1, Page(s) 142

    Abstract: Leishmaniasis is a tropical disease that leads to various clinical phenotypes. This study aimed to investigate protein expression changes in metacyclic and amastigote-like stages of L. tropica isolated from Iranian cutaneous leishmaniasis patients. ... ...

    Abstract Leishmaniasis is a tropical disease that leads to various clinical phenotypes. This study aimed to investigate protein expression changes in metacyclic and amastigote-like stages of L. tropica isolated from Iranian cutaneous leishmaniasis patients. Isolated samples were cultured and species type identified using PCR-RFLP technique. The promastigotes were grown in RPMI1640 media and differentiated to metacyclic and amastigote-like forms, followed by the extracted proteins of both successive stages carried out for proteomics and bioinformatics analysis. Using SWATH-MS quantitative proteomics technique, a total 176 and 155 distinct proteins were identified in metacyclic and axenic amastigote stages, respectively. Of these, 65 proteins were altered significantly (p-value < 0.05 and fold change ≥ 2) between studied stages. Several gene ontology (GO) categories were enriched for biological process during conversion of metacyclic promastigotes into amastigote-like, which "metabolic process" (GO: 0044281, P-Value: 6.52e-5), and "translation" (GO: 0006412, p-value: 5.01e-14) were disclosed as the top category in up and down-regulated proteins, respectively. Also, the KEGG pathway analysis indicated "metabolic pathways" and "ribosome" term as the most important pathways in up and down-regulated proteins, respectively. According to protein interaction network analysis, enolase (ENOL) has been detected as main hub proteins during differentiation, followed by Putative NADH-dependent fumarate reductase (LmjF.35.1180) and 40S ribosomal protein S2 (LmjF.32.0450). Overall, protein changes possibly play important roles in L. tropica biology. Anabolic pathways were down-regulated, whereas catabolic pathways were up-regulated during L. tropica differentiation. These protein expression changes could provide parasite survival in host macrophages, and could use as novel potential drug and vaccine targets for leishmaniasis.
    Language English
    Publishing date 2022-11-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2621432-5
    ISSN 2191-0855
    ISSN 2191-0855
    DOI 10.1186/s13568-022-01481-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Mass Spectrometry-Based Proteomics Research to Fight COVID-19: An Expert Review on Hopes and Challenges.

    Amiri-Dashatan, Nasrin / Koushki, Mehdi / Rezaei-Tavirani, Mostafa

    Omics : a journal of integrative biology

    2022  Volume 26, Issue 1, Page(s) 19–34

    Abstract: The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems ... ...

    Abstract The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems perspective remains incomplete. Moreover, there is currently only a limited description of this systemic disease. For precision diagnosis and treatment of SARS-CoV-2, multiomics technologies and systems science research offer significant prospects. This expert review offers a critical analysis of the prospects and challenges of the emerging mass spectrometry-based proteomics approaches to the study of COVID-19 as seen through a systems medicine lens. We also discuss the ways in which proteomics is poised to offer hope for diagnostics and therapeutics innovation on SARS-CoV-2 infection as the disease transitions from a pandemic to an endemic disease, and thus further challenging the health systems and services worldwide in the coming decade. Proteomics is an important high-throughput technology platform to achieve a functional overview of the ways in which COVID-19 changes host biology, and hence, can help identify possible points of entry for innovation in medicines and vaccines, among others.
    MeSH term(s) COVID-19 ; Humans ; Mass Spectrometry ; Pandemics ; Proteomics ; SARS-CoV-2
    Language English
    Publishing date 2022-01-07
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2030312-9
    ISSN 1557-8100 ; 1536-2310
    ISSN (online) 1557-8100
    ISSN 1536-2310
    DOI 10.1089/omi.2021.0182
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Screening the critical protein subnetwork to delineate potential mechanisms and protective agents associated with arsenic-induced cutaneous squamous cell carcinoma: A toxicogenomic study.

    Koushki, Mehdi / Amiri-Dashatan, Nasrin / Rezaei-Tavirani, Mostafa / Robati, Reza M / Fateminasab, Fatemeh / Rahimi, Shadi / Razzaghi, Zahra / Farahani, Masoumeh

    Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association

    2024  Volume 185, Page(s) 114451

    Abstract: Recent studies show that complex mechanisms are involved in arsenic-induced malignant transformation of cells. This study aimed to decipher molecular mechanisms associated with arsenic-induced cutaneous squamous cell carcinoma (cSCC) and suggest ... ...

    Abstract Recent studies show that complex mechanisms are involved in arsenic-induced malignant transformation of cells. This study aimed to decipher molecular mechanisms associated with arsenic-induced cutaneous squamous cell carcinoma (cSCC) and suggest potential protective factors. RNA-seq-based differentially expressed genes between arsenic-exposed human keratinocytes (HaCaT) and controls were used to construct a protein-protein interaction (PPI) network and discover critical subnetwork-based mechanisms. Protective compounds against arsenic toxicity were determined and their target interactions in the core sub-network were identified by the comparative toxicogenomic database (CTD). The binding affinity between the effective factor and target was calculated by molecular docking. A total of 15 key proteins were screened out as critical arsenic-responsive subnetwork (FN1, IL-1A, CCN2, PECAM1, FGF5, EDN1, FGF1, PXDN, DNAJB9, XBP1, ERN1, PDIA4, DNAJB11, FOS, PDIA6) and 7 effective protective agents were identified (folic acid, quercetin, zinc, acetylcysteine, methionine, catechin, selenium). The GeneMANIA predicted detailed interactions of the subnetwork and revealed terms related to unfolded protein response as the main processes. FN1, IL1A and CCN2, as top significant genes, had good docking affinity with folic acid and quercetin, as selected key compounds. Integration of gene expression and protein-protein interaction related to arsenic exposure in cSCC explored the potential mechanisms and protective agents.
    MeSH term(s) Humans ; Arsenic/toxicity ; Carcinoma, Squamous Cell/chemically induced ; Carcinoma, Squamous Cell/genetics ; Quercetin ; Molecular Docking Simulation ; Toxicogenetics ; Skin Neoplasms/chemically induced ; Skin Neoplasms/genetics ; Skin Neoplasms/metabolism ; Protective Agents ; Folic Acid/adverse effects ; Membrane Proteins ; Molecular Chaperones ; HSP40 Heat-Shock Proteins
    Chemical Substances Arsenic (N712M78A8G) ; Quercetin (9IKM0I5T1E) ; Protective Agents ; Folic Acid (935E97BOY8) ; DNAJB9 protein, human ; Membrane Proteins ; Molecular Chaperones ; HSP40 Heat-Shock Proteins
    Language English
    Publishing date 2024-01-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 782617-5
    ISSN 1873-6351 ; 0278-6915
    ISSN (online) 1873-6351
    ISSN 0278-6915
    DOI 10.1016/j.fct.2024.114451
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Critical review of therapeutic potential of silymarin in cancer: A bioactive polyphenolic flavonoid

    Koushki, Mehdi / Farrokhi Yekta, Reyhaneh / Amiri-Dashatan, Nasrin

    Journal of Functional Foods. 2023 May, v. 104 p.105502-

    2023  

    Abstract: Cancer is identified as second leading causes of death and imposes a significant psychological and economic burden on societies. Due to its high prevalence, and a main cause of death worldwide, there is a continuing need to discover new potential ... ...

    Abstract Cancer is identified as second leading causes of death and imposes a significant psychological and economic burden on societies. Due to its high prevalence, and a main cause of death worldwide, there is a continuing need to discover new potential anticancer compounds. Plant-derived compounds have recently attracted more attention among researchers for their potent anti-cancer properties. A numerous research, including in-vitro, in-vivo, preclinical, clinical, and epidemiological studies, has indicated that the flavonoid of silymarin have comprehensive preventive and therapeutic effects on array of inflammation-driven diseases, including cancer. Silymarin have clear anti-cancer activities through distinctive mechanisms including modulation of apoptosis in-vitro and survival in-vivo. The chemoprotection of silymarin and its constituent suggest they could be promising therapeutic agents in various cancer types. This review focus on the silymarin in vivo and in vitro effects in a variety of cancers, and explores signaling pathways that modulated by this compound.
    Keywords apoptosis ; death ; silymarin ; therapeutics ; Natural product ; Polyphenol ; Flavonoid ; Cancer ; Chemoprevention ; SMEDDS ; SLNs ; PVA ; SIL ; SILNPs ; SLM ; TMC ; WHO ; MAPK ; ERK ; BCl-2 ; Bcl-xL ; IL-6 ; STAT3 ; NF-κβ ; IL-1β ; PG-E2 ; IFN-γ ; NO ; TGF-β2 ; MMP-2 ; MMP-9 ; VEGFR1 ; GC ; CRC ; PTX ; HIF-1α ; C-MYC ; LC-MS/MS ; MMPs ; TGF-β ; TCF-4 ; ODC ; mRNA ; BPO ; BG ; SOD ; GPX ; AOM ; CAP ; UV ; BrCa ; ER-α ; ERBB2 ; DXL ; BCRP ; SMSWE ; REF ; AMAPK
    Language English
    Dates of publication 2023-05
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Use and reproduction
    ZDB-ID 2511964-3
    ISSN 1756-4646
    ISSN 1756-4646
    DOI 10.1016/j.jff.2023.105502
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Serum cortisol concentration and COVID-19 severity: a systematic review and meta-analysis.

    Amiri-Dashatan, Nasrin / Koushki, Mehdi / Parsamanesh, Negin / Chiti, Hossein

    Journal of investigative medicine : the official publication of the American Federation for Clinical Research

    2022  Volume 70, Issue 3, Page(s) 766–772

    Abstract: The novel COVID-19 outbreak is a major health threat to human beings with multiorgan injuries. However, its endocrine system manifestations are much less studied. In this study, we aimed to reassess the available findings on the association between ... ...

    Abstract The novel COVID-19 outbreak is a major health threat to human beings with multiorgan injuries. However, its endocrine system manifestations are much less studied. In this study, we aimed to reassess the available findings on the association between cortisol level and severity of COVID-19 infection. We conducted a systematic search on Medline/PubMed, Scopus, Web of Science, and Cochrane Library databases. To pool data, a random-effects model was performed depending on the heterogeneity among studies. Sensitivity analysis was also carried out by removing each study systematically. In addition, subgroup and meta-regression analyses were performed depending on the presence of the variables of sex and age. Subsequently, 11 studies (5 observational studies and 6 case reports) were included in the meta-analysis. Pooled analysis on the observational studies showed significantly higher levels of cortisol in patients with severe COVID-19 in comparison with those with mild-to-moderate COVID-19 (standardized mean difference: 1.48 µg/dL; 95% CI (0.51 to 2.46); p=0.003). Assessment of the results of case reports revealed that the patients with severe COVID-19 demonstrated higher cortisol levels than the patients with mild-to-moderate COVID-19. No publication bias was observed using the Begg's (p=0.08) and Egger's tests (p=0.09). Meta-regression illustrated a significant correlation between cortisol levels with sex. The serum cortisol level seems to be higher in patients with severe COVID-19 infection. This finding could be helpful to detect patients with poor prognosis at early stages of the disease, although age and sex may modify this level.
    MeSH term(s) Age Factors ; COVID-19/blood ; COVID-19/diagnosis ; Humans ; Hydrocortisone/blood ; SARS-CoV-2 ; Sex Factors
    Chemical Substances Hydrocortisone (WI4X0X7BPJ)
    Language English
    Publishing date 2022-01-20
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Systematic Review
    ZDB-ID 1217870-6
    ISSN 1708-8267 ; 0009-9279 ; 1081-5589
    ISSN (online) 1708-8267
    ISSN 0009-9279 ; 1081-5589
    DOI 10.1136/jim-2021-001989
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Comparison of gene expression of pyruvate kinase and tryparedoxin peroxidase in metacyclic promastigote forms of Leishmania (L.) tropica and L. major by real-time PCR

    Amiri-Dashatan, Nasrin / Koushki, Mehdi / Ahmadi, Nayebali

    Annals of parasitology

    2020  Volume 66, Issue 1, Page(s) 13–18

    MeSH term(s) Gene Expression Regulation, Enzymologic ; Humans ; Iran ; Leishmania tropica/enzymology ; Leishmania tropica/genetics ; Leishmaniasis, Cutaneous/parasitology ; Life Cycle Stages/genetics ; Peroxidases/genetics ; Protozoan Proteins/genetics ; Pyruvate Kinase/genetics ; Real-Time Polymerase Chain Reaction
    Chemical Substances Protozoan Proteins ; Peroxidases (EC 1.11.1.-) ; tryparedoxin peroxidase (EC 1.11.1.-) ; Pyruvate Kinase (EC 2.7.1.40)
    Language English
    Publishing date 2020-03-20
    Publishing country Poland
    Document type Journal Article
    ZDB-ID 2672322-0
    ISSN 2299-0631 ; 0043-5163
    ISSN 2299-0631 ; 0043-5163
    DOI 10.17420/ap6601.233
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Stage-Specific Differential Gene Expression of Glutathione Peroxidase in

    Amiri-Dashatan, Nasrin / Koushki, Mehdi / Rezaei-Tavirani, Mostafa / Ahmadi, Nayebalia

    Reports of biochemistry & molecular biology

    2021  Volume 9, Issue 3, Page(s) 324–330

    Abstract: Background: Leishmania (L) major: Methods: The samples were cultured in Novy-Nicolle-Mc Neal medium to obtain the promastigotes and identified using PCR-RFLP technique. They were then grown in RPMI1640 media for mass cultivation. The expression level ...

    Abstract Background: Leishmania (L) major
    Methods: The samples were cultured in Novy-Nicolle-Mc Neal medium to obtain the promastigotes and identified using PCR-RFLP technique. They were then grown in RPMI1640 media for mass cultivation. The expression level of TDPX gene was compared by Real-time PCR.
    Results: By comparison of expression level, up-regulation of TDPX gene was observed (5.37 and 2.29 folds) in
    Conclusion: Our data provide a foundation for identifying infectivity and high survival related factors in the
    Language English
    Publishing date 2021-03-01
    Publishing country Iran
    Document type Journal Article
    ZDB-ID 2743890-9
    ISSN 2322-3480
    ISSN 2322-3480
    DOI 10.29252/rbmb.9.3.324
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Identification of differential protein expression and putative drug target in metacyclic stage of Leishmania major and Leishmania tropica: A quantitative proteomics and computational view.

    Amiri-Dashatan, Nasrin / Ahmadi, Nayebali / Rezaei-Tavirani, Mostafa / Koushki, Mehdi

    Comparative immunology, microbiology and infectious diseases

    2021  Volume 75, Page(s) 101617

    Abstract: Cutaneous leishmaniasis (CL) is an infectious disease that commonly caused by Leishmania (L.) major and L.tropica. Recently there has been a growing interest in proteomics analysis on Leishmania for drug target discovery. Therefore, we aimed to ... ...

    Abstract Cutaneous leishmaniasis (CL) is an infectious disease that commonly caused by Leishmania (L.) major and L.tropica. Recently there has been a growing interest in proteomics analysis on Leishmania for drug target discovery. Therefore, we aimed to distinguish proteins which might be characteristic for each of the species from those shared by both to the detection of drug targets, which may become helpful for designing new drugs for CL. To identify differences in protein profiles of L. major and L. tropica, we conducted a Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) analysis. Totally 67 differentially expressed proteins (DEPs) (fold change> 2 and p < 0.05) were identified between species. Of these, 42 and 25 proteins were up-regulated in L. major and L. tropica, respectively. Several enriched GO terms were identified via biological process of up-regulated proteins. Furthermore, the small molecule metabolic process and translation were detected as significant biological processes for up-regulated proteins in L. major, while translation was identified for L. tropica. Also, KEGG analysis has revealed glycolysis/gluconeogenesis and translation as the top pathways in the proteins up-regulated in L. major and L. tropica, respectively. Finally glycosomal malate dehydrogenase was identified as putative drug target using network and homology analyses. The DEPs between the species are essential in host-pathogen interactions and parasite survival in the macrophage. Furthermore, L. major and L. tropica possibly uses different pathogenicity mechanisms that leads to anthroponotic or zoonotic CL. Our results may help in the drug discovery and chemotherapeutic interventions.
    MeSH term(s) Animals ; Leishmania major/genetics ; Leishmania tropica/genetics ; Leishmaniasis, Cutaneous/veterinary ; Pharmaceutical Preparations ; Proteomics
    Chemical Substances Pharmaceutical Preparations
    Language English
    Publishing date 2021-01-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 436522-7
    ISSN 1878-1667 ; 0147-9571
    ISSN (online) 1878-1667
    ISSN 0147-9571
    DOI 10.1016/j.cimid.2021.101617
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Identification of Agents with Potential Leishmania Malate Dehydrogenase Inhibitor Activity

    Nasrin Amiri-Dashatan / Mehdi Koushki / Marzieh Ashrafmansouri / Nayebali Ahmadi

    Journal of Mazandaran University of Medical Sciences, Vol 31, Iss 204, Pp 49-

    A Proteomic and Molecular Docking Approach

    2022  Volume 61

    Abstract: Background and purpose: Leishmaniasis is one of the most important infectious diseases caused by different species of the Leishmania, which is a public health problem worldwide. So far, no effective vaccine is introduced for this disease and drug therapy ...

    Abstract Background and purpose: Leishmaniasis is one of the most important infectious diseases caused by different species of the Leishmania, which is a public health problem worldwide. So far, no effective vaccine is introduced for this disease and drug therapy is associated with many side effects. Therefore, this study was designed to identify novel FDA-approved compounds with anti-leishmanial activity. Materials and methods: In this experimental study, proteomics, protein network analysis, and molecular docking were used. Protein profile was identified by LC-MS/MS and protein network analysis was performed using Cytoscape. Processing of the compound structure and molecular docking was performed by HyperChem and AutoDock Vina, respectively. Finally, docking results were interpreted by LigPlot+. Results: Based on proteomics and protein network analysis, glycosomal malate dehydrogenase was suggested as a potential drug target. Among the compounds, the best docking results were associated with Conivaptan and Avodart with a binding energy level of -10.5 and -10.2, respectively. Also, molecular docking studies showed that the most important bonds involved in drug-receptor binding were hydrogen and hydrophobic bonds. Conclusion: The current study demonstrated the importance of integrated proteomics, protein network and docking to identify novel compounds with anti-Leishmania properties. According to this study, Conivaptan and Avodart, also approved by the Food and Drug Administration, are effective inhibitors of glycosomal malate dehydrogenase in Leishmania major and Leishmania tropica which meanwhile require further in-vitro and in-vivo experiments.
    Keywords leishmania ; cutaneous leishmaniasis ; glycosomal malate dehydrogenase ; drug target ; molecular docking ; Medicine ; R ; Medicine (General) ; R5-920
    Subject code 540
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Mazandaran University of Medical Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: A quantitative proteomic and bioinformatics analysis of proteins in metacyclogenesis of Leishmania tropica.

    Amiri-Dashatan, Nasrin / Rezaei-Tavirani, Mostafa / Ahmadi, Nayebali

    Acta tropica

    2019  Volume 202, Page(s) 105227

    Abstract: Recently there has a growing interest in MS-based analysis on Leishmania for biology study, host-parasite interaction and drug target discovery. The aims of this study were to analyzed protein profiles in the procyclic and metacyclic stages of L. tropica, ...

    Abstract Recently there has a growing interest in MS-based analysis on Leishmania for biology study, host-parasite interaction and drug target discovery. The aims of this study were to analyzed protein profiles in the procyclic and metacyclic stages of L. tropica, and investigate their potential role in metacyclogenesis molecular mechanisms. Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) analysis was used to analyze protein profiles in each of procyclic and metacyclic stages. Proteins with a fold change>2 or <0.5 and p < 0.05 were considered to be significantly differentially expressed proteins (DEPs). The DEPs were subjected to gene ontology (GO), KEGG pathway and network analysis using PANTHER and STRING database, respectively. Quantitative real-time PCR of six selected genes validated the proteomic data. We quantified a total of 352 proteins in procyclic and metacyclic cells and 56 differentially expressed proteins (27 up/ 29down-regulated in metacyclic compared to procyclic). On the basis of biological processes in GO, the DEPs were primarily involved in ``metabolic process'' (GO: 0008152) and ``cellular process'' (GO: 0009987). In addition, several enriched GO terms were identified via molecular function, which among them ``catalytic activity'' (GO: 0003824) and ``binding'' (GO: 0005488) were disclosed as top category. The KEGG pathway analysis indicated ``metabolic pathways'' (p-value: 3.80E-08) including 17 genes term as the top pathway in DEPs. These findings bring a new insight in our understanding of the molecular characterization of metacyclogenesis and infective form in L. tropica. Comparative analysis of the proteome of both developmental stages of the L. tropica would help to the identification of proteins candidates for the development of new potential drug targets and vaccines.
    MeSH term(s) Computational Biology ; Leishmania tropica/metabolism ; Mass Spectrometry ; Proteome/analysis ; Proteomics/methods ; Protozoan Proteins/chemistry ; Protozoan Proteins/metabolism
    Chemical Substances Proteome ; Protozoan Proteins
    Language English
    Publishing date 2019-10-21
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2019.105227
    Database MEDical Literature Analysis and Retrieval System OnLINE

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