Understanding the complexity of Epimorphic Regeneration in zebrafish: A Transcriptomic and Proteomic approach.

Banu, Sarena; Gaur, Namami; Nair, Sowmya; Ravikrishnan, Tanuja; Khan, Shahida; Mani, Sandhya; Bharathi, Swarna; Mandal, Komal K.; Na, Kuram; Vuppaladadium, Sowmya; Cln, Murthy; Mir, Quoseena; N, Sarath Babu; Mm, Idris

doi:10.1101/2021.05.20.445069

Cited by 3 publications

(1 citation statement)

References 46 publications

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“…This is strikingly different from many other species, including humans, which can only regenerate a few specific tissues during the adult stages (Devarajan et al, 2003;Mao et al, 2014;Salamonsen, 2003). Many signaling pathways have been shown to play a role in the caudal fin regeneration pathway in zebrafish, the most important pathways seem to be Wnt, Retinoic Acid and FGF signaling (Banu et al, 2022;Blum & Begemann, 2012;Lee et al, 2005;Poss et al, 2000;Stoick-Cooper et al, 2007;Tal et al, 2010). However, the initial signal that triggers regeneration is still unclear.…”

Section: Introductionmentioning

confidence: 86%

Protein tyrosine phosphatases in zebrafish development and regeneration

Allers

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Protein tyrosine phosphatases (PTPs) have a central role in cell signaling, by dephosphorylating other proteins. PTPs are highly susceptible to oxidation, due to the low pKa of their active sites. Their reactive cysteine gets oxidized, which leads to the temporary inactivation of the PTP. It has been shown in many different species that a burst of Reactive Oxygen Species (ROS) is produced upon injury. This burst of ROS plays an important role in wound healing and regeneration. We hypothesized that the ROS could start a signaling cascade by oxidizing PTPs. Previously, eight PTPs were identified that were specifically oxidized in response to amputation of the tail fin of adult zebrafish. One of these PTPs, Shp2a, was shown to be essential for regeneration. In chapter 2 we describe how we generated zebrafish knockouts of 6 PTPs that were shown previously to be oxidized upon amputation of the caudal fin and their paralogs. We show that these PTPs were not essential for regeneration. In addition, we did not recapitulate all the phenotypes we expected. We hypothesize that this is due to genetic compensation. In chapter 3 we describe our investigation of zebrafish with a knockout of ptpn4a. We show that the majority of the mutant zebrafish died at the juvenile stage and suffered from epileptic seizures. This corresponds to human patients who suffer from intellectual disability and epileptic seizures due to nonsense mutations in PTPN4. We show that a minority of the mutant zebrafish compensated for the loss of Ptpn4a and survived, but also that a separate knockout line lost its compensation ability over time and showed enhanced lethality at the juvenile stage. In chapter 4 we describe our investigation of zebrafish with a knockout of ptpn6. We show that these mutant zebrafish displayed fully penetrant mortality at the larval stage and died from lethal hyperinflammation. This corresponds to the phenotype of the motheaten mice lacking SHP1 and human patients suffering from neutrophilic dermatoses and emphysema. We show that loss of Shp1 led to a reduced number of emerging HSPCs, increased HSPC proliferation, an increased number of macrophages and a decreased number of neutrophils. In addition, we show that loss of Shp1 affected the behavior of neutrophils and macrophages and led to reduced directional migration upon wounding. In chapter 5 we describe how we investigated the role of oxidation of Shp2a during regeneration, by creating a fusion protein consisting of Shp2a linked with Catalase. Due to the close vicinity, the Catalase protected Shp2a from oxidation. We show that by inhibiting oxidation of Shp2a, we inhibited regeneration. This indicates that transient oxidation of Shp2a is an essential step in the signaling cascade that results in regeneration. This research puts an end to the apparent paradox that Shp2a is oxidized during regeneration, but that catalytic activity of Shp2a is essential for regeneration to proceed. We hypothesize that transient oxidation of Shp2a leads to a reduction of a negative feedback loop, resulting in increased signaling activity once Shp2a is reduced again.

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Section: Introductionmentioning

confidence: 86%

Protein tyrosine phosphatases in zebrafish development and regeneration

Allers

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Gramicidin S and Melittin - Potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection

Enayathullah

Parekh

Banu

et al. 2021

Preprint

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The COVID19 pandemic has resulted in multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of gramicidin S and melittin peptides obtained from Bacillus brevis and bee venom respectively. Our in vitro antiviral assay results showed significant decrease in the viral load compared to the untreated group with no/very less cytotoxicity. The EC50 values for gramicidin S and melittin are calculated as 1.571μg and 0.656μg respectively. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 hours onwards with a maximal clearance after 24 hours post infection. Based on proteome analysis it was found that more than 250 proteins were found to be differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 hours post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.

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A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection

Banu

Idris

Nagaraj

2021

Preprint

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Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have earlier shown that several defensin genes are down regulated in cells from this region in patients who tested positive in the RTPCR test. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2 by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.

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Understanding the complexity of Epimorphic Regeneration in zebrafish: A Transcriptomic and Proteomic approach.

Cited by 3 publications

References 46 publications

Protein tyrosine phosphatases in zebrafish development and regeneration

Protein tyrosine phosphatases in zebrafish development and regeneration

Gramicidin S and Melittin - Potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection

A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection

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