Multi-Omics Studies towards Novel Modulators of Influenza A Virus–Host Interaction

Söderholm, Sandra; Fu, Yu; Gaelings, Lana; Belanov, Sergei; Yetukuri, Laxman; Berlinkov, Mikhail V.; Cheltsov, Anton; Anders, Simon; Aittokallio, Tero; Nyman, Tuula A.; Matikainen, Sampsa; Kainov, Denis E.

doi:10.3390/v8100269

Cited by 24 publications

(16 citation statements)

References 163 publications

(127 reference statements)

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“…Viruses have evolved to evade the host antiviral response at various stages starting from viral sensing to antiviral pro-inflammatory responses (Bowie and Unterholzner 2008, Navratil et al 2011, Garcia-Sastre 2017. Multiple studies attempted to understand global principles of the viral evasion employed by various viruses, including dengue virus (DENV), Ebola virus (EBOV), IAV and HIV (Pichlmair et al 2012, Rozenblatt-Rosen et al 2012, Jäger et al 2011, Shah et al 2018, Batra et al 2018, Söderholm et al 2016. Global systems-level approaches including functional RNAi screens, interactome mapping technologies such as affinitypreprint purification mass spectrometry (AP-MS), quantitative proteomics and CRISPR/Cas9-based screens have provided unparalleled details and insights into the dynamics of host proteome in immune cells (Weekes et al 2014, Nightingale et al 2018, Kandasamy et al 2016, Ersing et al 2017), host-virus interactome (Pichlmair et al 2012, Rozenblatt-Rosen et al 2012, Jäger et al 2011, Shapira et al 2009, Konig et al 2010, and also identified important host dependency factors of various viruses (Shapira et al 2009, Marceau et al 2016.…”

Section: Introductionmentioning

confidence: 99%

Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Bösl

Ianevski

Than

et al. 2019

Preprint

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Viruses are one of the major causes of various acute and chronic infectious diseases and thus a major contributor to the global burden of disease. Several studies have shown how viruses have evolved to hijack basic cellular pathways and evade innate immune response by modulating key host factors and signalling pathways. A collective view of these multiple studies could advance our understanding of viral evasion mechanisms and provide new therapeutic perspectives for the treatment of viral diseases. Here, we performed an integrative meta-analysis to elucidate the 17 different host-virus interactomes. Network and bioinformatics analyses showed how viruses with small genomes efficiently achieve the maximal effect by targeting multifunctional and highly connected host proteins with a high occurrence of disordered regions. We also identified the core cellular process subnetworks that are targeted by all the viruses. Integration with functional RNA interference (RNAi) datasets showed that a large proportion of the targets are required for viral replication. Furthermore, we performed an interactome-informed drug re-purposing screen and identified novel activities for broad-spectrum antiviral agents against hepatitis C virus and human metapneumovirus. Altogether, these orthogonal datasets could serve as a platform for hypothesis generation and follow-up studies to broaden our understanding of the viral evasion landscape. author/funder. All rights reserved. No reuse allowed without permission.

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Section: Introductionmentioning

confidence: 99%

Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Bösl

Ianevski

Than

et al. 2019

Preprint

Self Cite

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“…The vRNPs enter the nucleus through nuclear pore complexes [16]. In the nucleus viral genomic RNA is transcribed into positive-sense mRNA using viral polymerase [17,18]. The polymerase snatches 5' Caps from cellular RNA, performs RNA-dependent RNA polymerization and 3' RNA polyadenylation to make viral pre-mRNA.…”

Section: Iav Structure and Replication Cyclementioning

confidence: 99%

Influenza virus infection, interferon response, viral counter-response and apoptosis

Shim¹,

Kim²,

Min³

et al. 2017

Preprint

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Human influenza A viruses (IAVs) cause global pandemics and epidemics, which remain serious threats to public health because of the shortage of effective means of control. To combat the surge of viral outbreaks, new treatments are urgently needed. Developing new virus control modalities requires better understanding of virus-host interactions. Here we describe how IAV infection triggers cellular apoptosis, and how this process can be exploited towards development of new therapeutics, which might be more effective than the currently available anti-influenza drugs.

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“…It also seems plausible that a public “data driven” approach for data mining, integration, and reuse would improve the ‘omics field by no small measure . Despite the individual merit of the various ‘omics based approaches, an integrative multi‐omics approach would provide a more robust outcome both in the discovery and validation phases of the ‘omics based biomarker pipeline . Very few dermatological review articles have focused on the application of ‘omics based approaches in human skin, and there remains a dearth of human hair proteomics reviews.…”

Section: ‘Omics Based Approaches For Hair Researchmentioning

confidence: 99%

Emerging Diagnostic and Therapeutic Potentials of Human Hair Proteomics

Adeola

Wyk

Arowolo

et al. 2017

Proteomics Clinical Apps

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The use of noninvasive human substrates to interrogate pathophysiological conditions has become essential in the post- Human Genome Project era. Due to its high turnover rate, and its long term capability to incorporate exogenous and endogenous substances from the circulation, hair testing is emerging as a key player in monitoring long term drug compliance, chronic alcohol abuse, forensic toxicology, and biomarker discovery, among other things. Novel high-throughput 'omics based approaches like proteomics have been underutilized globally in comprehending human hair morphology and its evolving use as a diagnostic testing substrate in the era of precision medicine. There is paucity of scientific evidence that evaluates the difference in drug incorporation into hair based on lipid content, and very few studies have addressed hair growth rates, hair forms, and the biological consequences of hair grooming or bleaching. It is apparent that protein-based identification using the human hair proteome would play a major role in understanding these parameters akin to DNA single nucleotide polymorphism profiling, up to single amino acid polymorphism resolution. Hence, this work seeks to identify and discuss the progress made thus far in the field of molecular hair testing using proteomic approaches, and identify ways in which proteomics would improve the field of hair research, considering that the human hair is mostly composed of proteins. Gaps in hair proteomics research are identified and the potential of hair proteomics in establishing a historic medical repository of normal and disease-specific proteome is also discussed.

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Multi-Omics Studies towards Novel Modulators of Influenza A Virus–Host Interaction

Cited by 24 publications

References 163 publications

Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Influenza virus infection, interferon response, viral counter-response and apoptosis

Emerging Diagnostic and Therapeutic Potentials of Human Hair Proteomics

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