Reconstructing the cell–cell interaction network among mouse immune cells

Azadian, Somayeh; Doustmohammadi, Alireza; Naseri, Mohadeseh; Khodarahmi, Masoud; Arab, Seyed Shahriar; Yazdanifar, Mahboubeh; Zahiri, Javad; Lewis, Nathan E.

doi:10.1002/bit.28431

Cited by 4 publications

(2 citation statements)

References 33 publications

(47 reference statements)

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“…In fact, the immunoregulatory roles of BMP members have also been reported [26]. For example, the BMP pathway is one of the most significant contributors to the cell-cell interaction network among mouse immune cells in the reconstructed communication network [27]. A deficiency of BMP2, 4 or 7 results in decreased thymus size [16,17,[28][29][30][31].…”

Section: Discussionmentioning

confidence: 99%

Bmp4 in Zebrafish Enhances Antiviral Innate Immunity through p38 MAPK (Mitogen-Activated Protein Kinases) Pathway

Chen,

Zhong,

Wang

et al. 2023

IJMS

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Bone morphogenetic proteins (BMPs) are a group of structurally and functionally related signaling molecules that comprise a subfamily, belonging to the TGF-β superfamily. Most BMPs play roles in the regulation of embryonic development, stem cell differentiation, tumor growth and some cardiovascular and cerebrovascular diseases. Although evidence is emerging for the antiviral immunity of a few BMPs, more BMPs are needed to determine whether this function is universal. Here, we identified the zebrafish bmp4 ortholog, whose expression is up-regulated through challenge with grass carp reovirus (GCRV) or its mimic poly(I:C). The overexpression of bmp4 in epithelioma papulosum cyprini (EPC) cells significantly decreased the viral titer of GCRV-infected cells. Moreover, compared to wild-type zebrafish, viral load and mortality were significantly increased in both larvae and adults of bmp4−/− mutant zebrafish infected with GCRV virus. We further demonstrated that Bmp4 promotes the phosphorylation of Tbk1 and Irf3 through the p38 MAPK pathway, thereby inducing the production of type I IFNs in response to virus infection. These data suggest that Bmp4 plays an important role in the host defense against virus infection. Our study expands the understanding of BMP protein functions and opens up new targets for the control of viral infection.

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Section: Discussionmentioning

confidence: 99%

Bmp4 in Zebrafish Enhances Antiviral Innate Immunity through p38 MAPK (Mitogen-Activated Protein Kinases) Pathway

Chen,

Zhong,

Wang

et al. 2023

IJMS

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“…Fed-batch alone or in combination with perfusion were described by Fernandes-Platzgummer et al (2023) as a process to generate bone marrow-derived MsCs and MSC-EV in stirred tank bioreactors. To complement these experimental investigations, Azadian et al (2023) proposes an in silico approach (using mathematical models) to describe cell-to-cell communications important to immune cell's cell functions and ultimately immunotherapies.…”

Section: Stem Cells and Cell Therapiesmentioning

confidence: 99%

Advanced cell technologies: Making protein, cell, and gene therapies a reality

Geada,

Roldão,

Betenbaugh

et al. 2023

Biotech & Bioengineering

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Advanced cell technologies: Making protein, cell, and gene therapies a reality Researchers and engineers came together in Lisbon at the 27th Meeting of the European Society for Animal Cell Technology (ESACT 2022), to discuss the latest advances in technologies associated with protein-based biologics production, new modalities and cell, gene, and tissue therapies. Main contributions focused on how the capabilities of production platforms can be enhanced, and how to leverage them to generate new products. Some of the advances that were presented are discussed below, including those related to cell line development, metabolic engineering, analytics, chinese hamster ovary and insect cells platforms engineering, vesicle and viral vector production, and gene and cell therapy, along with some concluding remarks on the future of this important field.

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Integration of protein sequence and protein–protein interaction data by hypergraph learning to identify novel protein complexes

Xia,

Li,

Deng

et al. 2024

Briefings in Bioinformatics

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Protein–protein interactions (PPIs) are the basis of many important biological processes, with protein complexes being the key forms implementing these interactions. Understanding protein complexes and their functions is critical for elucidating mechanisms of life processes, disease diagnosis and treatment and drug development. However, experimental methods for identifying protein complexes have many limitations. Therefore, it is necessary to use computational methods to predict protein complexes. Protein sequences can indicate the structure and biological functions of proteins, while also determining their binding abilities with other proteins, influencing the formation of protein complexes. Integrating these characteristics to predict protein complexes is very promising, but currently there is no effective framework that can utilize both protein sequence and PPI network topology for complex prediction. To address this challenge, we have developed HyperGraphComplex, a method based on hypergraph variational autoencoder that can capture expressive features from protein sequences without feature engineering, while also considering topological properties in PPI networks, to predict protein complexes. Experiment results demonstrated that HyperGraphComplex achieves satisfactory predictive performance when compared with state-of-art methods. Further bioinformatics analysis shows that the predicted protein complexes have similar attributes to known ones. Moreover, case studies corroborated the remarkable predictive capability of our model in identifying protein complexes, including 3 that were not only experimentally validated by recent studies but also exhibited high-confidence structural predictions from AlphaFold-Multimer. We believe that the HyperGraphComplex algorithm and our provided proteome-wide high-confidence protein complex prediction dataset will help elucidate how proteins regulate cellular processes in the form of complexes, and facilitate disease diagnosis and treatment and drug development. Source codes are available at https://github.com/LiDlab/HyperGraphComplex.

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Reconstructing the cell–cell interaction network among mouse immune cells

Cited by 4 publications

References 33 publications

Bmp4 in Zebrafish Enhances Antiviral Innate Immunity through p38 MAPK (Mitogen-Activated Protein Kinases) Pathway

Bmp4 in Zebrafish Enhances Antiviral Innate Immunity through p38 MAPK (Mitogen-Activated Protein Kinases) Pathway

Advanced cell technologies: Making protein, cell, and gene therapies a reality

Integration of protein sequence and protein–protein interaction data by hypergraph learning to identify novel protein complexes

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