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Transcriptome signatures of host tissue infected with African swine fever virus reveal differential expression of associated oncogenes

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Abstract

African swine fever (ASF) has emerged as a threat to swine production worldwide. Evasion of host immunity by ASF virus (ASFV) is well understood. However, the role of ASFV in triggering oncogenesis is still unclear. In the present study, ASFV-infected kidney tissue samples were subjected to Illumina-based transcriptome analysis. A total of 2463 upregulated and 825 downregulated genes were differentially expressed (p < 0.05). A literature review revealed that the majority of the differentially expressed host genes were key molecules in signaling pathways involved in oncogenesis. Bioinformatic analysis indicated the activation of certain oncogenic KEGG pathways, including basal cell carcinoma, breast cancer, transcriptional deregulation in cancer, and hepatocellular carcinoma. Analysis of host-virus interactions revealed that the upregulated oncogenic RELA (p65 transcription factor) protein of Sus scrofa can interact with the A238L (hypothetical protein of unknown function) of ASFV. Differential expression of oncogenes was confirmed by qRT-PCR, using the H3 histone family 3A gene (H3F3A) as an internal control to confirm the RNA-Seq data. The levels of gene expression indicated by qRT-PCR matched closely to those determined through RNA-Seq. These findings open up new possibilities for investigation of the mechanisms underlying ASFV infection and offer insights into the dynamic interaction between viral infection and oncogenic processes. However, as these investigations were conducted on pigs that died from natural ASFV infection, the role of ASFV in oncogenesis still needs to be investigated in controlled experimental studies.

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Data availability

The data that support this study will be shared upon reasonable request to the corresponding author.

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Acknowledgements

The authors would like to express their gratitude to the Director of the ICAR-National Research Centre on Pig in Guwahati, Assam, India, for providing the essential facilities for the current study. The authors are grateful to the Indian Council of Agricultural Research in New Delhi for providing funding for Illumina high-throughput transcriptome sequencing. The authors would also like to express their gratitude to the Department of Biotechnology, Government of India (BT/PR46409/AAQ/1/852/2022), for providing partial financial assistance. Mr. Bimal Rajbangshi, Field Assistant, deserves special recognition for his assistance with sample collecting and processing.

Funding

This study is funded by Department of Biotechnology, Ministry of Science and Technology, India (BT/PR46409/AAQ/1/852/2022).

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Author notes

  1. Rajib Deb, Gyanendra Singh Sengar and Joyshikh Sonowal have contributed equally to this work.

Authors and Affiliations

  1. ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India

    Rajib Deb, Gyanendra Singh Sengar, Joyshikh Sonowal, Seema Rani Pegu, Pranab Jyoti Das, Nitin Attupurum, Swaraj Rajkhowa & Vivek Kumar Gupta

  2. Banaras Hindu University, Varanasi, India

    Indra Singh

  3. ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India

    Soumendu Chakravarti & Arutkumaran Selvaradjou

  4. Pirbright Institute, Ash Road, Pirbright, Surrey, United Kingdom

    Soumendu Chakravarti

  5. Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat, Assam, 785001, India

    Joyshikh Sonowal

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Contributions

RD and VKG: design of the concept. NA and SRP: sample collection and processing. GSS, RD, SRP, PJD: wet lab work. IS and JS: dry lab work. RD, SC, AS and NA: manuscript drafting. JS, SC, SR and VK: proofreading of the manuscript. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Rajib Deb, Pranab Jyoti Das or Vivek Kumar Gupta.

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Ethical statement

Tissue samples were collected with the approval of the Institutional Animal Ethics Committee (IAEC) with the approval code no. NRCP/IAEC/1658/2023-24/90, dated 25-04-2023.

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Deb, R., Sengar, G.S., Sonowal, J. et al. Transcriptome signatures of host tissue infected with African swine fever virus reveal differential expression of associated oncogenes. Arch Virol 169, 54 (2024). https://doi.org/10.1007/s00705-023-05959-4

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