Transcriptomics in the Study of Antiviral Innate Immunity

Diamond MS, Kanneganti TD (2022) Innate immunity: the first line of defense against SARS-CoV-2. Nat Immunol 23:165–176. https://doi.org/10.1038/s41590-021-01091-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK (2024) SARS-CoV-2 and innate immunity: the good, the bad, and the “goldilocks”. Cell Mol Immunol 21:171–183. https://doi.org/10.1038/s41423-023-01104-y

Article  CAS  PubMed  Google Scholar 

Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620. https://doi.org/10.1016/j.molcel.2015.04.005

Article  CAS  PubMed  Google Scholar 

Danishuddin, Khan S, Kim JJ (2024) Spatial transcriptomics data and analytical methods: an updated perspective. Drug Discov Today 29:103889. https://doi.org/10.1016/j.drudis.2024.103889

Article  CAS  PubMed  Google Scholar 

Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T (2017) Transcriptomics technologies. PLoS Comput Biol 13:e1005457. https://doi.org/10.1371/journal.pcbi.1005457

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA (2023) Single-cell RNA-seq methods to interrogate virus–host interactions. Semin Immunopathol 45:71–89. https://doi.org/10.1007/s00281-022-00972-2

Article  CAS  PubMed  Google Scholar 

Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y (2022) Single-cell RNA sequencing technologies and applications: a brief overview. Clin Transl Med 12:e694. https://doi.org/10.1002/ctm2.694

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wyler E, Franke V, Menegatti J, Kocks C, Boltengagen A, Praktiknjo S et al (2019) Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program. Nat Commun 10:4878. https://doi.org/10.1038/s41467-019-12894-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zanini F, Robinson ML, Croote D, Sahoo MK, Sanz AM, Ortiz-Lasso E et al (2018) Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proc Natl Acad Sci USA 115:E12363–e12369. https://doi.org/10.1073/pnas.1813819115

Article  CAS  PubMed  PubMed Central  Google Scholar 

Steuerman Y, Cohen M, Peshes-Yaloz N, Valadarsky L, Cohn O, David E et al (2018) Dissection of influenza infection in vivo by single-cell RNA sequencing. Cell Syst 6:679–691.e674. https://doi.org/10.1016/j.cels.2018.05.008

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL et al (2020) A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med 26:1070–1076. https://doi.org/10.1038/s41591-020-0944-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A (2018) Single-cell RNA-Seq reveals transcriptional heterogeneity in latent and reactivated HIV-infected cells. Cell Rep 23:942–950. https://doi.org/10.1016/j.celrep.2018.03.102

Article  CAS  PubMed  Google Scholar 

Oh T, Kim G, Baek SH, Woo Y, Koo BS, Hwang EH et al (2023) Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques. Commun Biol 6:879. https://doi.org/10.1038/s42003-023-05253-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao M, Shao F, Liu Z, Ma J, Yu D, Zhang H et al (2023) Spatially resolved transcriptomics reveals distinct pulmonary immune responses during influenza virus and SARS-CoV-2 infections. Sci Bull 68:3137–3141. https://doi.org/10.1016/j.scib.2023.11.001

Article  Google Scholar 

Rendeiro AF, Ravichandran H, Bram Y, Chandar V, Kim J, Meydan C et al (2021) The spatial landscape of lung pathology during COVID-19 progression. Nature 593:564–569. https://doi.org/10.1038/s41586-021-03475-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Netzband R, Pager CT (2020) Epitranscriptomic marks: emerging modulators of RNA virus gene expression. Wiley Interdiscip Rev RNA 11:e1576. https://doi.org/10.1002/wrna.1576

Article  CAS  PubMed  Google Scholar 

Comments (0)

No login
gif