SARS-CoV-2 infection in hiPSC-derived neurons is cathepsin-dependent and causes differential accumulation of HIF1ɑ and phosphorylated tau

  • Mol Ther Nucleic Acids. 2025 Sep 30;36(4):102726. doi: 10.1016/j.omtn.2025.102726.
Pinja Kettunen  1 ,  Janika Ruuska  2 ,  Tania Quirin  2 ,  Ravi Ojha  2 ,  Saber H Saber  3  4  5 ,  Julian D J Sng  6 ,  Sean Morrison  2 ,  Bahaa Al-Mhanawi  2 ,  Mohammed R Shaker  2  7  8 ,  Simon De Neck  9 ,  Anja Kipar  9 ,  Lassi Paavolainen  10 ,  Ernst Wolvetang  2 ,  Merja Joensuu  3 ,  Jari Koistinaho  1  11 ,  Taisia Rolova  1 ,  Giuseppe Balistreri  1  2
Affiliations
  • 1. Helsinki Institute of Life Science (HiLIFE), Neuroscience Center, University of Helsinki, Helsinki, Finland.
  • 2. Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
  • 3. Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
  • 4. Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
  • 5. Zoology and Entomology Department, Faculty of Science, Assiut University, Assiut 71516, Egypt.
  • 6. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
  • 7. Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
  • 8. College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
  • 9. Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
  • 10. Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
  • 11. Drug Research Program, Division of Pharmacology and Pharmacotherapy, University of Helsinki, Helsinki, Finland.
PMID: 41216428 DOI: 10.1016/j.omtn.2025.102726
Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to infect areas of the human brain and a subset of neurons in vitro. We have previously demonstrated that the virus enters human induced pluripotent stem cell (hiPSC)-derived neurons via an endosomal-lysosomal pathway. Here, we show that neuronal Infection with both SARS-CoV-2 Wuhan and Omicron XBB.1.5 variants is dependent on cathepsins and can be blocked by an inhibitor of Cathepsin B. The result was reproducible in non-transgenic hiPSC-derived cortical organoids. We further show that SARS-CoV-2 can replicate in neuron cultures, but the infectivity of the newly produced virions declined at 24 h post-infection despite a further increase in released viral RNA at later time points. The number of infected neurons decreased within five days, suggesting virus-induced neuronal cell death. The Infection also caused the accumulation of the hypoxia-inducible stress factor HIF1-α in infected neurons under normoxia. Finally, expanding previous findings, in SARS-CoV-2 infected neurons, the microtubule-associated protein tau was hyperphosphorylated at multiple loci, including S202/T205, and mislocalized to the soma of infected 2D-neuronal cultures, but not in 3D-organotypic models. Hence, the neurodegenerative potential of SARS-CoV-2 Infection should be carefully considered in different Infection models.

Keywords
CA-004 ME; HIF-1α; MT: Clinical Applications; SARS-COV-2; antivirals; cathepsins; microglia; neurodegeneration; tau; virus entry.
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