Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Advertisement

Scientific Reports
  • View all journals
  • Search
  • My Account Login
  • Content Explore content
  • About the journal
  • Publish with us
  • Sign up for alerts
  • RSS feed
  1. nature
  2. scientific reports
  3. articles
  4. article
Genome-wide screens identify core regulators of cell surface prion protein expression
Download PDF
Download PDF
  • Article
  • Open access
  • Published: 21 January 2026

Genome-wide screens identify core regulators of cell surface prion protein expression

  • Kathryn S. Beauchemin1 &
  • Surachai Supattapone1,2 

Scientific Reports , Article number:  (2026) Cite this article

  • 773 Accesses

  • 7 Altmetric

  • Metrics details

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Biotechnology
  • Cell biology
  • Molecular biology
  • Neuroscience

Abstract

Expression of the cellular prion protein, PrPC, on the surface of neurons plays an important role in the pathogenesis of prion disease. We performed genome-wide CRISPR/Cas9 knockout screens in prion-infectible cells of neuronal origin (CAD5) to identify regulators of cell surface PrPC expression. We identified and validated 46 positive and 21 negative regulators of cell surface PrPC expression in undifferentiated CAD5 cells. Pathway analysis of the screening dataset showed that genes involved in the glycophosphatidylinositol (GPI) anchor and N-glycosylation biosynthetic pathways were overrepresented as positive regulators of cell surface PrPC. We also sought to determine whether the same or different genes regulate cell surface PrPC in CAD5 cells that have been differentiated to a more neuronal state and validated 41 positive and 13 negative regulators of CAD5 cell surface PrPC expression in the differentiated state. We identified 23 core genes as shared between the undifferentiated and differentiated cell states, including many positive regulators involved in GPI anchor biosynthesis. Intriguingly, unique regulators were also identified in the undifferentiated and differentiated cell states, suggesting that some mechanisms regulating cell surface PrPC expression in CAD5 cells are dependent on cell state. This list of core genes involved in regulating cell surface PrPC expression in a prion-susceptible, neuron-like cell type offers a valuable guide for future research and may help identify potential therapeutic targets for prion disease and other neurodegenerative diseases.

Similar content being viewed by others

Novel anti-prion compounds screening in prion-infected cell culture model combined with surface plasmon resonance analysis

Article Open access 26 November 2025

Characterization of PANoptosis-related genes in Crohn’s disease by integrated bioinformatics, machine learning and experiments

Article Open access 22 May 2024

Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis

Article 24 May 2021

Data availability

Raw .fastq files from all screening samples have been deposited with Mendeley Data and can be found using the following DOIs: 10.17632/jv32cvpn3r.1, 10.17632/5pfdty7zd6.1, 10.17632/p5t6d78zn8.1, 10.17632/vs9fwhbcvj.1, 10.17632/tmkn3zsjts.1, 10.17632/jb89dp34d8.1.

References

  1. Hadlow, W. J. Scrapie and Kuru. Lancet 1959, 289–290 (1959).

  2. Klatzo, I., Gajdusek, D. C. & Zigas, V. Pathology of Kuru. Lab. Invest. 8, 799–847 (1959).

    Google Scholar 

  3. Prusiner, S. B. Prions. Proc. Natl. Acad. Sci. U S A 95, 13363–13383 (1998).

  4. Alper, T., Cramp, W. A., Haig, D. A. & Clarke, M. C. Does the agent of scrapie replicate without nucleic acid? Nature 214, 764–766 (1967).

    Google Scholar 

  5. Prusiner, S. B. Novel proteinaceous infectious particles cause scrapie. Science 216, 136–144 (1982).

    Google Scholar 

  6. Basler, K. et al. Scrapie and cellular PrP isoforms are encoded by the same chromosomal gene. Cell 46, 417–428 (1986).

    Google Scholar 

  7. Pan, K. M. et al. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins. Proc. Natl. Acad. Sci. U S A. 90, 10962–10966 (1993).

    Google Scholar 

  8. McKinley, M. P., Bolton, D. C. & Prusiner, S. B. A protease-resistant protein is a structural component of the scrapie prion. Cell 35, 57–62 (1983).

    Google Scholar 

  9. Prusiner, S. B. et al. Scrapie prions aggregate to form amyloid-like birefringent rods. Cell 35, 349–358 (1983).

    Google Scholar 

  10. Budka, H. Neuropathology of prion diseases. Br. Med. Bull. 66, 121–130 (2003).

    Google Scholar 

  11. Stahl, N., Borchelt, D. R., Hsiao, K. & Prusiner, S. B. Scrapie prion protein contains a phosphatidylinositol glycolipid. Cell 51, 229–240 (1987).

    Google Scholar 

  12. Endo, T., Groth, D., Prusiner, S. B. & Kobata, A. Diversity of oligosaccharide structures linked to asparagines of the scrapie prion protein. Biochemistry 28, 8380–8388 (1989).

    Google Scholar 

  13. Turk, E., Teplow, D. B., Hood, L. E. & Prusiner, S. B. Purification and properties of the cellular and scrapie hamster prion proteins. Eur. J. Biochem. 176, 21–30 (1988).

    Google Scholar 

  14. Stahl, N. et al. Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry 32, 1991–2002 (1993).

    Google Scholar 

  15. Haraguchi, T. et al. Asparagine-linked glycosylation of the scrapie and cellular prion proteins. Arch. Biochem. Biophys. 274, 1–13 (1989).

    Google Scholar 

  16. Wopfner, F. et al. Analysis of 27 mammalian and 9 avian PrPs reveals high conservation of flexible regions of the prion protein. J. Mol. Biol. 289, 1163–1178 (1999).

    Google Scholar 

  17. Bendheim, P. E. et al. Nearly ubiquitous tissue distribution of the scrapie agent precursor protein. Neurology 42, 149–156 (1992).

    Google Scholar 

  18. Campana, V., Sarnataro, D. & Zurzolo, C. The highways and byways of prion protein trafficking. Trends Cell. Biol. 15, 102–111. https://doi.org/10.1016/j.tcb.2004.12.002 (2005).

    Google Scholar 

  19. Vey, M. et al. Subcellular colocalization of the cellular and scrapie prion proteins in caveolae-like membranous domains. Proc. Natl. Acad. Sci. U S A. 93, 14945–14949 (1996).

    Google Scholar 

  20. Taraboulos, A. et al. Cholesterol depletion and modification of COOH-terminal targeting sequence of the prion protein inhibit formation of the scrapie isoform. J. Cell. Biol. 129, 121–132 (1995).

    Google Scholar 

  21. Shyng, S. L., Huber, M. T. & Harris, D. A. A prion protein cycles between the cell surface and an endocytic compartment in cultured neuroblastoma cells. J. Biol. Chem. 268, 15922–15928 (1993).

    Google Scholar 

  22. Shyng, S. L., Heuser, J. E. & Harris, D. A. A glycolipid-anchored prion protein is endocytosed via clathrin-coated pits. J. Cell. Biol. 125, 1239–1250 (1994).

    Google Scholar 

  23. Castle, A. R. & Westaway, D. Prion protein endoproteolysis: cleavage Sites, mechanisms and connections to prion disease. J. Neurochem. 169, e16310. https://doi.org/10.1111/jnc.16310 (2025).

    Google Scholar 

  24. Watts, J. C., Bourkas, M. E. C. & Arshad, H. The function of the cellular prion protein in health and disease. Acta Neuropathol. 135, 159–178. https://doi.org/10.1007/s00401-017-1790-y (2018).

    Google Scholar 

  25. Bueler, H. et al. Normal development and behaviour of mice lacking the neuronal cell- surface PrP protein. Nature 356, 577–582 (1992).

    Google Scholar 

  26. Bueler, H. et al. Mice devoid of PrP are resistant to scrapie. Cell 73, 1339–1347 (1993).

    Google Scholar 

  27. Sakaguchi, S. et al. Accumulation of proteinase K-resistant prion protein (PrP) is restricted by the expression level of normal PrP in mice inoculated with a mouse-adapted strain of the Creutzfeldt-Jakob disease agent. J. Virol. 69, 7586–7592 (1995).

    Google Scholar 

  28. Mallucci, G. et al. Depleting neuronal PrP in prion infection prevents disease and reverses spongiosis. Science 302, 871–874 (2003).

    Google Scholar 

  29. Richt, J. A. et al. Production of cattle lacking prion protein. Nat. Biotechnol. 25, 132–138. https://doi.org/10.1038/nbt1271 (2007).

    Google Scholar 

  30. Benestad, S. L., Austbo, L., Tranulis, M. A., Espenes, A. & Olsaker, I. Healthy goats naturally devoid of prion protein. Vet. Res. 43, 87. https://doi.org/10.1186/1297-9716-43-87 (2012).

    Google Scholar 

  31. Aguzzi, A., Lakkaraju, A. K. K. & Frontzek, K. Toward therapy of human prion diseases. Annu. Rev. Pharmacol. Toxicol. 58, 331–351. https://doi.org/10.1146/annurev-pharmtox-010617-052745 (2018).

    Google Scholar 

  32. Bueler, H. et al. High prion and PrPSc levels but delayed onset of disease in scrapie- inoculated mice heterozygous for a disrupted PrP gene. Mol. Med. 1, 19–30 (1994).

    Google Scholar 

  33. Minikel, E. V. et al. Prion protein Lowering is a disease-modifying therapy across prion disease stages, strains and endpoints. Nucleic Acids Res. 48, 10615–10631. https://doi.org/10.1093/nar/gkaa616 (2020).

    Google Scholar 

  34. Gentile, J. E. et al. Divalent siRNA for prion disease. bioRxiv (2024). https://doi.org/10.1101/2024.12.05.627039.

  35. Chou, S.-W. Zinc Finger repressors mediate widespread PRNP; lowering in the nonhuman primate brain and profoundly extend survival in prion disease mice. bioRxiv https://doi.org/10.1101/2025.03.05.636713 (2025).

  36. Heinzer, D. et al. Novel regulators of PrPC biosynthesis revealed by genome-wide RNA interference. PLoS Pathog. 17, e1010013. https://doi.org/10.1371/journal.ppat.1010013 (2021).

    Google Scholar 

  37. Raymond, G. J. et al. Antisense oligonucleotides extend survival of prion-infected mice. JCI Insight. 5, 256. https://doi.org/10.1172/jci.insight.131175 (2019).

  38. Mortberg, M. A. et al. Regional variability and genotypic and pharmacodynamic effects on PrP concentration in the CNS. JCI Insight. 7, 96. https://doi.org/10.1172/jci.insight.156532 (2022).

  39. Bender, H. et al. PrPC knockdown by liposome-siRNA-peptide complexes (LSPCs) prolongs survival and normal behavior of prion-infected mice immunotolerant to treatment. PLoS One. 14, e0219995. https://doi.org/10.1371/journal.pone.0219995 (2019).

    Google Scholar 

  40. An, M. et al. In vivo base editing extends lifespan of a humanized mouse model of prion disease. Nat. Med. 31, 1319–1328. https://doi.org/10.1038/s41591-024-03466-w (2025).

    Google Scholar 

  41. Neumann, E. N. et al. Brainwide Silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor. Science 384, ado7082. https://doi.org/10.1126/science.ado7082 (2024).

    Google Scholar 

  42. Citron, M. et al. Mutant presenilins of alzheimer’s disease increase production of 42-residue amyloid beta-protein in both transfected cells and Transgenic mice. Nat. Med. 3, 67–72. https://doi.org/10.1038/nm0197-67 (1997).

    Google Scholar 

  43. Cleary, J. P. et al. Natural oligomers of the amyloid-beta protein specifically disrupt cognitive function. Nat. Neurosci. 8, 79–84. https://doi.org/10.1038/nn1372 (2005).

    Google Scholar 

  44. Lauren, J., Gimbel, D. A., Nygaard, H. B., Gilbert, J. W. & Strittmatter, S. M. Cellular prion protein mediates impairment of synaptic plasticity by amyloid-beta oligomers. Nature 457, 1128–1132. https://doi.org/10.1038/nature07761 (2009).

    Google Scholar 

  45. Gimbel, D. A. et al. Memory impairment in Transgenic alzheimer mice requires cellular prion protein. J. Neurosci. 30, 6367–6374. https://doi.org/10.1523/JNEUROSCI.0395-10.2010 (2010).

    Google Scholar 

  46. Purro, S. A., Nicoll, A. J. & Collinge, J. Prion protein as a toxic acceptor of Amyloid-beta oligomers. Biol. Psychiatry. 83, 358–368. https://doi.org/10.1016/j.biopsych.2017.11.020 (2018).

    Google Scholar 

  47. Salazar, S. V. et al. Conditional deletion of Prnp rescues behavioral and synaptic deficits after disease onset in Transgenic alzheimer’s disease. J. Neurosci. 37, 9207–9221. https://doi.org/10.1523/JNEUROSCI.0722-17.2017 (2017).

    Google Scholar 

  48. Kostylev, M. A. et al. Prion-Protein-interacting Amyloid-beta oligomers of high molecular weight are tightly correlated with memory impairment in multiple alzheimer mouse models. J. Biol. Chem. 290, 17415–17438. https://doi.org/10.1074/jbc.M115.643577 (2015).

    Google Scholar 

  49. Chung, E. et al. Anti-PrPC monoclonal antibody infusion as a novel treatment for cognitive deficits in an alzheimer’s disease model mouse. BMC Neurosci. 11, 130. https://doi.org/10.1186/1471-2202-11-130 (2010).

    Google Scholar 

  50. Freir, D. B. et al. Interaction between prion protein and toxic amyloid beta assemblies can be therapeutically targeted at multiple sites. Nat. Commun. 2, 336. https://doi.org/10.1038/ncomms1341 (2011).

    Google Scholar 

  51. Klyubin, I. et al. Peripheral administration of a humanized anti-PrP antibody blocks alzheimer’s disease Abeta synaptotoxicity. J. Neurosci. 34, 6140–6145. https://doi.org/10.1523/JNEUROSCI.3526-13.2014 (2014).

    Google Scholar 

  52. Peters, C., Espinoza, M. P., Gallegos, S., Opazo, C. & Aguayo, L. G. Alzheimer’s Abeta interacts with cellular prion protein inducing neuronal membrane damage and synaptotoxicity. Neurobiol. Aging. 36, 1369–1377. https://doi.org/10.1016/j.neurobiolaging.2014.11.019 (2015).

    Google Scholar 

  53. Cox, T. O. et al. Anti-PrP(C) antibody rescues cognition and synapses in Transgenic alzheimer mice. Ann. Clin. Transl Neurol. 6, 554–574. https://doi.org/10.1002/acn3.730 (2019).

    Google Scholar 

  54. Gunther, E. C. et al. Rescue of Transgenic alzheimer’s pathophysiology by polymeric cellular prion protein antagonists. Cell. Rep. 26, 1368. https://doi.org/10.1016/j.celrep.2019.01.064 (2019).

    Google Scholar 

  55. Stoner, A. et al. Neuronal transcriptome, tau and synapse loss in Alzheimer’s knock-in mice require prion protein. Alzheimers Res. Ther. 15, 69. https://doi.org/10.1186/s13195-023-01345-z (2023).

  56. De Cecco, E. et al. The uptake of Tau amyloid fibrils is facilitated by the cellular prion protein and hampers prion propagation in cultured cells. J. Neurochem. 155, 577–591. https://doi.org/10.1111/jnc.15040 (2020).

    Google Scholar 

  57. Corbett, G. T. et al. PrP is a central player in toxicity mediated by soluble aggregates of neurodegeneration-causing proteins. Acta Neuropathol. 139, 503–526. https://doi.org/10.1007/s00401-019-02114-9 (2020).

    Google Scholar 

  58. Vieira, T., Barros, C. A., Domingues, R. & Outeiro, T. F. PrP Meets alpha-synuclein: molecular mechanisms and implications for disease. J. Neurochem. 168, 1625–1639. https://doi.org/10.1111/jnc.15992 (2024).

    Google Scholar 

  59. Scialo, C. et al. The cellular prion protein increases the uptake and toxicity of TDP-43 fibrils. Viruses 13, 85. https://doi.org/10.3390/v13081625 (2021).

  60. Davis, E. M. et al. Comparative haploid genetic screens reveal divergent pathways in the biogenesis and trafficking of Glycophosphatidylinositol-Anchored proteins. Cell. Rep. 11, 1727–1736. https://doi.org/10.1016/j.celrep.2015.05.026 (2015).

    Google Scholar 

  61. Pease, D. et al. Genome-wide identification of MicroRNAs regulating the human prion protein. Brain Pathol. 29, 232–244. https://doi.org/10.1111/bpa.12679 (2019).

    Google Scholar 

  62. Yin, J. A. et al. Arrayed CRISPR libraries for the genome-wide activation, deletion and Silencing of human protein-coding genes. Nat. Biomed. Eng. 9, 127–148. https://doi.org/10.1038/s41551-024-01278-4 (2025).

    Google Scholar 

  63. Mahal, S. P. et al. Prion strain discrimination in cell culture: the cell panel assay. Proc. Natl. Acad. Sci. U S A. 104, 20908–20913 (2007).

    Google Scholar 

  64. Browning, S. et al. Abrogation of complex glycosylation by swainsonine results in strain- and cell-specific Inhibition of prion replication. J. Biol. Chem. 286, 40962–40973. https://doi.org/10.1074/jbc.M111.283978 (2011).

    Google Scholar 

  65. Berry, D. B. et al. Drug resistance confounding prion therapeutics. Proc. Natl. Acad. Sci. U S A. 110, E4160–4169. https://doi.org/10.1073/pnas.1317164110 (2013).

    Google Scholar 

  66. McKinnon, C. et al. Prion-mediated neurodegeneration is associated with early impairment of the ubiquitin-proteasome system. Acta Neuropathol. 131, 411–425. https://doi.org/10.1007/s00401-015-1508-y (2016).

    Google Scholar 

  67. Bourkas, M. E. C. et al. Engineering a murine cell line for the stable propagation of hamster prions. J. Biol. Chem. 294, 4911–4923. https://doi.org/10.1074/jbc.RA118.007135 (2019).

    Google Scholar 

  68. Walia, R., Ho, C. C., Lee, C., Gilch, S. & Schatzl, H. M. Gene-edited murine cell lines for propagation of chronic wasting disease prions. Sci. Rep. 9, 11151. https://doi.org/10.1038/s41598-019-47629-z (2019).

    Google Scholar 

  69. Arshad, H. et al. A single protective polymorphism in the prion protein blocks cross-species prion replication in cultured cells. J. Neurochem. 165, 230–245. https://doi.org/10.1111/jnc.15739 (2023).

    Google Scholar 

  70. Frontzek, K. et al. A conformational switch controlling the toxicity of the prion protein. Nat. Struct. Mol. Biol. 29, 831–840. https://doi.org/10.1038/s41594-022-00814-7 (2022).

    Google Scholar 

  71. Avar, M. et al. An arrayed genome-wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate-limiting for prion propagation. EMBO J. 41, e112338. https://doi.org/10.15252/embj.2022112338 (2022).

    Google Scholar 

  72. Ali, T. et al. Oral administration of repurposed drug targeting Cyp46A1 increases survival times of prion infected mice. Acta Neuropathol. Commun. 9, 963. https://doi.org/10.1186/s40478-021-01162-1 (2021).

  73. Shim, S. Y., Karri, S., Law, S., Schatzl, H. M. & Gilch, S. Prion infection impairs lysosomal degradation capacity by interfering with rab7 membrane attachment in neuronal cells. Sci. Rep. 6, 21658. https://doi.org/10.1038/srep21658 (2016).

    Google Scholar 

  74. Fremuntova, Z. et al. Simple 3D spheroid cell culture model for studies of prion infection. Eur. J. Neurosci. 60, 4437–4452. https://doi.org/10.1111/ejn.16444 (2024).

    Google Scholar 

  75. Fremuntova, Z. et al. Changes in cellular prion protein expression, processing and localisation during differentiation of the neuronal cell line CAD 5. Biol. Cell. 112, 1–21. https://doi.org/10.1111/boc.201900045 (2020).

    Google Scholar 

  76. Arshad, H. & Watts, J. C. Genetically engineered cellular models of prion propagation. Cell. Tissue Res. 392, 63–80. https://doi.org/10.1007/s00441-022-03630-z (2023).

    Google Scholar 

  77. Arshad, H. et al. The molecular determinants of a universal prion acceptor. PLoS Pathog. 20, e1012538. https://doi.org/10.1371/journal.ppat.1012538 (2024).

    Google Scholar 

  78. Arshad, H. et al. The aminoglycoside G418 hinders de Novo prion infection in cultured cells. J. Biol. Chem. 297, 101073. https://doi.org/10.1016/j.jbc.2021.101073 (2021).

    Google Scholar 

  79. Qi, Y., Wang, J. K., McMillian, M. & Chikaraishi, D. M. Characterization of a CNS cell line, CAD, in which morphological differentiation is initiated by serum deprivation. J. Neurosci. 17, 1217–1225 (1997).

    Google Scholar 

  80. Abdulrahman, B. A., Abdelaziz, D. H. & Schatzl, H. M. Autophagy regulates Exosomal release of prions in neuronal cells. J. Biol. Chem. 293, 8956–8968. https://doi.org/10.1074/jbc.RA117.000713 (2018).

    Google Scholar 

  81. Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554. https://doi.org/10.1186/s13059-014-0554-4 (2014).

    Google Scholar 

  82. Wang, B. et al. Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. Nat. Protoc. 14, 756–780. https://doi.org/10.1038/s41596-018-0113-7 (2019).

    Google Scholar 

  83. Kanehisa, M. Toward Understanding the origin and evolution of cellular organisms. Protein Sci. 28, 1947–1951. https://doi.org/10.1002/pro.3715 (2019).

    Google Scholar 

  84. Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30. https://doi.org/10.1093/nar/28.1.27 (2000).

    Google Scholar 

  85. Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Res. 53, D672–D677. https://doi.org/10.1093/nar/gkae909 (2025).

    Google Scholar 

  86. Doench, J. G. et al. Optimized SgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191. https://doi.org/10.1038/nbt.3437 (2016).

    Google Scholar 

  87. DeWeirdt, P. C. et al. Genetic screens in isogenic mammalian cell lines without single cell cloning. Nat. Commun. 11, 752. https://doi.org/10.1038/s41467-020-14620-6 (2020).

    Google Scholar 

  88. Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods. 11, 783–784. https://doi.org/10.1038/nmeth.3047 (2014).

    Google Scholar 

  89. Mayer, M. P. & Bukau, B. Hsp70 chaperones: cellular functions and molecular mechanism. Cell. Mol. Life Sci. 62, 670–684. https://doi.org/10.1007/s00018-004-4464-6 (2005).

    Google Scholar 

  90. Jin, T. et al. The chaperone protein bip binds to a mutant prion protein and mediates its degradation by the proteasome. J. Biol. Chem. 275, 38699–38704 (2000).

    Google Scholar 

  91. Abrams, J. et al. Functional genomics screen identifies proteostasis targets that modulate prion protein (PrP) stability. Cell. Stress Chaperones. 26, 443–452. https://doi.org/10.1007/s12192-021-01191-8 (2021).

    Google Scholar 

  92. Shoup, D. & Priola, S. A. Grp78 destabilization of infectious prions is strain-specific and modified by multiple factors including accessory chaperones and pH. J. Biol. Chem. 300, 107346. https://doi.org/10.1016/j.jbc.2024.107346 (2024).

    Google Scholar 

  93. Shoup, D. & Priola, S. A. Chaperone-mediated disaggregation of infectious prions releases particles that seed new prion formation in a strain-specific manner. J. Biol. Chem. 301, 108062. https://doi.org/10.1016/j.jbc.2024.108062 (2025).

    Google Scholar 

  94. Chesebro, B. et al. Anchorless prion protein results in infectious amyloid disease without clinical scrapie. Science 308, 1435–1439 (2005).

    Google Scholar 

  95. Chesebro, B. et al. Fatal transmissible amyloid encephalopathy: a new type of prion disease associated with lack of prion protein membrane anchoring. PLoS Pathog. 6, e1000800. https://doi.org/10.1371/journal.ppat.1000800 (2010).

    Google Scholar 

  96. Stohr, J. et al. Spontaneous generation of anchorless prions in Transgenic mice. Proc. Natl. Acad. Sci. U S A. 108, 21223–21228. https://doi.org/10.1073/pnas.1117827108 (2011).

    Google Scholar 

  97. Lang, S. et al. Different effects of Sec61alpha, Sec62 and Sec63 depletion on transport of polypeptides into the Endoplasmic reticulum of mammalian cells. J. Cell Sci. 125, 1958–1969. https://doi.org/10.1242/jcs.096727 (2012).

    Google Scholar 

  98. Kim, S. J. & Hegde, R. S. Cotranslational partitioning of nascent prion protein into multiple populations at the translocation channel. Mol. Biol. Cell 13, 3775–3786. https://doi.org/10.1091/mbc.e02-05-0293 (2002).

  99. Conti, B. J., Devaraneni, P. K., Yang, Z., David, L. L. & Skach, W. R. Cotranslational stabilization of Sec62/63 within the ER Sec61 translocon is controlled by distinct substrate-driven translocation events. Mol. Cell. 58, 269–283. https://doi.org/10.1016/j.molcel.2015.02.018 (2015).

    Google Scholar 

  100. Pobre, K. F. R., Poet, G. J. & Hendershot, L. M. The Endoplasmic reticulum (ER) chaperone bip is a master regulator of ER functions: getting by with a little help from ERdj friends. J. Biol. Chem. 294, 2098–2108. https://doi.org/10.1074/jbc.REV118.002804 (2019).

    Google Scholar 

  101. Ziska, A. et al. The signal peptide plus a cluster of positive charges in prion protein dictate chaperone-mediated Sec61 channel gating. Biol. Open. 8, 69. https://doi.org/10.1242/bio.040691 (2019).

  102. Park, K. W. et al. The Endoplasmic reticulum chaperone GRP78/BiP modulates prion propagation in vitro and in vivo. Sci. Rep. 7, 44723. https://doi.org/10.1038/srep44723 (2017).

    Google Scholar 

  103. Matera, A. G. & Wang, Z. A day in the life of the spliceosome. Nat. Rev. Mol. Cell. Biol. 15, 108–121. https://doi.org/10.1038/nrm3742 (2014).

    Google Scholar 

  104. Maeder, C. I. et al. The THO complex coordinates transcripts for synapse development and dopamine neuron survival. Cell 174, 1436–1449 e1420. https://doi.org/10.1016/j.cell.2018.07.046 (2018).

  105. Vonk, W. I. M. et al. Differentiation drives widespread rewiring of the neural stem cell chaperone network. Mol. Cell 78, 329–345 e329. https://doi.org/10.1016/j.molcel.2020.03.009 (2020).

  106. Thiruvalluvan, A. et al. DNAJB6, a key factor in neuronal sensitivity to amyloidogenesis. Mol. Cell 78, 346–358 e349. https://doi.org/10.1016/j.molcel.2020.02.022 (2020).

  107. Kimura, K. et al. Glycoproteomic analysis of the changes in protein N-glycosylation during neuronal differentiation in human-induced pluripotent stem cells and derived neuronal cells. Sci. Rep. 11, 11169. https://doi.org/10.1038/s41598-021-90102-z (2021).

    Google Scholar 

  108. Nairn, A. V. et al. Regulation of glycan structures in murine embryonic stem cells: combined transcript profiling of glycan-related genes and glycan structural analysis. J. Biol. Chem. 287, 37835–37856. https://doi.org/10.1074/jbc.M112.405233 (2012).

    Google Scholar 

  109. An, H. J. et al. Extensive determination of glycan heterogeneity reveals an unusual abundance of high mannose glycans in enriched plasma membranes of human embryonic stem cells. Mol. Cell. Proteomics: MCP 11, M111 010660. https://doi.org/10.1074/mcp.M111.010660 (2012).

  110. Terashima, M., Amano, M., Onodera, T., Nishimura, S. & Iwasaki, N. Quantitative glycomics monitoring of induced pluripotent- and embryonic stem cells during neuronal differentiation. Stem Cell. Res. 13, 454–464. https://doi.org/10.1016/j.scr.2014.10.006 (2014).

    Google Scholar 

  111. Cindric, A. et al. Total cell N-glycosylation is altered during differentiation of induced pluripotent stem cells to neural stem cells and is disturbed by trisomy 21. BBA Adv. 7, 100137. https://doi.org/10.1016/j.bbadva.2024.100137 (2025).

    Google Scholar 

  112. Ermonval, M., Petit, D., Le Duc, A., Kellermann, O. & Gallet, P. F. Glycosylation-related genes are variably expressed depending on the differentiation state of a bioaminergic neuronal cell line: implication for the cellular prion protein. Glycoconj. J. (2008).

  113. Rogers, M., Taraboulos, A., Scott, M., Groth, D. & Prusiner, S. B. Intracellular accumulation of the cellular prion protein after mutagenesis of its Asn-linked glycosylation sites. Glycobiology 1, 101–109 (1990).

    Google Scholar 

  114. Gao, Z. et al. Glycan-deficient PrP stimulates VEGFR2 signaling via glycosaminoglycan. Cell. Signal. 28, 652–662. https://doi.org/10.1016/j.cellsig.2016.03.010 (2016).

    Google Scholar 

  115. Yi, C. W. et al. Glycosylation significantly inhibits the aggregation of human prion protein and decreases its cytotoxicity. Sci. Rep. 8, 12603. https://doi.org/10.1038/s41598-018-30770-6 (2018).

    Google Scholar 

  116. Cancellotti, E. et al. Altered glycosylated PrP proteins can have different neuronal trafficking in brain but do not acquire scrapie-like properties. J. Biol. Chem. 280, 42909–42918 (2005).

    Google Scholar 

  117. Wiseman, F. K. et al. The glycosylation status of PrPC is a key factor in determining transmissible spongiform encephalopathy transmission between species. J. Virol. 89, 4738–4747. https://doi.org/10.1128/JVI.02296-14 (2015).

    Google Scholar 

  118. Tuzi, N. L. et al. Host PrP glycosylation: a major factor determining the outcome of prion infection. PLoS Biol. 6, e100 (2008).

    Google Scholar 

  119. Aguilar-Calvo, P., Callender, J. A. & Sigurdson, C. J. Short and sweet: how glycans impact prion conversion, cofactor interactions, and cross-species transmission. PLoS Pathog. 17, e1009123. https://doi.org/10.1371/journal.ppat.1009123 (2021).

    Google Scholar 

  120. Grasbon-Frodl, E. et al. Loss of glycosylation associated with the T183A mutation in human prion disease. Acta Neuropathol. 108, 476–484. https://doi.org/10.1007/s00401-004-0913-4 (2004).

    Google Scholar 

  121. Cracco, L. et al. Efficient transmission of human prion diseases to a glycan-free prion protein-expressing host. Brain: J. Neurol. 147, 1539–1552. https://doi.org/10.1093/brain/awad399 (2024).

    Google Scholar 

  122. Camacho, M. V., Telling, G., Kong, Q., Gambetti, P. & Notari, S. Role of prion protein glycosylation in replication of human prions by protein misfolding Cyclic amplification. Lab. Invest. 99, 1741–1748. https://doi.org/10.1038/s41374-019-0282-1 (2019).

    Google Scholar 

  123. Katorcha, E., Makarava, N., Savtchenko, R. & Baskakov, I. V. Sialylation of the prion protein glycans controls prion replication rate and glycoform ratio. Sci. Rep. 5, 16912. https://doi.org/10.1038/srep16912 (2015).

    Google Scholar 

  124. Srivastava, S. et al. Sialylation controls prion fate in vivo. J. Biol. Chem. 292, 2359–2368. https://doi.org/10.1074/jbc.M116.768010 (2017).

    Google Scholar 

  125. Burke, C. M. et al. Cofactor and glycosylation preferences for in vitro prion conversion are predominantly determined by strain conformation. PLoS Pathog. 16, e1008495. https://doi.org/10.1371/journal.ppat.1008495 (2020).

    Google Scholar 

  126. Piro, J. R. et al. Prion protein glycosylation is not required for strain-specific neurotropism. J. Virol. 83, 5321–5328 (2009).

    Google Scholar 

  127. Nishina, K. A. et al. The stoichiometry of host PrPC glycoforms modulates the efficiency of PrPSc formation in vitro. Biochemistry 45, 14129–14139 (2006).

    Google Scholar 

  128. Sevillano, A. M. et al. Prion protein glycans reduce intracerebral fibril formation and spongiosis in prion disease. J. Clin. Investig. 130, 1350–1362. https://doi.org/10.1172/JCI131564 (2020).

    Google Scholar 

  129. Kang, H. E. et al. Incomplete glycosylation during prion infection unmasks a prion protein epitope that facilitates prion detection and strain discrimination. J. Biol. Chem. 295, 10420–10433. https://doi.org/10.1074/jbc.RA120.012796 (2020).

    Google Scholar 

  130. Cancellotti, E. et al. Glycosylation of PrPC determines timing of neuroinvasion and targeting in the brain following transmissible spongiform encephalopathy infection by a peripheral route. J. Virol. 84, 3464–3475. https://doi.org/10.1128/JVI.02374-09 (2010).

    Google Scholar 

  131. Cancellotti, E. et al. Post-translational changes to PrP alter transmissible spongiform encephalopathy strain properties. EMBO J. 32, 756–769. https://doi.org/10.1038/emboj.2013.6 (2013).

    Google Scholar 

  132. Neuendorf, E. et al. Glycosylation deficiency at either one of the two glycan attachment sites of cellular prion protein preserves susceptibility to bovine spongiform encephalopathy and scrapie infections. J. Biol. Chem. 279, 53306–53316 (2004).

    Google Scholar 

  133. Xiao, X. et al. Glycoform-selective prion formation in sporadic and Familial forms of prion disease. PLoS One. 8, e58786. https://doi.org/10.1371/journal.pone.0058786 (2013).

    Google Scholar 

  134. Callender, J. A. et al. Prion protein post-translational modifications modulate Heparan sulfate binding and limit aggregate size in prion disease. Neurobiol. Dis. 142, 104955. https://doi.org/10.1016/j.nbd.2020.104955 (2020).

    Google Scholar 

  135. Guardia, C. M., De Pace, R., Mattera, R. & Bonifacino, J. S. Neuronal functions of adaptor complexes involved in protein sorting. Curr. Opin. Neurobiol. 51, 103–110. https://doi.org/10.1016/j.conb.2018.02.021 (2018).

    Google Scholar 

  136. Zhang, M. et al. A Translocation pathway for vesicle-mediated unconventional protein secretion. Cell 181, 637–652 e615. https://doi.org/10.1016/j.cell.2020.03.031 (2020).

  137. Daverkausen-Fischer, L., Draga, M. & Prols, F. Regulation of Translation, Translocation, and degradation of proteins at the membrane of the Endoplasmic reticulum. Int. J. Mol. Sci. 23, 96. https://doi.org/10.3390/ijms23105576 (2022).

  138. Padhan, P., Simran, Kumar, N., Verma, S. & Glutathione, S. Transferase: a keystone in parkinson’s disease pathogenesis and therapy. Mol. Cell. Neurosci. 132, 103981. https://doi.org/10.1016/j.mcn.2024.103981 (2025).

    Google Scholar 

  139. Hayes, J. D., Flanagan, J. U. & Jowsey, I. R. Glutathione transferases. Annu. Rev. Pharmacol. Toxicol. 45, 51–88. https://doi.org/10.1146/annurev.pharmtox.45.120403.095857 (2005).

    Google Scholar 

  140. Coccia, E. et al. SIVA-1 regulates apoptosis and synaptic function by modulating XIAP interaction with the death receptor antagonist FAIM-L. Cell. Death Dis. 11, 82. https://doi.org/10.1038/s41419-020-2282-x (2020).

    Google Scholar 

  141. Willemse, S. W. et al. UNC13A in amyotrophic lateral sclerosis: from genetic association to therapeutic target. J. Neurol. Neurosurg. Psychiatry. 94, 649–656. https://doi.org/10.1136/jnnp-2022-330504 (2023).

    Google Scholar 

  142. Lauretti, E., Dincer, O. & Pratico, D. Glycogen synthase kinase-3 signaling in alzheimer’s disease. Biochim. Biophys. Acta Mol. Cell. Res. 1867, 118664. https://doi.org/10.1016/j.bbamcr.2020.118664 (2020).

    Google Scholar 

  143. Neizer-Ashun, F., Bhattacharya, R. & Reality, C. H. E. K. Understanding the biology and clinical potential of CHK1. Cancer Lett. 497, 202–211. https://doi.org/10.1016/j.canlet.2020.09.016 (2021).

    Google Scholar 

  144. Deng, M. et al. Identification and functional analysis of a novel Cyclin e/cdk2 substrate ankrd17. J. Biol. Chem. 284, 7875–7888. https://doi.org/10.1074/jbc.M807827200 (2009).

    Google Scholar 

  145. Zenobio, E. G. et al. Blood clot stability and bone formation following maxillary sinus membrane elevation and space maintenance by means of immediate implant placement in humans. A computed tomography study. J. Craniomaxillofac. Surg. 47, 1803–1808. https://doi.org/10.1016/j.jcms.2018.10.004 (2019).

    Google Scholar 

  146. Stahl, N., Baldwin, M. A., Burlingame, A. L. & Prusiner, S. B. Identification of Glycoinositol phospholipid linked and truncated forms of the scrapie prion protein. Biochemistry 29, 8879–8884 (1990).

    Google Scholar 

  147. Stahl, N. et al. Glycosylinositol phospholipid anchors of the scrapie and cellular prion proteins contain Sialic acid. Biochemistry 31, 5043–5053 (1992).

    Google Scholar 

  148. Kamilaris, C. D. C. & Stratakis, C. A. Multiple endocrine neoplasia type 1 (MEN1): an update and the significance of early genetic and clinical diagnosis. Front. Endocrinol. (Lausanne). 10, 339. https://doi.org/10.3389/fendo.2019.00339 (2019).

    Google Scholar 

  149. Mariani, M. et al. Two murine and human homologs of mab-21, a cell fate determination gene involved in caenorhabditis elegans neural development. Hum. Mol. Genet. 8, 2397–2406. https://doi.org/10.1093/hmg/8.13.2397 (1999).

    Google Scholar 

  150. Wong, R. L., Chan, K. K. & Chow, K. L. Developmental expression of Mab21l2 during mouse embryogenesis. Mech. Dev. 87, 185–188. https://doi.org/10.1016/s0925-4773(99)00127-6 (1999).

    Google Scholar 

  151. Srivastava, D. et al. Regulation of cardiac mesodermal and neural crest development by the bHLH transcription factor, dHAND. Nat. Genet. 16, 154–160. https://doi.org/10.1038/ng0697-154 (1997).

    Google Scholar 

  152. Glenewinkel, F. et al. The adaptor protein DCAF7 mediates the interaction of the adenovirus E1A oncoprotein with the protein kinases DYRK1A and HIPK2. Sci. Rep. 6, 28241. https://doi.org/10.1038/srep28241 (2016).

    Google Scholar 

  153. Gao, J. et al. The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis. Elife 4, 896. https://doi.org/10.7554/eLife.07539 (2015).

  154. Fujii, R. et al. Identification of a neuropeptide modified with bromine as an endogenous ligand for GPR7. J. Biol. Chem. 277, 34010–34016. https://doi.org/10.1074/jbc.M205883200 (2002).

    Google Scholar 

  155. AJ, C. Q., Bugai, A. & Barboric, M. Cracking the control of RNA polymerase II elongation by 7SK SnRNP and P-TEFb. Nucleic Acids Res. 44, 7527–7539. https://doi.org/10.1093/nar/gkw585 (2016).

    Google Scholar 

  156. Cascon, A. et al. Whole-exome sequencing identifies MDH2 as a new Familial paraganglioma gene. J. Natl. Cancer Inst. 107, 96. https://doi.org/10.1093/jnci/djv053 (2015).

Download references

Acknowledgements

The authors wish to thank Elisabeth Sergison for creating the Cas9-expressing CAD5 monoclonal line, Gary Ward for FACS of the genome-wide libraries, Chris Shoemaker for use of the Sony SH800 sorter as well as technical and scientific guidance, Margaret Ackerman for scientific guidance, Tamutenda Chidawanyika and Kenneth Mark for guidance with CRISPR/Cas9 screening procedures and bioinformatic analysis, Lisa Francomacaro, Rachel Pepin, Abigail Schwind, and Francesca Salerno for scientific guidance and support. Kathryn Beauchemin would also like to thank her husband, Marc Beauchemin, for his unwavering support. This study was funded by the National Institute for Neurological Diseases and Stroke (1R37NS125431, R01NS117276 and R01NS118796 to S.S.) and the National Institutes of Health (P20-GM113132 to Dean Madden).

Funding

This study was funded by the National Institute for Neurological Diseases and Stroke (1R37NS125431, R01NS117276 and R01NS118796 to S.S.) and the National Institutes of Health (5T32AI007519-22 to Deborah Hogan) (P20-GM113132 to Dean Madden).

Author information

Authors and Affiliations

  1. Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, 7200 Vail Building, Hanover, NH, 03755, USA

    Kathryn S. Beauchemin & Surachai Supattapone

  2. Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA

    Surachai Supattapone

Authors
  1. Kathryn S. Beauchemin
    View author publications

    Search author on:PubMed Google Scholar

  2. Surachai Supattapone
    View author publications

    Search author on:PubMed Google Scholar

Contributions

K.S.B. performed all of the experiments, wrote the main manuscript text, and prepared figures, participated in project design, experimental troubleshooting, and reviewed and edited the manuscript text. S.S. participated in project design, experimental troubleshooting, and reviewed and edited the manuscript text.

Corresponding author

Correspondence to Surachai Supattapone.

Ethics declarations

Competing interests

K.S.B. and S.S. are named inventors on a patent application related to this work.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary Material 1

Supplementary Material 2

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Beauchemin, K.S., Supattapone, S. Genome-wide screens identify core regulators of cell surface prion protein expression. Sci Rep (2026). https://doi.org/10.1038/s41598-026-37137-2

Download citation

  • Received: 10 July 2025

  • Accepted: 20 January 2026

  • Published: 21 January 2026

  • DOI: https://doi.org/10.1038/s41598-026-37137-2

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

Keywords

  • CRISPR
  • N-glycosylation
  • Differentiation
  • CAD5
  • Prion
Download PDF

Advertisement

Explore content

  • Research articles
  • News & Comment
  • Collections
  • Subjects
  • Follow us on Facebook
  • Follow us on Twitter
  • Sign up for alerts
  • RSS feed

About the journal

  • About Scientific Reports
  • Contact
  • Journal policies
  • Guide to referees
  • Calls for Papers
  • Editor's Choice
  • Journal highlights
  • Open Access Fees and Funding

Publish with us

  • For authors
  • Language editing services
  • Open access funding
  • Submit manuscript

Search

Advanced search

Quick links

  • Explore articles by subject
  • Find a job
  • Guide to authors
  • Editorial policies

Scientific Reports (Sci Rep)

ISSN 2045-2322 (online)

nature.com sitemap

About Nature Portfolio

  • About us
  • Press releases
  • Press office
  • Contact us

Discover content

  • Journals A-Z
  • Articles by subject
  • protocols.io
  • Nature Index

Publishing policies

  • Nature portfolio policies
  • Open access

Author & Researcher services

  • Reprints & permissions
  • Research data
  • Language editing
  • Scientific editing
  • Nature Masterclasses
  • Research Solutions

Libraries & institutions

  • Librarian service & tools
  • Librarian portal
  • Open research
  • Recommend to library

Advertising & partnerships

  • Advertising
  • Partnerships & Services
  • Media kits
  • Branded content

Professional development

  • Nature Awards
  • Nature Careers
  • Nature Conferences

Regional websites

  • Nature Africa
  • Nature China
  • Nature India
  • Nature Japan
  • Nature Middle East
  • Privacy Policy
  • Use of cookies
  • Legal notice
  • Accessibility statement
  • Terms & Conditions
  • Your US state privacy rights
Springer Nature

© 2026 Springer Nature Limited

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research