Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia.

David H Brann, Tatsuya Tsukahara, Caleb Weinreb, Marcela Lipovsek, Koen Van den Berge, Boying Gong, Rebecca Chance, Iain C Macaulay, Hsin-Jung Chou, Russell B Fletcher, Diya Das, Kelly Street, Hector Roux de Bezieux, Yoon-Gi Choi, Davide Risso, Sandrine Dudoit, Elizabeth Purdom, Jonathan Mill, Ralph Abi Hachem, Hiroaki Matsunami, Darren W Logan, Bradley J Goldstein, Matthew S Grubb, John Ngai, Sandeep Robert Datta
Author Information
  1. David H Brann: Harvard Medical School Department of Neurobiology, Boston MA 02115 USA. ORCID
  2. Tatsuya Tsukahara: Harvard Medical School Department of Neurobiology, Boston MA 02115 USA. ORCID
  3. Caleb Weinreb: Harvard Medical School Department of Neurobiology, Boston MA 02115 USA. ORCID
  4. Marcela Lipovsek: Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London SE1 1UL, UK. ORCID
  5. Koen Van den Berge: Department of Statistics, University of California, Berkeley, CA 94720.
  6. Boying Gong: Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720.
  7. Rebecca Chance: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720. ORCID
  8. Iain C Macaulay: Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. ORCID
  9. Hsin-Jung Chou: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.
  10. Russell B Fletcher: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.
  11. Diya Das: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720. ORCID
  12. Kelly Street: Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA. ORCID
  13. Hector Roux de Bezieux: Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720. ORCID
  14. Yoon-Gi Choi: QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720.
  15. Davide Risso: Department of Statistical Sciences, University of Padova, Padova, Italy. ORCID
  16. Sandrine Dudoit: Department of Statistics, University of California, Berkeley, CA 94720.
  17. Elizabeth Purdom: Department of Statistics, University of California, Berkeley, CA 94720. ORCID
  18. Jonathan Mill: University of Exeter Medical School, College of Medicine & Health, University of Exeter, Exeter EX2 5DW, UK. ORCID
  19. Ralph Abi Hachem: Duke University School of Medicine Department of Head and Neck Surgery & Communication Sciences, Durham, NC 27717 USA.
  20. Hiroaki Matsunami: Duke University School of Medicine Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Durham, NC 27717 US. ORCID
  21. Darren W Logan: Waltham Petcare Science Institute, Leicestershire LE14 4RT, UK. ORCID
  22. Bradley J Goldstein: Duke University School of Medicine Department of Head and Neck Surgery & Communication Sciences, Durham, NC 27717 USA. ORCID
  23. Matthew S Grubb: Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London SE1 1UL, UK. ORCID
  24. John Ngai: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720. ORCID
  25. Sandeep Robert Datta: Harvard Medical School Department of Neurobiology, Boston MA 02115 USA. srdatta@hms.harvard.edu. ORCID

Abstract

Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.

References

  1. Nat Commun. 2015 Oct 15;6:8557 [PMID: 26469390]
  2. J Virol. 2011 Dec;85(24):13363-72 [PMID: 21994442]
  3. J Physiol. 2005 Feb 1;562(Pt 3):785-99 [PMID: 15611020]
  4. JAMA. 2020 Apr 7;323(13):1239-1242 [PMID: 32091533]
  5. Nature. 2020 Mar;579(7798):270-273 [PMID: 32015507]
  6. Elife. 2018 Apr 20;7: [PMID: 29676260]
  7. Clin Infect Dis. 2020 Jul 28;71(15):889-890 [PMID: 32215618]
  8. N Engl J Med. 2020 Aug 6;383(6):590-592 [PMID: 32402155]
  9. J Infect Dis. 2005 Mar 1;191(5):755-60 [PMID: 15688292]
  10. Nucleic Acids Res. 1999 Nov 15;27(22):4324-7 [PMID: 10536138]
  11. Cell. 2015 May 21;161(5):1202-1214 [PMID: 26000488]
  12. Front Neurol. 2021 Jan 20;11:573095 [PMID: 33551947]
  13. J Comp Neurol. 2015 Feb 15;523(3):406-30 [PMID: 25271146]
  14. iScience. 2020 Dec 18;23(12):101839 [PMID: 33251489]
  15. N Engl J Med. 2020 Feb 20;382(8):727-733 [PMID: 31978945]
  16. PLoS Comput Biol. 2018 Sep 4;14(9):e1006378 [PMID: 30180157]
  17. Am J Respir Crit Care Med. 2020 Dec 15;202(12):1636-1645 [PMID: 32726565]
  18. J Korean Med Sci. 2020 May 11;35(18):e174 [PMID: 32383370]
  19. J Virol. 2004 Sep;78(18):10156-65 [PMID: 15331748]
  20. Nat Med. 2019 Jul;25(7):1153-1163 [PMID: 31209336]
  21. Neurology. 2020 Aug 4;95(5):224-225 [PMID: 32444492]
  22. Nat Neurosci. 2018 Jun;21(6):869-880 [PMID: 29686262]
  23. Sci Rep. 2015 Dec 16;5:18178 [PMID: 26670777]
  24. J Otolaryngol Head Neck Surg. 2020 May 4;49(1):26 [PMID: 32366299]
  25. Bioinformatics. 2018 Apr 1;34(7):1246-1248 [PMID: 29228172]
  26. Neuron. 2014 Aug 20;83(4):823-38 [PMID: 25123312]
  27. JAMA. 2020 May 26;323(20):2089-2090 [PMID: 32320008]
  28. Gigascience. 2018 Jul 1;7(7): [PMID: 30010766]
  29. N Engl J Med. 2020 Apr 30;382(18):1708-1720 [PMID: 32109013]
  30. Cell. 2018 Aug 9;174(4):999-1014.e22 [PMID: 30096314]
  31. Eur Respir J. 2020 Sep 24;56(3): [PMID: 32817004]
  32. Radiology. 2020 Aug;296(2):E119-E120 [PMID: 32228363]
  33. JAMA Neurol. 2020 Aug 1;77(8):1028-1029 [PMID: 32469400]
  34. J Virol. 2008 Aug;82(15):7264-75 [PMID: 18495771]
  35. Front Cell Neurosci. 2018 Oct 26;12:386 [PMID: 30416428]
  36. Cell Syst. 2019 Apr 24;8(4):315-328.e8 [PMID: 31022373]
  37. Neuron. 2010 Nov 18;68(4):682-94 [PMID: 21092858]
  38. Eur Arch Otorhinolaryngol. 2020 Aug;277(8):2251-2261 [PMID: 32253535]
  39. Nat Biotechnol. 2016 May;34(5):525-7 [PMID: 27043002]
  40. Nat Rev Drug Discov. 2016 May;15(5):327-47 [PMID: 26868298]
  41. Chem Senses. 2001 Oct;26(8):953-63 [PMID: 11595672]
  42. Nature. 2003 Nov 27;426(6965):450-4 [PMID: 14647384]
  43. Biol Open. 2018 Nov 19;7(11): [PMID: 30455179]
  44. Adv Virus Res. 2018;100:163-188 [PMID: 29551135]
  45. J Neurol Neurosurg Psychiatry. 2020 Aug;91(8):889-891 [PMID: 32354768]
  46. Genome Biol. 2018 Feb 6;19(1):15 [PMID: 29409532]
  47. Virology. 1993 May;194(1):185-91 [PMID: 8386871]
  48. Cell Host Microbe. 2020 Jul 8;28(1):124-133.e4 [PMID: 32485164]
  49. Elife. 2020 Jul 07;9: [PMID: 32633720]
  50. ACS Chem Neurosci. 2020 Jun 3;11(11):1555-1562 [PMID: 32379417]
  51. Cell. 2020 May 28;181(5):1016-1035.e19 [PMID: 32413319]
  52. Am J Physiol Regul Integr Comp Physiol. 2007 Jan;292(1):R373-81 [PMID: 16946085]
  53. Neurology. 2020 Oct 6;95(14):e2016-e2027 [PMID: 32546654]
  54. Handb Clin Neurol. 2019;164:361-387 [PMID: 31604558]
  55. Cell. 2020 Jul 23;182(2):429-446.e14 [PMID: 32526206]
  56. Nat Commun. 2020 Oct 12;11(1):5139 [PMID: 33046696]
  57. Nature. 2020 May;581(7809):465-469 [PMID: 32235945]
  58. Cell. 2016 Oct 6;167(2):566-580.e19 [PMID: 27716510]
  59. J Biol Chem. 2018 Jul 27;293(30):11709-11726 [PMID: 29887526]
  60. Cell. 2018 Aug 23;174(5):1229-1246.e17 [PMID: 30078709]
  61. PLoS One. 2015 Jan 15;10(1):e0113170 [PMID: 25590618]
  62. ORL J Otorhinolaryngol Relat Spec. 2020;82(4):175-180 [PMID: 32526759]
  63. Nat Methods. 2012 Jun 28;9(7):676-82 [PMID: 22743772]
  64. Alzheimers Res Ther. 2016 Nov 25;8(1):50 [PMID: 27884212]
  65. JAMA. 2020 Jun 23;323(24):2518-2520 [PMID: 32437497]
  66. Nat Neurosci. 2020 Mar;23(3):323-326 [PMID: 32066986]
  67. Chem Senses. 2020 Oct 9;45(7):609-622 [PMID: 32564071]
  68. Cell Stem Cell. 2019 Oct 3;25(4):501-513.e5 [PMID: 31523027]
  69. J Pathol. 2004 Jun;203(2):631-7 [PMID: 15141377]
  70. Cell. 2018 May 17;173(5):1280-1292.e18 [PMID: 29681453]
  71. Arch Otolaryngol Head Neck Surg. 1995 Oct;121(10):1183-7 [PMID: 7546588]
  72. Sci Adv. 2019 Jul 31;5(7):eaax0396 [PMID: 31392275]
  73. Laryngoscope. 2018 Jan;128(1):10-15 [PMID: 28556265]
  74. Nature. 2018 Aug;560(7718):377-381 [PMID: 30069046]
  75. Nat Protoc. 2016 Nov;11(11):2081-103 [PMID: 27685099]
  76. Int Forum Allergy Rhinol. 2020 Jul;10(7):814-820 [PMID: 32271490]
  77. Cell. 2016 Aug 25;166(5):1308-1323.e30 [PMID: 27565351]
  78. Science. 2020 Feb 14;367(6479): [PMID: 31974159]
  79. Environ Health Perspect. 1990 Apr;85:171-6 [PMID: 2384061]
  80. Int Forum Allergy Rhinol. 2020 Jul;10(7):806-813 [PMID: 32279441]
  81. BMJ. 2020 Mar 26;368:m1091 [PMID: 32217556]
  82. N Engl J Med. 2020 Jun 4;382(23):2268-2270 [PMID: 32294339]
  83. J Autoimmun. 2020 May;109:102433 [PMID: 32113704]
  84. Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9 [PMID: 29174333]
  85. Cell Syst. 2019 Apr 24;8(4):281-291.e9 [PMID: 30954476]
  86. Cell. 2020 Jul 9;182(1):50-58.e8 [PMID: 32516571]
  87. PLoS One. 2012;7(4):e35876 [PMID: 22558251]
  88. Med J Islam Repub Iran. 2020 Jun 15;34:62 [PMID: 32974228]
  89. Nature. 2020 Jul;583(7818):830-833 [PMID: 32380511]
  90. Eur Rev Med Pharmacol Sci. 2020 Mar;24(5):2781-2783 [PMID: 32196628]
  91. Bioinformatics. 2017 Apr 15;33(8):1179-1186 [PMID: 28088763]
  92. Cell Syst. 2019 Apr 24;8(4):329-337.e4 [PMID: 30954475]
  93. Cell Rep. 2018 Jan 9;22(2):441-455 [PMID: 29320739]
  94. Adv Otorhinolaryngol. 2006;63:125-132 [PMID: 16733337]
  95. Genome Biol. 2016 Apr 27;17:75 [PMID: 27122128]
  96. Exp Neurol. 1995 Dec;136(2):225-33 [PMID: 7498412]
  97. Laryngoscope Investig Otolaryngol. 2018 Feb 06;3(1):35-42 [PMID: 29492466]
  98. Nat Neurosci. 2016 Oct;19(10):1331-40 [PMID: 27571008]
  99. BMC Dev Biol. 2001;1:4 [PMID: 11299042]
  100. Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8 [PMID: 28506465]
  101. Vet Pathol. 1995 Jan;32(1):1-10 [PMID: 7725592]
  102. Cell. 2019 Jun 13;177(7):1888-1902.e21 [PMID: 31178118]
  103. J Comp Neurol. 1996 Dec 23;376(4):509-17 [PMID: 8978466]
  104. Nat Med. 2020 Jul;26(7):1037-1040 [PMID: 32393804]
  105. Nat Neurosci. 2015 Jan;18(1):145-53 [PMID: 25420068]
  106. Nat Med. 2005 Aug;11(8):875-9 [PMID: 16007097]
  107. J Intern Med. 2020 Sep;288(3):335-344 [PMID: 32352202]
  108. N Engl J Med. 2020 Apr 23;382(17):e38 [PMID: 32268022]
  109. Nature. 2020 Sep;585(7824):268-272 [PMID: 32396922]
  110. Nat Neurosci. 2017 Feb;20(2):176-188 [PMID: 27991900]
  111. Nat Protoc. 2007;2(11):2924-9 [PMID: 18007629]
  112. Nat Biotechnol. 2014 Sep;32(9):896-902 [PMID: 25150836]
  113. Science. 2020 Jul 3;369(6499):50-54 [PMID: 32358202]
  114. Cell. 2020 Apr 16;181(2):271-280.e8 [PMID: 32142651]
  115. J Comp Neurol. 2017 Mar 1;525(4):1034-1054 [PMID: 27560601]
  116. Front Cell Neurosci. 2019 Jun 28;13:282 [PMID: 31316352]
  117. Nat Med. 2020 May;26(5):681-687 [PMID: 32327758]
  118. JAMA Otolaryngol Head Neck Surg. 2020 Jul 1;146(7):674-675 [PMID: 32267483]
  119. J Virol. 2004 Oct;78(20):11429-33 [PMID: 15452268]
  120. Chem Senses. 2001 Oct;26(8):937-52 [PMID: 11595671]

Grants

  1. R01 DC014423/NIDCD NIH HHS
  2. R01 DC016222/NIDCD NIH HHS
  3. R011DC016222/NIH HHS
  4. F31 DC019017/NIDCD NIH HHS
  5. R01 DC016224/NIDCD NIH HHS
  6. /Medical Research Council
  7. R01 DC007235/NIDCD NIH HHS
  8. U19 NS112953/NINDS NIH HHS
  9. R01 DC016859/NIDCD NIH HHS
  10. P30 NS072030/NINDS NIH HHS

MeSH Term

Angiotensin-Converting Enzyme 2
Animals
Betacoronavirus
COVID-19
Callithrix
Coronavirus Infections
Humans
Macaca
Mice
Olfaction Disorders
Olfactory Mucosa
Olfactory Receptor Neurons
Pandemics
Peptidyl-Dipeptidase A
Pneumonia, Viral
SARS-CoV-2
Serine Endopeptidases
Smell
Virus Internalization

Chemicals

Peptidyl-Dipeptidase A
ACE2 protein, human
Ace2 protein, mouse
Angiotensin-Converting Enzyme 2
Serine Endopeptidases
TMPRSS2 protein, human