A Roadmap for the Human Gut Cell Atlas.
Journal
Nature reviews. Gastroenterology & hepatology
ISSN: 1759-5053
Titre abrégé: Nat Rev Gastroenterol Hepatol
Pays: England
ID NLM: 101500079
Informations de publication
Date de publication:
09 2023
09 2023
Historique:
accepted:
14
04
2023
medline:
28
8
2023
pubmed:
1
6
2023
entrez:
31
5
2023
Statut:
ppublish
Résumé
The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.
Identifiants
pubmed: 37258747
doi: 10.1038/s41575-023-00784-1
pii: 10.1038/s41575-023-00784-1
pmc: PMC10527367
mid: NIHMS1908204
doi:
Types de publication
Journal Article
Review
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
597-614Subventions
Organisme : NIDDK NIH HHS
ID : R01 DK115806
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK128200
Pays : United States
Organisme : CSRD VA
ID : I01 CX002171
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : BLRD VA
ID : I01 BX004366
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK103831
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK058404
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK034987
Pays : United States
Informations de copyright
© 2023. Springer Nature Limited.
Références
Cell. 2021 Feb 4;184(3):810-826.e23
pubmed: 33406409
Science. 2019 Sep 27;365(6460):1401-1405
pubmed: 31604266
Nat Rev Microbiol. 2018 Jul;16(7):410-422
pubmed: 29795328
Semin Cell Dev Biol. 2020 Jan;97:172-180
pubmed: 31587964
Cell Rep. 2021 Mar 9;34(10):108819
pubmed: 33691112
Nucleic Acids Res. 2022 Jan 7;50(D1):D129-D140
pubmed: 34850121
Nature. 2022 May;605(7908):160-165
pubmed: 35477756
Nat Immunol. 2020 Mar;21(3):343-353
pubmed: 32066951
Nature. 2020 Nov;587(7835):619-625
pubmed: 33208946
Nat Commun. 2022 Apr 1;13(1):1742
pubmed: 35365629
Nat Immunol. 2019 Feb;20(2):163-172
pubmed: 30643263
Elife. 2017 Dec 05;6:
pubmed: 29206104
Nat Med. 2020 Sep;26(9):1480-1490
pubmed: 32747828
Nucleic Acids Res. 2020 Jul 2;48(W1):W403-W414
pubmed: 32449934
Nat Protoc. 2021 Aug;16(8):3802-3835
pubmed: 34215862
Nat Rev Genet. 2021 Oct;22(10):627-644
pubmed: 34145435
Mol Syst Biol. 2019 Oct;15(10):e9005
pubmed: 31657111
Nat Biotechnol. 2020 Dec;38(12):1384-1386
pubmed: 33188371
Genome Biol. 2021 Jul 26;22(1):215
pubmed: 34311752
Nat Rev Immunol. 2016 May 27;16(6):341-52
pubmed: 27231050
Cell Syst. 2017 Sep 27;5(3):251-267.e3
pubmed: 28957658
Cell. 2019 Dec 12;179(7):1636-1646.e15
pubmed: 31787378
Diagn Histopathol (Oxf). 2013 Sep;19(9):322-330
pubmed: 24639889
Nat Med. 2022 Apr;28(4):766-779
pubmed: 35190725
Commun Biol. 2020 Oct 9;3(1):565
pubmed: 33037292
Bioessays. 2022 Nov;44(11):e2200084
pubmed: 36068142
Front Cell Dev Biol. 2023 Jan 10;10:1102978
pubmed: 36704202
Cell. 2020 Sep 17;182(6):1606-1622.e23
pubmed: 32888429
BMC Med Inform Decis Mak. 2023 Feb 15;23(1):36
pubmed: 36793076
Nat Commun. 2022 Mar 10;13(1):1246
pubmed: 35273156
Cell Mol Gastroenterol Hepatol. 2022;13(5):1554-1589
pubmed: 35176508
Curr Opin Pediatr. 2017 Oct;29(5):566-571
pubmed: 28700415
Cell. 2019 Dec 12;179(7):1455-1467
pubmed: 31835027
Nat Immunol. 2019 Mar;20(3):301-312
pubmed: 30664737
Best Pract Res Clin Gastroenterol. 2022 Feb-Mar;56-57:101784
pubmed: 35331396
Cell Mol Gastroenterol Hepatol. 2022;13(6):1717-1740
pubmed: 35158099
Gastroenterology. 2019 Feb;156(3):812-815.e22
pubmed: 30391472
Nat Methods. 2021 Apr;18(4):327-328
pubmed: 33782609
Nat Methods. 2014 Aug;11(8):817-820
pubmed: 25042786
Gut. 2022 Sep;71(9):1892-1908
pubmed: 35636923
J Exp Med. 2020 Feb 3;217(2):
pubmed: 31753849
Cell. 2018 Aug 9;174(4):968-981.e15
pubmed: 30078711
Cell. 2021 Sep 2;184(18):4734-4752.e20
pubmed: 34450029
Nat Med. 2020 May;26(5):792-802
pubmed: 32405060
Am J Public Health. 2011 Dec;101 Suppl 1:S359-64
pubmed: 21164086
PLoS Comput Biol. 2018 Jun 25;14(6):e1006245
pubmed: 29939984
Bioinformatics. 2022 Mar 4;38(6):1756-1760
pubmed: 34935911
PLoS Comput Biol. 2020 Aug 18;16(8):e1008135
pubmed: 32810127
Nat Genet. 2022 Jul;54(7):985-995
pubmed: 35726067
Nat Methods. 2019 Dec;16(12):1289-1296
pubmed: 31740819
Curr Opin Endocrinol Diabetes Obes. 2022 Apr 1;29(2):169-176
pubmed: 35066539
NAR Genom Bioinform. 2020 Sep;2(3):lqaa052
pubmed: 32766548
Transl Gastroenterol Hepatol. 2022 Jan 25;7:7
pubmed: 35243116
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Nat Neurosci. 2021 Apr;24(4):584-594
pubmed: 33723434
Cell Stem Cell. 2021 Mar 4;28(3):568-580.e4
pubmed: 33278341
Nat Genet. 2020 Jun;52(6):594-603
pubmed: 32451460
Exp Mol Med. 2021 Oct;53(10):1451-1458
pubmed: 34663935
Nat Cell Biol. 2018 Jun;20(6):721-734
pubmed: 29802404
Expert Rev Gastroenterol Hepatol. 2016;10(4):481-95
pubmed: 26581857
Cell. 2018 Oct 4;175(2):372-386.e17
pubmed: 30270042
Elife. 2017 Jun 27;6:
pubmed: 28653622
Mol Cells. 2023 Feb 28;46(2):106-119
pubmed: 36859475
Nat Protoc. 2021 Sep;16(9):4177-4200
pubmed: 34349282
Nat Methods. 2017 Nov;14(11):1083-1086
pubmed: 28991892
Cell. 2020 Jun 11;181(6):1291-1306.e19
pubmed: 32407674
Am J Respir Cell Mol Biol. 2019 Jul;61(1):31-41
pubmed: 30995076
Gut. 2021 Mar;70(3):464-475
pubmed: 32532891
Nat Biotechnol. 2018 Oct 29;:
pubmed: 30371680
Genome Biol. 2020 May 11;21(1):111
pubmed: 32393329
Nat Biotechnol. 2022 May;40(5):661-671
pubmed: 35027729
Nat Protoc. 2020 Nov;15(11):3632-3662
pubmed: 33046898
Cell Res. 2020 Sep;30(9):745-762
pubmed: 32561858
Science. 2022 May 13;376(6594):eabl4896
pubmed: 35549404
Cell. 2021 Jun 10;184(12):3281-3298.e22
pubmed: 34019796
Gastroenterology. 2022 Mar;162(3):859-876
pubmed: 34780721
Nature. 2022 Nov;611(7937):810-817
pubmed: 36385528
Nature. 2019 Mar;567(7746):49-55
pubmed: 30814735
Genome Med. 2017 Aug 18;9(1):75
pubmed: 28821273
Cell. 2019 Nov 14;179(5):1160-1176.e24
pubmed: 31730855
Nature. 2021 Sep;597(7875):250-255
pubmed: 34497389
JCI Insight. 2023 Feb 22;8(4):
pubmed: 36810249
Gastroenterology. 2021 Apr;160(5):1679-1693
pubmed: 33359089
Front Cell Dev Biol. 2018 Sep 04;6:108
pubmed: 30234113
Gastroenterology. 2020 Aug;159(2):591-608.e10
pubmed: 32428507
Dev Cell. 2020 Dec 21;55(6):771-783.e5
pubmed: 33290721
Front Pediatr. 2021 Aug 05;9:638093
pubmed: 34422713
Nat Commun. 2021 Mar 26;12(1):1921
pubmed: 33771991
Genome Biol. 2020 Jan 16;21(1):12
pubmed: 31948481
Elife. 2021 Jan 04;10:
pubmed: 33393902
Sci Rep. 2019 May 22;9(1):7721
pubmed: 31118500
Nat Rev Genet. 2021 Feb;22(2):71-88
pubmed: 33168968
Nat Genet. 2022 Jul;54(7):963-975
pubmed: 35773407
Nat Genet. 2017 May;49(5):708-718
pubmed: 28319088
Am J Public Health. 2013 Dec;103(12):e7-e14
pubmed: 24134352
Science. 2021 Aug 13;373(6556):760-767
pubmed: 34385390
Annu Rev Biomed Data Sci. 2021 Jul 20;4:145-164
pubmed: 34465167
Cell Stem Cell. 2022 Sep 1;29(9):1333-1345.e6
pubmed: 36002022
Genome Biol. 2021 Dec 28;22(1):351
pubmed: 34963480
Front Cardiovasc Med. 2020 Mar 13;7:29
pubmed: 32232057
PLoS Biol. 2023 May 19;21(5):e3002124
pubmed: 37205711
Nat Genet. 2021 Sep;53(9):1334-1347
pubmed: 34493872
Nat Biotechnol. 2022 Oct;40(10):1458-1466
pubmed: 35501393
Gastroenterology. 2021 Apr;160(5):1709-1724
pubmed: 33421512
Nat Commun. 2018 Feb 22;9(1):781
pubmed: 29472610
Cell. 2020 Apr 16;181(2):442-459.e29
pubmed: 32302573
Cell. 2021 Dec 22;184(26):6262-6280.e26
pubmed: 34910928
Cell Discov. 2021 Sep 7;7(1):80
pubmed: 34489408
Genome Biol. 2021 Mar 8;22(1):78
pubmed: 33685491
Cancer Discov. 2022 Mar 1;12(3):670-691
pubmed: 34642171
Cell. 2019 Jul 25;178(3):714-730.e22
pubmed: 31348891
Gastroenterology. 2022 Nov;163(5):1391-1406.e24
pubmed: 35963362
Nat Commun. 2022 Aug 22;13(1):4920
pubmed: 35995787
Nature. 2018 Dec;564(7735):268-272
pubmed: 30479382
Science. 2022 May 13;376(6594):eabl5197
pubmed: 35549406
Cell. 2021 Jul 22;184(15):4090-4104.e15
pubmed: 34129837
Dev Cell. 2021 Feb 8;56(3):383-397.e8
pubmed: 33238152
Exp Mol Med. 2018 Aug 7;50(8):1-14
pubmed: 30089861
Adv Exp Med Biol. 2020;1255:7-27
pubmed: 32949387
Brief Bioinform. 2022 Mar 10;23(2):
pubmed: 35048116
Cell. 2019 Sep 5;178(6):1493-1508.e20
pubmed: 31474370
Neurogastroenterol Motil. 2022 Jul;34(7):e14303
pubmed: 34913225
Nat Rev Gastroenterol Hepatol. 2018 Sep;15(9):525-535
pubmed: 29789682
EMBO Mol Med. 2021 Oct 7;13(10):e14123
pubmed: 34409732
Science. 2020 Nov 13;370(6518):
pubmed: 33184181
Gastroenterology. 2021 Dec;161(6):1940-1952
pubmed: 34529988
Cell. 2020 Aug 6;182(3):655-671.e22
pubmed: 32603654
J Exp Med. 2022 Feb 9;219(3):
pubmed: 35139155
Nat Commun. 2018 Nov 6;9(1):4638
pubmed: 30401874
Nature. 2021 Sep;597(7875):196-205
pubmed: 34497388
J Cell Biochem. 2022 Sep;123(9):1481-1494
pubmed: 35894175
Nat Methods. 2018 May;15(5):343-346
pubmed: 29553579
Cell Host Microbe. 2018 Jun 13;23(6):705-715
pubmed: 29902436
Nat Protoc. 2020 Apr;15(4):1484-1506
pubmed: 32103204
Nature. 2017 Oct 18;550(7677):451-453
pubmed: 29072289
Nat Rev Microbiol. 2019 Dec;17(12):742-753
pubmed: 31541197
Nat Methods. 2020 Feb;17(2):147-154
pubmed: 31907445
Gastroenterology. 2017 Feb;152(3):497-514
pubmed: 28063287
Biochem J. 2020 Apr 30;477(8):1427-1442
pubmed: 32339226
Mil Med Res. 2022 Dec 2;9(1):68
pubmed: 36461064
Immunity. 2023 Feb 14;56(2):444-458.e5
pubmed: 36720220
Nat Biotechnol. 2019 Aug;37(8):916-924
pubmed: 31235917
Nat Methods. 2015 Jun;12(6):519-22
pubmed: 25915121
Bioinformatics. 2019 Jun 1;35(12):2159-2161
pubmed: 30445495