Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells,...
Saved in:
| Published in | Cell Vol. 175; no. 2; pp. 372 - 386.e17 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
04.10.2018
Cell Press |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0092-8674 1097-4172 1097-4172 |
| DOI | 10.1016/j.cell.2018.08.067 |
Cover
| Abstract | Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD.
[Display omitted]
•Single-cell census of the colonic mesenchyme reveals unexpected heterogeneity•Identification of the colonic crypt niche mesenchymal cell expressing SOX6 and Wnts•Definition of fundamental aspects of mesenchymal remodeling in colitis•Analysis of colitis-associated mesenchymal cells reveals pathogenicity drivers
Single-cell profiling of human colonic mesenchymal cells identifies a colitis-associated population that expresses factors contributing to epithelial cell dysfunction and inflammation. |
|---|---|
| AbstractList | Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD. Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD. [Display omitted] •Single-cell census of the colonic mesenchyme reveals unexpected heterogeneity•Identification of the colonic crypt niche mesenchymal cell expressing SOX6 and Wnts•Definition of fundamental aspects of mesenchymal remodeling in colitis•Analysis of colitis-associated mesenchymal cells reveals pathogenicity drivers Single-cell profiling of human colonic mesenchymal cells identifies a colitis-associated population that expresses factors contributing to epithelial cell dysfunction and inflammation. Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo . Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD. • Single-cell census of the colonic mesenchyme reveals unexpected heterogeneity • Identification of the colonic crypt niche mesenchymal cell expressing SOX6 and Wnts • Definition of fundamental aspects of mesenchymal remodeling in colitis • Analysis of colitis-associated mesenchymal cells reveals pathogenicity drivers Single-cell profiling of human colonic mesenchymal cells identifies a colitis-associated population that expresses factors contributing to epithelial cell dysfunction and inflammation. Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD.Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD. Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD. |
| Author | Chen, Hannah H. Koohy, Hashem Simmons, Alison Parikh, Kaushal Bowden, Rory Attar, Moustafa Ashley, Neil Fawkner-Corbett, David Gervais, Francois Jagielowicz, Marta Kinchen, James Mellado-Gomez, Esther Richter, Felix C. Sharma, Eshita Ahern, David Cubitt, Laura Puri, Kamal D. Henault, Jill Antanaviciute, Agne Wills, Quin |
| AuthorAffiliation | 8 Translational Development, Celgene Corporation, Cambridge, MA, USA 6 Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK 1 MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK 7 OncoResponse, Inc., Seattle, WA 98104, USA 9 Novo Nordisk Research Centre Oxford, Oxford, UK 3 MRC WIMM Centre For Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK 5 Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK 4 Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK 2 Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK |
| AuthorAffiliation_xml | – name: 6 Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK – name: 3 MRC WIMM Centre For Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – name: 4 Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – name: 9 Novo Nordisk Research Centre Oxford, Oxford, UK – name: 5 Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK – name: 8 Translational Development, Celgene Corporation, Cambridge, MA, USA – name: 7 OncoResponse, Inc., Seattle, WA 98104, USA – name: 1 MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – name: 2 Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK |
| Author_xml | – sequence: 1 givenname: James surname: Kinchen fullname: Kinchen, James organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 2 givenname: Hannah H. surname: Chen fullname: Chen, Hannah H. organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 3 givenname: Kaushal surname: Parikh fullname: Parikh, Kaushal organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 4 givenname: Agne surname: Antanaviciute fullname: Antanaviciute, Agne organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 5 givenname: Marta surname: Jagielowicz fullname: Jagielowicz, Marta organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 6 givenname: David surname: Fawkner-Corbett fullname: Fawkner-Corbett, David organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 7 givenname: Neil surname: Ashley fullname: Ashley, Neil organization: Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 8 givenname: Laura surname: Cubitt fullname: Cubitt, Laura organization: Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK – sequence: 9 givenname: Esther surname: Mellado-Gomez fullname: Mellado-Gomez, Esther organization: Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK – sequence: 10 givenname: Moustafa surname: Attar fullname: Attar, Moustafa organization: Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK – sequence: 11 givenname: Eshita surname: Sharma fullname: Sharma, Eshita organization: Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK – sequence: 12 givenname: Quin surname: Wills fullname: Wills, Quin organization: Novo Nordisk Research Centre Oxford, Oxford, UK – sequence: 13 givenname: Rory surname: Bowden fullname: Bowden, Rory organization: Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK – sequence: 14 givenname: Felix C. surname: Richter fullname: Richter, Felix C. organization: Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK – sequence: 15 givenname: David surname: Ahern fullname: Ahern, David organization: Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK – sequence: 16 givenname: Kamal D. surname: Puri fullname: Puri, Kamal D. organization: OncoResponse, Inc., Seattle, WA 98104, USA – sequence: 17 givenname: Jill surname: Henault fullname: Henault, Jill organization: Translational Development, Celgene Corporation, Cambridge, MA, USA – sequence: 18 givenname: Francois surname: Gervais fullname: Gervais, Francois organization: Translational Development, Celgene Corporation, Cambridge, MA, USA – sequence: 19 givenname: Hashem surname: Koohy fullname: Koohy, Hashem organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK – sequence: 20 givenname: Alison surname: Simmons fullname: Simmons, Alison email: alison.simmons@imm.ox.ac.uk organization: MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30270042$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFUU1v1DAQtVAR3Rb-AAfkI5csYyeOEwkhwfLRSkVIFM6Wa0-6XiV2sZ2i_fc42hYBhyKNNId5782beSfkyAePhDxnsGbA2le7tcFxXHNg3RpKtfIRWTHoZdUwyY_ICqDnVdfK5picpLQDgE4I8YQc18AlQMNX5PIyx9nkOeqRfsUpWBydv6ZhoHmL9GyetKebMAbvDP2MCb3Z7iekztNzP4x6mnQOcU_fhZ840vcuoU74lDwe9Jjw2V0_Jd8_fvi2Oasuvnw637y9qIwQTa4sYzWr-cBtIzhYY2TdX_V9h8JijcUfDg1YhgY57wfdoe1Biq7vGTJRy7o-JW8Oujfz1YTWoM_lDHUT3aTjXgXt1N8T77bqOtyqlsm2k6wIvLwTiOHHjCmryaXlp9pjmJPinDNoyjL4P5QxwaWQ0BXoiz9t_fZz__QC6A4AE0NKEQdlXNbZhcWlGxUDteSrdmpZoJZ8FZRqZaHyf6j36g-SXh9IWMK4dRhVMq4kidZFNFnZ4B6i_wIxeL7R |
| CitedBy_id | crossref_primary_10_2147_MNM_S263813 crossref_primary_10_1242_dev_166173 crossref_primary_10_2139_ssrn_4149949 crossref_primary_10_1371_journal_pbio_3001532 crossref_primary_10_1038_s41556_020_0567_z crossref_primary_10_1016_j_stem_2021_07_008 crossref_primary_10_1038_s41467_022_28020_5 crossref_primary_10_1084_jem_20232148 crossref_primary_10_1111_imr_12987 crossref_primary_10_1016_j_jcmgh_2019_04_001 crossref_primary_10_1093_bioinformatics_btaf094 crossref_primary_10_1186_s13059_021_02452_6 crossref_primary_10_1002_eji_201847758 crossref_primary_10_3390_jcm14020608 crossref_primary_10_1093_database_baac050 crossref_primary_10_3389_fimmu_2022_1057932 crossref_primary_10_3390_ijms26051807 crossref_primary_10_1002_glia_24632 crossref_primary_10_1038_s43018_020_0089_4 crossref_primary_10_1016_j_devcel_2024_07_012 crossref_primary_10_1016_j_stem_2023_03_004 crossref_primary_10_1111_imr_12974 crossref_primary_10_1093_bib_bbac327 crossref_primary_10_1136_gutjnl_2021_325522 crossref_primary_10_1080_1744666X_2024_2330604 crossref_primary_10_1038_s41586_020_2166_3 crossref_primary_10_1155_2021_9929461 crossref_primary_10_1016_j_ccell_2024_04_010 crossref_primary_10_1038_s41591_020_1003_4 crossref_primary_10_1016_j_cell_2020_12_016 crossref_primary_10_1111_cpr_13566 crossref_primary_10_1152_physrev_00048_2019 crossref_primary_10_3390_ijms21124478 crossref_primary_10_1093_ibd_izae255 crossref_primary_10_1038_s43856_024_00504_z crossref_primary_10_1186_s13619_021_00086_4 crossref_primary_10_3389_fnins_2023_1098612 crossref_primary_10_1172_JCI149538 crossref_primary_10_3390_cells10061331 crossref_primary_10_1111_cas_16436 crossref_primary_10_1038_s41575_023_00784_1 crossref_primary_10_1007_s10555_024_10194_7 crossref_primary_10_1016_j_mucimm_2023_01_006 crossref_primary_10_1016_j_celrep_2020_107857 crossref_primary_10_1038_s41385_021_00470_y crossref_primary_10_2147_JIR_S455862 crossref_primary_10_3389_fimmu_2024_1484483 crossref_primary_10_3390_biom10070974 crossref_primary_10_1111_acel_13015 crossref_primary_10_1016_j_clim_2023_109849 crossref_primary_10_1016_j_immuni_2021_11_014 crossref_primary_10_1002_lio2_388 crossref_primary_10_1093_intimm_dxae068 crossref_primary_10_1016_j_ajpath_2021_01_001 crossref_primary_10_1053_j_gastro_2020_04_073 crossref_primary_10_1053_j_gastro_2019_08_025 crossref_primary_10_3390_cancers13081749 crossref_primary_10_1242_dev_200167 crossref_primary_10_1038_s41467_021_22164_6 crossref_primary_10_3390_biology13070461 crossref_primary_10_1002_mnfr_202200773 crossref_primary_10_1016_j_intimp_2024_113896 crossref_primary_10_1016_j_neulet_2023_137215 crossref_primary_10_3390_biom12030452 crossref_primary_10_23868_202205001 crossref_primary_10_1053_j_gastro_2024_12_011 crossref_primary_10_3390_biomedicines11123229 crossref_primary_10_12688_f1000research_20805_1 crossref_primary_10_1016_j_tcb_2023_06_001 crossref_primary_10_1016_j_intimp_2023_111109 crossref_primary_10_1016_j_stem_2020_06_013 crossref_primary_10_1152_ajpgi_00199_2020 crossref_primary_10_1056_NEJMra2002697 crossref_primary_10_14309_ctg_0000000000000576 crossref_primary_10_1111_all_15781 crossref_primary_10_1177_00220345221110768 crossref_primary_10_1136_gutjnl_2024_334165 crossref_primary_10_1038_s41467_021_24235_0 crossref_primary_10_1093_jmcb_mjab026 crossref_primary_10_1128_mbio_01857_23 crossref_primary_10_1016_j_tcb_2020_11_010 crossref_primary_10_1002_bies_202200186 crossref_primary_10_1371_journal_pone_0276195 crossref_primary_10_5483_BMBRep_2024_0039 crossref_primary_10_1136_jitc_2023_008628 crossref_primary_10_3390_ijms22137043 crossref_primary_10_1016_j_apmt_2024_102143 crossref_primary_10_1093_stmcls_sxab020 crossref_primary_10_1016_j_berh_2022_101742 crossref_primary_10_1016_j_ejphar_2024_176318 crossref_primary_10_1242_dmm_049692 crossref_primary_10_1186_s13578_023_01139_8 crossref_primary_10_1016_j_xpro_2023_102686 crossref_primary_10_1038_s41467_022_31571_2 crossref_primary_10_3390_ijms23010137 crossref_primary_10_1016_j_trsl_2024_12_002 crossref_primary_10_1038_s41467_024_47173_z crossref_primary_10_3389_fimmu_2023_1137659 crossref_primary_10_1093_ibd_izaa089 crossref_primary_10_1111_jcpe_13912 crossref_primary_10_1039_D4FO04931D crossref_primary_10_1093_ibd_izac264 crossref_primary_10_1242_bio_049809 crossref_primary_10_1172_jci_insight_137905 crossref_primary_10_1111_imr_12748 crossref_primary_10_1242_dev_201690 crossref_primary_10_1242_dmm_049332 crossref_primary_10_3389_fimmu_2020_00410 crossref_primary_10_1016_j_isci_2022_104318 crossref_primary_10_1053_j_gastro_2024_12_026 crossref_primary_10_3390_life13071557 crossref_primary_10_1038_s42003_021_01730_0 crossref_primary_10_1042_CS20210889 crossref_primary_10_1038_s41586_024_07571_1 crossref_primary_10_1111_imr_12990 crossref_primary_10_1039_D4FO00432A crossref_primary_10_1096_fj_202301218R crossref_primary_10_1038_s41598_021_92384_9 crossref_primary_10_1016_j_stemcr_2024_06_006 crossref_primary_10_1186_s12916_024_03611_9 crossref_primary_10_1038_s41598_024_64672_7 crossref_primary_10_1053_j_gastro_2021_11_014 crossref_primary_10_1172_JCI147614 crossref_primary_10_3390_pharmaceutics15030845 crossref_primary_10_3390_biomedicines10020226 crossref_primary_10_1016_j_celrep_2020_107597 crossref_primary_10_1038_s41467_023_37353_8 crossref_primary_10_3390_ijms241512348 crossref_primary_10_2147_JIR_S470520 crossref_primary_10_1038_s41575_024_00980_7 crossref_primary_10_3748_wjg_v29_i28_4397 crossref_primary_10_1016_j_jcmgh_2024_101423 crossref_primary_10_1172_jci_insight_165566 crossref_primary_10_3389_fimmu_2022_1058862 crossref_primary_10_1016_j_mucimm_2023_11_004 crossref_primary_10_1038_s41586_023_05915_x crossref_primary_10_1093_ibd_izab116 crossref_primary_10_1038_s41598_021_89119_1 crossref_primary_10_1093_ibd_izac201 crossref_primary_10_1152_ajpgi_00216_2022 crossref_primary_10_1016_j_xpro_2021_100890 crossref_primary_10_1002_pmic_202400104 crossref_primary_10_1016_j_jcmgh_2023_07_011 crossref_primary_10_1038_s41385_022_00577_w crossref_primary_10_1016_j_ygeno_2021_05_034 crossref_primary_10_1186_s13619_023_00174_7 crossref_primary_10_3390_ijms241512475 crossref_primary_10_1016_j_stemcr_2020_06_017 crossref_primary_10_1002_smll_202207350 crossref_primary_10_1016_j_jcmgh_2022_05_003 crossref_primary_10_1016_j_jcmgh_2021_04_004 crossref_primary_10_1111_imm_13191 crossref_primary_10_1016_j_jcmgh_2021_04_008 crossref_primary_10_1172_JCI179472 crossref_primary_10_1186_s12915_023_01667_2 crossref_primary_10_1016_j_ymthe_2024_02_021 crossref_primary_10_3390_ijms231911210 crossref_primary_10_1371_journal_pbio_3002124 crossref_primary_10_1038_s41576_022_00449_w crossref_primary_10_1016_j_immuni_2023_01_002 crossref_primary_10_1016_j_jcmgh_2024_02_003 crossref_primary_10_1016_j_cels_2020_02_008 crossref_primary_10_1038_s41467_022_29366_6 crossref_primary_10_1186_s12967_022_03679_y crossref_primary_10_1053_j_gastro_2023_07_014 crossref_primary_10_4110_in_2020_20_e13 crossref_primary_10_1038_s41392_023_01501_9 crossref_primary_10_1093_ibd_izaa045 crossref_primary_10_32604_biocell_2024_053983 crossref_primary_10_1093_ibd_izab251 crossref_primary_10_1002_advs_202403461 crossref_primary_10_1016_j_intimp_2024_112693 crossref_primary_10_1126_sciadv_adp8783 crossref_primary_10_7554_eLife_62810 crossref_primary_10_1016_j_molmed_2024_10_003 crossref_primary_10_1016_j_trsl_2021_06_001 crossref_primary_10_1080_19490976_2023_2251646 crossref_primary_10_1242_dev_201416 crossref_primary_10_1016_j_ebiom_2021_103690 crossref_primary_10_3390_ijms252313008 crossref_primary_10_3389_fimmu_2022_924866 crossref_primary_10_1038_s41422_020_0355_0 crossref_primary_10_3390_organoids4010006 crossref_primary_10_1016_j_jcmgh_2024_01_013 crossref_primary_10_1042_BST20221083 crossref_primary_10_3389_fcell_2024_1258859 crossref_primary_10_3389_fonc_2022_878920 crossref_primary_10_1016_j_mucimm_2024_06_009 crossref_primary_10_1038_s41598_024_78908_z crossref_primary_10_3389_fcell_2024_1452258 crossref_primary_10_1016_j_jare_2024_12_030 crossref_primary_10_1016_j_autrev_2024_103529 crossref_primary_10_1053_j_gastro_2021_03_052 crossref_primary_10_1038_s41598_022_16885_x crossref_primary_10_3390_cells11030335 crossref_primary_10_1016_j_cgh_2020_09_023 crossref_primary_10_1080_13543784_2021_1965122 crossref_primary_10_1016_j_neo_2021_03_010 crossref_primary_10_1016_j_diff_2019_06_001 crossref_primary_10_2147_JIR_S340452 crossref_primary_10_1126_sciimmunol_abb4432 crossref_primary_10_1111_exd_13978 crossref_primary_10_3390_cancers13020183 crossref_primary_10_1038_s41467_019_12349_5 crossref_primary_10_1038_s42003_022_04298_5 crossref_primary_10_3389_fimmu_2024_1353402 crossref_primary_10_1016_j_cell_2024_03_013 crossref_primary_10_3389_fcell_2024_1420313 crossref_primary_10_1038_s41467_023_40156_6 crossref_primary_10_1186_s12915_022_01492_z crossref_primary_10_1093_stcltm_szad003 crossref_primary_10_1242_dev_199906 crossref_primary_10_1016_j_cell_2019_10_027 crossref_primary_10_1038_s41577_021_00540_z crossref_primary_10_1038_s41577_023_00942_1 crossref_primary_10_1002_ueg2_12770 crossref_primary_10_1038_s41584_023_01007_2 crossref_primary_10_1007_s00508_021_01905_z crossref_primary_10_1007_s13770_023_00600_6 crossref_primary_10_3389_fimmu_2024_1337384 crossref_primary_10_1002_msp2_29 crossref_primary_10_1016_j_jcmgh_2021_11_008 crossref_primary_10_1016_j_jcmgh_2024_01_007 crossref_primary_10_1126_scisignal_aay3258 crossref_primary_10_1016_j_jcmgh_2024_01_003 crossref_primary_10_1038_s41467_024_51411_9 crossref_primary_10_3389_fcell_2020_00558 crossref_primary_10_3389_fcell_2021_685665 crossref_primary_10_1016_j_ijpharm_2021_121125 crossref_primary_10_3839_jabc_2025_008 crossref_primary_10_1016_j_biopha_2022_112988 crossref_primary_10_3389_fimmu_2023_1291990 crossref_primary_10_3389_fnut_2025_1550880 crossref_primary_10_1111_apha_13699 crossref_primary_10_1016_j_heliyon_2024_e34519 crossref_primary_10_1016_j_ccell_2023_04_011 crossref_primary_10_7554_eLife_81525 crossref_primary_10_1111_jvim_16688 crossref_primary_10_3389_fimmu_2019_01281 crossref_primary_10_3389_fimmu_2022_966067 crossref_primary_10_1016_j_biopha_2024_116722 crossref_primary_10_3390_cells8060535 crossref_primary_10_1038_s41590_021_00981_7 crossref_primary_10_1038_s41467_023_39729_2 crossref_primary_10_1080_19490976_2021_1990827 crossref_primary_10_1186_s12859_022_04676_0 crossref_primary_10_1016_j_isci_2021_102863 crossref_primary_10_1038_s41467_020_17886_y crossref_primary_10_1038_s41573_025_01158_9 crossref_primary_10_1152_ajpgi_00277_2024 crossref_primary_10_1016_j_mucimm_2022_11_001 crossref_primary_10_1038_s41467_023_37952_5 crossref_primary_10_1016_j_anndiagpath_2025_152461 crossref_primary_10_1053_j_gastro_2020_07_035 crossref_primary_10_3389_fimmu_2022_1014881 crossref_primary_10_1038_s41586_020_2938_9 crossref_primary_10_3390_ijms24021526 crossref_primary_10_1080_03009734_2019_1689209 crossref_primary_10_3390_biom13101516 crossref_primary_10_1186_s40001_024_01932_2 crossref_primary_10_1016_j_isci_2021_102618 crossref_primary_10_1038_s41588_020_0636_z crossref_primary_10_3389_fimmu_2023_1152140 crossref_primary_10_1038_s41588_022_01156_2 crossref_primary_10_1016_j_smim_2023_101819 crossref_primary_10_1053_j_gastro_2021_10_035 crossref_primary_10_1093_ecco_jcc_jjab001 crossref_primary_10_3390_ph15091080 crossref_primary_10_1016_j_tcb_2023_03_007 crossref_primary_10_1016_j_gde_2024_102276 crossref_primary_10_1016_j_stem_2022_05_007 crossref_primary_10_1038_s41598_022_08398_4 crossref_primary_10_1093_gastro_goae090 crossref_primary_10_1038_s41392_023_01554_w crossref_primary_10_1038_s41586_023_06139_9 crossref_primary_10_1038_s41467_020_17740_1 crossref_primary_10_1038_s41598_023_45176_2 crossref_primary_10_1016_j_devcel_2024_12_030 crossref_primary_10_3390_ijms25010148 crossref_primary_10_3390_ijms26030885 crossref_primary_10_3390_ijms24032696 crossref_primary_10_1038_s41467_022_31950_9 crossref_primary_10_1159_000528312 crossref_primary_10_1016_j_devcel_2020_11_010 crossref_primary_10_1093_ecco_jcc_jjaa009 crossref_primary_10_1042_EBC20180072 crossref_primary_10_1038_s41568_018_0090_8 crossref_primary_10_3389_fcell_2022_915654 crossref_primary_10_1016_j_intimp_2024_112298 crossref_primary_10_1038_s41586_021_03852_1 crossref_primary_10_1038_s41419_022_04566_6 crossref_primary_10_1073_pnas_2100293118 crossref_primary_10_1042_BST20210223 crossref_primary_10_1016_j_medj_2024_03_021 crossref_primary_10_4049_jimmunol_2300762 crossref_primary_10_1016_j_envpol_2023_121708 crossref_primary_10_1016_j_coi_2020_03_009 crossref_primary_10_3390_jcm12093280 crossref_primary_10_1080_19490976_2023_2263210 crossref_primary_10_1038_s41421_022_00434_x crossref_primary_10_3390_ijms25105108 crossref_primary_10_62347_VUFU1836 crossref_primary_10_1097_CM9_0000000000003545 crossref_primary_10_1038_s41590_022_01285_0 crossref_primary_10_1186_s12865_019_0322_z crossref_primary_10_1038_s41467_024_50438_2 crossref_primary_10_1038_s41467_024_45665_6 crossref_primary_10_1038_s41467_024_54180_7 crossref_primary_10_1038_s41586_021_03283_y crossref_primary_10_1080_00207454_2024_2313022 crossref_primary_10_1186_s13287_020_02025_7 crossref_primary_10_1096_fj_202400211RR crossref_primary_10_1016_j_cell_2021_04_028 crossref_primary_10_1038_s41590_023_01669_w crossref_primary_10_1002_glia_24272 crossref_primary_10_1016_j_devcel_2024_03_034 crossref_primary_10_3390_biomedicines12081674 crossref_primary_10_14814_phy2_14604 crossref_primary_10_1016_j_csbj_2024_07_011 crossref_primary_10_1038_s41598_020_75186_3 crossref_primary_10_1126_sciimmunol_abe8856 crossref_primary_10_1016_j_matbio_2024_01_002 crossref_primary_10_1126_sciadv_adj7666 crossref_primary_10_1186_s13619_020_00061_5 crossref_primary_10_3390_cancers17020219 crossref_primary_10_1021_acsptsci_2c00035 crossref_primary_10_1016_j_ceb_2020_08_009 crossref_primary_10_1177_2050640620975324 crossref_primary_10_3390_ijms241411585 crossref_primary_10_1038_s41389_023_00492_0 crossref_primary_10_1038_s41590_020_0741_2 crossref_primary_10_3390_ijms23137017 crossref_primary_10_1038_s41420_024_02015_1 crossref_primary_10_1136_gutjnl_2023_329963 crossref_primary_10_1016_j_canlet_2024_216822 crossref_primary_10_1038_s41385_021_00389_4 crossref_primary_10_1038_s41586_019_0992_y crossref_primary_10_1152_ajpheart_00545_2023 crossref_primary_10_1038_s41586_021_03549_5 crossref_primary_10_1016_j_advms_2019_12_001 crossref_primary_10_1016_j_gde_2021_05_005 crossref_primary_10_1084_jem_20191130 crossref_primary_10_1007_s13258_021_01045_8 crossref_primary_10_1038_s41435_023_00242_7 crossref_primary_10_1038_s41591_021_01551_y crossref_primary_10_1084_jem_20211938 crossref_primary_10_1007_s00109_024_02477_x crossref_primary_10_1016_j_biomaterials_2022_121696 crossref_primary_10_1096_fj_202101817RR crossref_primary_10_1146_annurev_physiol_031620_094324 crossref_primary_10_1111_imr_13051 crossref_primary_10_3389_fimmu_2022_893803 crossref_primary_10_1126_scitranslmed_abb5071 crossref_primary_10_1002_path_6408 crossref_primary_10_1038_s41586_020_2424_4 crossref_primary_10_3389_fmicb_2023_1188455 crossref_primary_10_3389_fgene_2021_797490 crossref_primary_10_1016_j_stem_2020_01_008 crossref_primary_10_1038_s41590_021_00894_5 crossref_primary_10_1038_s41573_024_01053_9 crossref_primary_10_1007_s11906_022_01175_8 crossref_primary_10_1038_s41586_021_03484_5 crossref_primary_10_1097_MD_0000000000032775 crossref_primary_10_1016_j_jcmgh_2022_10_014 crossref_primary_10_1038_s41575_020_0273_0 crossref_primary_10_1113_JP284620 crossref_primary_10_1016_j_jcmgh_2022_10_019 crossref_primary_10_1038_s41568_023_00549_7 crossref_primary_10_3389_fimmu_2021_749708 crossref_primary_10_3389_fmed_2022_1033817 crossref_primary_10_1016_j_immuni_2019_03_017 crossref_primary_10_1002_ctd2_186 crossref_primary_10_1038_s41525_022_00335_8 crossref_primary_10_1038_s41586_021_04006_z crossref_primary_10_3390_jcm8111989 crossref_primary_10_3892_ol_2024_14390 crossref_primary_10_1007_s00018_021_04071_7 crossref_primary_10_1016_j_stem_2022_07_007 crossref_primary_10_3389_fimmu_2024_1357632 crossref_primary_10_3389_fimmu_2024_1434804 crossref_primary_10_1538_expanim_23_0166 crossref_primary_10_3390_gastroent15020034 crossref_primary_10_1016_j_celrep_2021_109484 crossref_primary_10_1186_s41232_024_00355_0 crossref_primary_10_1016_j_stem_2020_11_008 crossref_primary_10_3390_ijms241914799 crossref_primary_10_3390_ijms23095181 crossref_primary_10_1093_ecco_jcc_jjad025 crossref_primary_10_1016_j_coisb_2019_10_005 crossref_primary_10_1038_s41590_024_01994_8 crossref_primary_10_4049_jimmunol_2200326 crossref_primary_10_1101_gad_351069_123 crossref_primary_10_1016_j_isci_2024_111246 crossref_primary_10_1016_j_matbio_2022_09_001 crossref_primary_10_1177_09636897221105252 crossref_primary_10_1038_s41586_020_2025_2 crossref_primary_10_4049_jimmunol_2200652 crossref_primary_10_1016_S2468_1253_24_00390_X crossref_primary_10_1002_JLB_3MIR0120_567R crossref_primary_10_1016_j_biomaterials_2020_120248 crossref_primary_10_1007_s00018_022_04570_1 crossref_primary_10_3390_ijms23031419 crossref_primary_10_1242_dev_175018 crossref_primary_10_1093_ibd_izae081 crossref_primary_10_1002_jcp_30756 crossref_primary_10_1016_j_stem_2021_10_004 crossref_primary_10_1039_D4TB02868F crossref_primary_10_1515_jcim_2022_0239 crossref_primary_10_1038_s41467_023_38780_3 crossref_primary_10_14309_ctg_0000000000000721 crossref_primary_10_1016_j_intimp_2024_111993 crossref_primary_10_1084_jem_20220236 crossref_primary_10_1038_s41467_020_20351_5 crossref_primary_10_1038_s41467_022_30633_9 crossref_primary_10_1038_s41575_022_00604_y crossref_primary_10_1016_j_cellsig_2022_110552 crossref_primary_10_1016_j_stem_2022_06_013 crossref_primary_10_1038_s41586_020_2729_3 crossref_primary_10_1016_j_medj_2022_05_002 crossref_primary_10_1101_gr_273961_120 crossref_primary_10_1111_jre_13057 crossref_primary_10_1111_cpr_13536 crossref_primary_10_3389_fimmu_2022_840935 crossref_primary_10_1177_1934578X231182905 crossref_primary_10_1016_j_stem_2025_02_009 crossref_primary_10_2217_fon_2020_0384 crossref_primary_10_1038_s41467_020_15714_x crossref_primary_10_1016_j_coi_2019_11_003 crossref_primary_10_1038_s43588_023_00464_9 crossref_primary_10_1038_s41536_021_00153_z crossref_primary_10_1016_j_cell_2023_11_004 crossref_primary_10_1172_JCI154993 crossref_primary_10_3390_cells10112954 crossref_primary_10_1038_s41467_022_29734_2 crossref_primary_10_3892_mmr_2024_13281 crossref_primary_10_1186_s41232_021_00174_7 crossref_primary_10_1186_s12967_023_04281_6 crossref_primary_10_1038_s41467_024_46076_3 crossref_primary_10_1093_ibd_izad084 crossref_primary_10_1016_j_isci_2023_107943 crossref_primary_10_1016_j_immuni_2022_11_002 crossref_primary_10_1093_ibd_izae292 crossref_primary_10_1136_gutjnl_2021_325516 crossref_primary_10_1111_iep_12488 crossref_primary_10_1016_j_devcel_2023_02_012 crossref_primary_10_1038_s41385_021_00472_w crossref_primary_10_2147_JIR_S288412 crossref_primary_10_1101_cshperspect_a040865 crossref_primary_10_3389_fimmu_2019_01093 crossref_primary_10_1093_hmg_ddaa130 crossref_primary_10_1016_j_chom_2024_07_020 crossref_primary_10_1007_s10620_020_06609_4 crossref_primary_10_1016_j_ceb_2020_01_004 crossref_primary_10_1111_1751_7915_13661 crossref_primary_10_3389_fimmu_2024_1388496 crossref_primary_10_1016_j_immuni_2020_02_009 crossref_primary_10_3390_cells10092242 crossref_primary_10_1053_j_gastro_2021_09_077 crossref_primary_10_1038_s41591_021_01520_5 crossref_primary_10_3390_cancers13051000 crossref_primary_10_1126_sciimmunol_aax0416 crossref_primary_10_3389_fimmu_2020_547102 crossref_primary_10_1242_jcs_260248 crossref_primary_10_1016_j_diff_2019_01_002 |
| Cites_doi | 10.1016/S1535-6108(04)00081-9 10.1186/1471-2105-15-182 10.1186/1471-2105-12-77 10.1093/bioinformatics/btw354 10.1038/ncb2610 10.1186/1471-2105-9-559 10.1016/j.cell.2016.11.040 10.1016/j.diff.2017.08.003 10.1016/S0079-6603(01)70012-8 10.1126/science.1223821 10.1093/biostatistics/kxj037 10.1179/his.2010.33.1.31 10.1186/1471-2105-11-367 10.1016/j.jcmgh.2015.12.004 10.1371/journal.pone.0076871 10.1053/j.gastro.2011.07.050 10.1038/nrm3721 10.1016/j.diff.2016.05.002 10.1093/nar/30.1.207 10.1038/s41586-018-0190-3 10.1186/s13059-016-0947-7 10.1136/gut.2008.148395 10.1038/nature11965 10.1038/nmeth.3317 10.1016/j.ymeth.2015.06.021 10.1073/pnas.1603534113 10.1038/nbt.2931 10.1038/nbt.3192 10.1038/s41586-018-0084-4 10.1242/dev.02141 10.1172/JCI29159 10.1093/bioinformatics/btt656 10.1152/ajpgi.00001.2013 10.1016/j.stemcr.2013.12.012 10.1016/j.stem.2013.09.006 10.1053/j.gastro.2008.07.016 10.1089/omi.2011.0118 10.1093/bioinformatics/btv715 10.1038/nbt.4091 10.1093/bioinformatics/btw777 |
| ContentType | Journal Article |
| Copyright | 2018 The Author(s) Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved. 2018 The Author(s) 2018 |
| Copyright_xml | – notice: 2018 The Author(s) – notice: Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved. – notice: 2018 The Author(s) 2018 |
| DBID | 6I. AAFTH AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6 5PM |
| DOI | 10.1016/j.cell.2018.08.067 |
| DatabaseName | ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic AGRICOLA AGRICOLA - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic AGRICOLA |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1097-4172 |
| EndPage | 386.e17 |
| ExternalDocumentID | PMC6176871 30270042 10_1016_j_cell_2018_08_067 S0092867418311681 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GrantInformation_xml | – fundername: Wellcome Trust – fundername: Medical Research Council grantid: MC_UU_12009/16 – fundername: Medical Research Council grantid: MC_UU_00016/15 – fundername: Medical Research Council grantid: MC_UU_12010/7 – fundername: Department of Health grantid: NIHR-RP-R3-12-026 – fundername: Medical Research Council grantid: MR/M00919X/1 – fundername: Medical Research Council grantid: MC_UU_00008/7 – fundername: Wellcome Trust grantid: 102974/Z/13/Z – fundername: Medical Research Council grantid: G84/6443 |
| GroupedDBID | --- --K -DZ -ET -~X 0R~ 0WA 1RT 1~5 29B 2FS 2WC 3EH 4.4 457 4G. 53G 5GY 5RE 62- 6I. 6J9 7-5 85S AACTN AAEDW AAFTH AAFWJ AAIAV AAKRW AAKUH AALRI AAUCE AAVLU AAXUO ABCQX ABJNI ABMAC ABMWF ABOCM ABVKL ACGFO ACGFS ACNCT ADBBV ADEZE ADJPV AEFWE AENEX AEXQZ AFTJW AGHSJ AGKMS AHHHB AITUG ALKID ALMA_UNASSIGNED_HOLDINGS AMRAJ ASPBG AVWKF AZFZN BAWUL CS3 DIK DU5 E3Z EBS EJD F5P FCP FDB FIRID HH5 IH2 IHE IXB J1W JIG K-O KOO KQ8 L7B LX5 M3Z M41 N9A NCXOZ O-L O9- OK1 P2P RCE RIG RNS ROL RPZ SCP SDG SDP SES SSZ TAE TN5 TR2 TWZ UKR UPT VQA WH7 WQ6 YZZ ZA5 ZCA .-4 .55 .GJ .HR 1CY 1VV 2KS 3O- 5VS 6TJ 9M8 AAEDT AAHBH AAIKJ AAMRU AAQFI AAQXK AAYJJ AAYWO AAYXX ABDGV ABDPE ABEFU ABWVN ACRPL ACVFH ADCNI ADMUD ADNMO ADVLN ADXHL AETEA AEUPX AFPUW AGCQF AGHFR AGQPQ AI. AIDAL AIGII AKAPO AKBMS AKRWK AKYEP APXCP CITATION FEDTE FGOYB G-2 HVGLF HZ~ H~9 MVM OHT OMK OZT PUQ R2- UBW UHB VH1 X7M YYP YYQ ZGI ZHY ZKB ZY4 CGR CUY CVF ECM EFKBS EIF NPM 7X8 7S9 L.6 5PM |
| ID | FETCH-LOGICAL-c554t-d113132f2d4520dcc739b998e5de3e700ef40d1ece229fa8ed90758991e153733 |
| IEDL.DBID | IXB |
| ISSN | 0092-8674 1097-4172 |
| IngestDate | Thu Aug 21 18:28:17 EDT 2025 Sun Sep 28 02:20:17 EDT 2025 Sun Sep 28 09:08:54 EDT 2025 Mon Jul 21 06:08:08 EDT 2025 Tue Jul 01 02:17:01 EDT 2025 Thu Apr 24 23:13:29 EDT 2025 Fri Feb 23 02:27:20 EST 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 2 |
| Keywords | stromal cell mesenchyme target discovery TNFSF14 stratification single-cell RNA-seq SOX6 crypt niche CyTOF inflammatory bowel disease Wnts |
| Language | English |
| License | This is an open access article under the CC BY license. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c554t-d113132f2d4520dcc739b998e5de3e700ef40d1ece229fa8ed90758991e153733 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Lead Contact These authors contributed equally |
| OpenAccessLink | https://www.sciencedirect.com/science/article/pii/S0092867418311681 |
| PMID | 30270042 |
| PQID | 2115275708 |
| PQPubID | 23479 |
| PageCount | 15 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_6176871 proquest_miscellaneous_2221041530 proquest_miscellaneous_2115275708 pubmed_primary_30270042 crossref_citationtrail_10_1016_j_cell_2018_08_067 crossref_primary_10_1016_j_cell_2018_08_067 elsevier_sciencedirect_doi_10_1016_j_cell_2018_08_067 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2018-10-04 |
| PublicationDateYYYYMMDD | 2018-10-04 |
| PublicationDate_xml | – month: 10 year: 2018 text: 2018-10-04 day: 04 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Cell |
| PublicationTitleAlternate | Cell |
| PublicationYear | 2018 |
| Publisher | Elsevier Inc Cell Press |
| Publisher_xml | – name: Elsevier Inc – name: Cell Press |
| References | Hsia, Ashley, Ouaret, Wang, Wilding, Bodmer (bib14) 2016; 113 Kurahashi, Nakano, Peri, Townsend, Ward, Sanders (bib20) 2013; 304 Torgo (bib40) 2010 Risso, Ngai, Speed, Dudoit (bib31) 2014; 32 Brown, Riehl, Walker, Geske, Doherty, Stenson, Stappenbeck (bib6) 2007; 117 Johnson, Li, Rabinovic (bib16) 2007; 8 Liaw, M (bib23) 2002; 2 Haghverdi, Lun, Morgan, Marioni (bib13) 2018; 36 Roulis, Flavell (bib33) 2016; 92 McCarthy, Campbell, Lun, Wills (bib25) 2017; 33 Van Der Loos (bib41) 2010; 33 Sato, Stange, Ferrante, Vries, Van Es, Van den Brink, Van Houdt, Pronk, Van Gorp, Siersema, Clevers (bib36) 2011; 141 Degirmenci, Valenta, Dimitrieva, Hausmann, Basler (bib9) 2018; 558 Ewels, Magnusson, Lundin, Kaller (bib11) 2016; 32 Gaujoux, Seoighe (bib12) 2010; 11 Angerer, Haghverdi, Büttner, Theis, Marr, Buettner (bib1) 2016; 32 Barker (bib4) 2014; 15 Scialdone, Natarajan, Saraiva, Proserpio, Teichmann, Stegle, Marioni, Buettner (bib38) 2015; 85 Wilm, Ipenberg, Hastie, Burch, Bader (bib42) 2005; 132 San Roman, Jayewickreme, Murtaugh, Shivdasani (bib34) 2014; 2 Satija, Farrell, Gennert, Schier, Regev (bib35) 2015; 33 Jiang, Lei, Ding, Zhu (bib15) 2014; 15 Pinchuk, Saada, Beswick, Boya, Qiu, Mifflin, Raju, Reyes, Powell (bib29) 2008; 135 Langfelder, Horvath (bib21) 2008; 9 Nowarski, Jackson, Flavell (bib28) 2017; 168 Schwank, Andersson-Rolf, Koo, Sasaki, Clevers (bib37) 2013; 8 Edgar, Domrachev, Lash (bib10) 2002; 30 Bernardo, Fibbe (bib5) 2013; 13 Koch (bib18) 2017; 97 Rinkevich, Mori, Sahoo, Xu, Bermingham, Weissman (bib30) 2012; 14 Yu, Wang, Han, He (bib43) 2012; 16 Csiszar (bib8) 2001; 70 Robin, Turck, Hainard, Tiberti, Lisacek, Sanchez, Müller (bib32) 2011; 12 Buczacki, Zecchini, Nicholson, Russell, Vermeulen, Kemp, Winton (bib7) 2013; 495 Lun, Bach, Marioni (bib24) 2016; 17 Aoki, Shoshkes-Carmel, Gao, Shin, May, Golson, Zahm, Ray, Wiser, Wright, Kaestner (bib2) 2016; 2 Liao, Smyth, Shi (bib22) 2014; 30 Miyoshi, Ajima, Luo, Yamaguchi, Stappenbeck (bib26) 2012; 338 Kim, Langmead, Salzberg (bib17) 2015; 12 Bao, Ouyang, Bai, Huang, Ma, Liu, Shao, Anderson, Rich, Wang (bib3) 2004; 5 Shoshkes-Carmel, Wang, Wangensteen, Tóth, Kondo, Massasa, Itzkovitz, Kaestner (bib39) 2018; 557 Kuhn (bib19) 2008; 28 Noble, Abbas, Cornelius, Lees, Ho, Toy, Modrusan, Pal, Zhong, Chalasani (bib27) 2008; 57 Shoshkes-Carmel (10.1016/j.cell.2018.08.067_bib39) 2018; 557 Degirmenci (10.1016/j.cell.2018.08.067_bib9) 2018; 558 Wilm (10.1016/j.cell.2018.08.067_bib42) 2005; 132 Risso (10.1016/j.cell.2018.08.067_bib31) 2014; 32 Torgo (10.1016/j.cell.2018.08.067_bib40) 2010 Sato (10.1016/j.cell.2018.08.067_bib36) 2011; 141 Csiszar (10.1016/j.cell.2018.08.067_bib8) 2001; 70 Roulis (10.1016/j.cell.2018.08.067_bib33) 2016; 92 Johnson (10.1016/j.cell.2018.08.067_bib16) 2007; 8 Edgar (10.1016/j.cell.2018.08.067_bib10) 2002; 30 Kuhn (10.1016/j.cell.2018.08.067_bib19) 2008; 28 Angerer (10.1016/j.cell.2018.08.067_bib1) 2016; 32 San Roman (10.1016/j.cell.2018.08.067_bib34) 2014; 2 Noble (10.1016/j.cell.2018.08.067_bib27) 2008; 57 Buczacki (10.1016/j.cell.2018.08.067_bib7) 2013; 495 Langfelder (10.1016/j.cell.2018.08.067_bib21) 2008; 9 Satija (10.1016/j.cell.2018.08.067_bib35) 2015; 33 Scialdone (10.1016/j.cell.2018.08.067_bib38) 2015; 85 Pinchuk (10.1016/j.cell.2018.08.067_bib29) 2008; 135 Ewels (10.1016/j.cell.2018.08.067_bib11) 2016; 32 Haghverdi (10.1016/j.cell.2018.08.067_bib13) 2018; 36 Gaujoux (10.1016/j.cell.2018.08.067_bib12) 2010; 11 Schwank (10.1016/j.cell.2018.08.067_bib37) 2013; 8 Jiang (10.1016/j.cell.2018.08.067_bib15) 2014; 15 Liao (10.1016/j.cell.2018.08.067_bib22) 2014; 30 Liaw (10.1016/j.cell.2018.08.067_bib23) 2002; 2 Miyoshi (10.1016/j.cell.2018.08.067_bib26) 2012; 338 Aoki (10.1016/j.cell.2018.08.067_bib2) 2016; 2 Bao (10.1016/j.cell.2018.08.067_bib3) 2004; 5 Barker (10.1016/j.cell.2018.08.067_bib4) 2014; 15 Nowarski (10.1016/j.cell.2018.08.067_bib28) 2017; 168 Kurahashi (10.1016/j.cell.2018.08.067_bib20) 2013; 304 Lun (10.1016/j.cell.2018.08.067_bib24) 2016; 17 Yu (10.1016/j.cell.2018.08.067_bib43) 2012; 16 Kim (10.1016/j.cell.2018.08.067_bib17) 2015; 12 Brown (10.1016/j.cell.2018.08.067_bib6) 2007; 117 Koch (10.1016/j.cell.2018.08.067_bib18) 2017; 97 Bernardo (10.1016/j.cell.2018.08.067_bib5) 2013; 13 Van Der Loos (10.1016/j.cell.2018.08.067_bib41) 2010; 33 Rinkevich (10.1016/j.cell.2018.08.067_bib30) 2012; 14 McCarthy (10.1016/j.cell.2018.08.067_bib25) 2017; 33 Robin (10.1016/j.cell.2018.08.067_bib32) 2011; 12 Hsia (10.1016/j.cell.2018.08.067_bib14) 2016; 113 |
| References_xml | – volume: 495 start-page: 65 year: 2013 end-page: 69 ident: bib7 article-title: Intestinal label-retaining cells are secretory precursors expressing Lgr5 publication-title: Nature – volume: 338 start-page: 108 year: 2012 end-page: 113 ident: bib26 article-title: Wnt5a potentiates TGF-β signaling to promote colonic crypt regeneration after tissue injury publication-title: Science – volume: 33 start-page: 31 year: 2010 end-page: 40 ident: bib41 article-title: Chromogens in multiple immunohistochemical staining used for visual assessment and spectral imaging: The colorful future publication-title: J. Histotechnol. – volume: 15 start-page: 19 year: 2014 end-page: 33 ident: bib4 article-title: Adult intestinal stem cells: Critical drivers of epithelial homeostasis and regeneration publication-title: Nat. Rev. Mol. Cell Biol. – volume: 13 start-page: 392 year: 2013 end-page: 402 ident: bib5 article-title: Mesenchymal stromal cells: Sensors and switchers of inflammation publication-title: Cell Stem Cell – volume: 30 start-page: 207 year: 2002 end-page: 210 ident: bib10 article-title: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository publication-title: Nucleic Acids Res. – volume: 8 start-page: 118 year: 2007 end-page: 127 ident: bib16 article-title: Adjusting batch effects in microarray expression data using empirical Bayes methods publication-title: Biostatistics – volume: 30 start-page: 923 year: 2014 end-page: 930 ident: bib22 article-title: featureCounts: An efficient general purpose program for assigning sequence reads to genomic features publication-title: Bioinformatics – volume: 14 start-page: 1251 year: 2012 end-page: 1260 ident: bib30 article-title: Identification and prospective isolation of a mesothelial precursor lineage giving rise to smooth muscle cells and fibroblasts for mammalian internal organs, and their vasculature publication-title: Nat. Cell Biol. – volume: 557 start-page: 242 year: 2018 end-page: 246 ident: bib39 article-title: Subepithelial telocytes are an important source of Wnts that supports intestinal crypts publication-title: Nature – volume: 2 start-page: 18 year: 2002 end-page: 22 ident: bib23 article-title: Classification and regression by randomForest publication-title: R News – volume: 141 start-page: 1762 year: 2011 end-page: 1772 ident: bib36 article-title: Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium publication-title: Gastroenterology – volume: 168 start-page: 362 year: 2017 end-page: 375 ident: bib28 article-title: The stromal intervention: Regulation of immunity and inflammation at the epithelial-mesenchymal barrier publication-title: Cell – volume: 117 start-page: 258 year: 2007 end-page: 269 ident: bib6 article-title: Myd88-dependent positioning of Ptgs2-expressing stromal cells maintains colonic epithelial proliferation during injury publication-title: J. Clin. Invest. – volume: 32 start-page: 896 year: 2014 end-page: 902 ident: bib31 article-title: Normalization of RNA-seq data using factor analysis of control genes or samples publication-title: Nat. Biotechnol. – volume: 11 start-page: 367 year: 2010 ident: bib12 article-title: A flexible R package for nonnegative matrix factorization publication-title: BMC Bioinformatics – volume: 2 start-page: 127 year: 2014 end-page: 134 ident: bib34 article-title: Wnt secretion from epithelial cells and subepithelial myofibroblasts is not required in the mouse intestinal stem cell niche in vivo publication-title: Stem Cell Reports – volume: 8 start-page: e76871 year: 2013 ident: bib37 article-title: Generation of BAC transgenic epithelial organoids publication-title: PLoS ONE – volume: 132 start-page: 5317 year: 2005 end-page: 5328 ident: bib42 article-title: The serosal mesothelium is a major source of smooth muscle cells of the gut vasculature publication-title: Development – volume: 32 start-page: 1241 year: 2016 end-page: 1243 ident: bib1 article-title: destiny: Diffusion maps for large-scale single-cell data in R publication-title: Bioinformatics – volume: 33 start-page: 495 year: 2015 end-page: 502 ident: bib35 article-title: Spatial reconstruction of single-cell gene expression data publication-title: Nat. Biotechnol. – volume: 32 start-page: 3047 year: 2016 end-page: 3048 ident: bib11 article-title: MultiQC: summarize analysis results for multiple tools and samples in a single report publication-title: Bioinformatics – volume: 85 start-page: 54 year: 2015 end-page: 61 ident: bib38 article-title: Computational assignment of cell-cycle stage from single-cell transcriptome data publication-title: Methods – volume: 28 year: 2008 ident: bib19 article-title: Building predictive models in R using the caret package publication-title: J. Stat. Softw. – volume: 304 start-page: G823 year: 2013 end-page: G834 ident: bib20 article-title: A novel population of subepithelial platelet-derived growth factor receptor α-positive cells in the mouse and human colon publication-title: Am. J. Physiol. Gastrointest. Liver Physiol. – volume: 36 start-page: 421 year: 2018 end-page: 427 ident: bib13 article-title: Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors publication-title: Nat. Biotechnol. – volume: 558 start-page: 449 year: 2018 end-page: 453 ident: bib9 article-title: GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells publication-title: Nature – year: 2010 ident: bib40 article-title: Data Mining with R, Learning with Case Studies – volume: 97 start-page: 1 year: 2017 end-page: 8 ident: bib18 article-title: Extrinsic control of Wnt signaling in the intestine publication-title: Differentiation – volume: 113 start-page: E2162 year: 2016 end-page: E2171 ident: bib14 article-title: Myofibroblasts are distinguished from activated skin fibroblasts by the expression of AOC3 and other associated markers publication-title: Proc. Natl. Acad. Sci. USA – volume: 135 start-page: 1228 year: 2008 end-page: 1237 ident: bib29 article-title: PD-1 ligand expression by human colonic myofibroblasts/fibroblasts regulates CD4+ T-cell activity publication-title: Gastroenterology – volume: 2 start-page: 175 year: 2016 end-page: 188 ident: bib2 article-title: Foxl1-expressing mesenchymal cells constitute the intestinal stem cell niche publication-title: Cell. Mol. Gastroenterol. Hepatol. – volume: 15 start-page: 182 year: 2014 ident: bib15 article-title: Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads publication-title: BMC Bioinformatics – volume: 33 start-page: 1179 year: 2017 end-page: 1186 ident: bib25 article-title: Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R publication-title: Bioinformatics – volume: 92 start-page: 116 year: 2016 end-page: 131 ident: bib33 article-title: Fibroblasts and myofibroblasts of the intestinal lamina propria in physiology and disease publication-title: Differentiation – volume: 70 start-page: 1 year: 2001 end-page: 32 ident: bib8 article-title: Lysyl oxidases: a novel multifunctional amine oxidase family publication-title: Prog. Nucleic Acid Res. Mol. Biol. – volume: 5 start-page: 329 year: 2004 end-page: 339 ident: bib3 article-title: Periostin potently promotes metastatic growth of colon cancer by augmenting cell survival via the Akt/PKB pathway publication-title: Cancer Cell – volume: 17 start-page: 75 year: 2016 ident: bib24 article-title: Pooling across cells to normalize single-cell RNA sequencing data with many zero counts publication-title: Genome Biol. – volume: 57 start-page: 1398 year: 2008 end-page: 1405 ident: bib27 article-title: Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis publication-title: Gut – volume: 16 start-page: 284 year: 2012 end-page: 287 ident: bib43 article-title: clusterProfiler: An R package for comparing biological themes among gene clusters publication-title: OMICS – volume: 12 start-page: 357 year: 2015 end-page: 360 ident: bib17 article-title: HISAT: A fast spliced aligner with low memory requirements publication-title: Nat. Methods – volume: 9 start-page: 559 year: 2008 ident: bib21 article-title: WGCNA: An R package for weighted correlation network analysis publication-title: BMC Bioinformatics – volume: 12 start-page: 77 year: 2011 ident: bib32 article-title: pROC: an open-source package for R and S+ to analyze and compare ROC curves publication-title: BMC Bioinformatics – volume: 5 start-page: 329 year: 2004 ident: 10.1016/j.cell.2018.08.067_bib3 article-title: Periostin potently promotes metastatic growth of colon cancer by augmenting cell survival via the Akt/PKB pathway publication-title: Cancer Cell doi: 10.1016/S1535-6108(04)00081-9 – volume: 15 start-page: 182 year: 2014 ident: 10.1016/j.cell.2018.08.067_bib15 article-title: Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-15-182 – volume: 12 start-page: 77 year: 2011 ident: 10.1016/j.cell.2018.08.067_bib32 article-title: pROC: an open-source package for R and S+ to analyze and compare ROC curves publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-77 – volume: 32 start-page: 3047 year: 2016 ident: 10.1016/j.cell.2018.08.067_bib11 article-title: MultiQC: summarize analysis results for multiple tools and samples in a single report publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw354 – volume: 14 start-page: 1251 year: 2012 ident: 10.1016/j.cell.2018.08.067_bib30 article-title: Identification and prospective isolation of a mesothelial precursor lineage giving rise to smooth muscle cells and fibroblasts for mammalian internal organs, and their vasculature publication-title: Nat. Cell Biol. doi: 10.1038/ncb2610 – volume: 9 start-page: 559 year: 2008 ident: 10.1016/j.cell.2018.08.067_bib21 article-title: WGCNA: An R package for weighted correlation network analysis publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-9-559 – volume: 168 start-page: 362 year: 2017 ident: 10.1016/j.cell.2018.08.067_bib28 article-title: The stromal intervention: Regulation of immunity and inflammation at the epithelial-mesenchymal barrier publication-title: Cell doi: 10.1016/j.cell.2016.11.040 – volume: 97 start-page: 1 year: 2017 ident: 10.1016/j.cell.2018.08.067_bib18 article-title: Extrinsic control of Wnt signaling in the intestine publication-title: Differentiation doi: 10.1016/j.diff.2017.08.003 – volume: 70 start-page: 1 year: 2001 ident: 10.1016/j.cell.2018.08.067_bib8 article-title: Lysyl oxidases: a novel multifunctional amine oxidase family publication-title: Prog. Nucleic Acid Res. Mol. Biol. doi: 10.1016/S0079-6603(01)70012-8 – volume: 338 start-page: 108 year: 2012 ident: 10.1016/j.cell.2018.08.067_bib26 article-title: Wnt5a potentiates TGF-β signaling to promote colonic crypt regeneration after tissue injury publication-title: Science doi: 10.1126/science.1223821 – volume: 8 start-page: 118 year: 2007 ident: 10.1016/j.cell.2018.08.067_bib16 article-title: Adjusting batch effects in microarray expression data using empirical Bayes methods publication-title: Biostatistics doi: 10.1093/biostatistics/kxj037 – volume: 33 start-page: 31 year: 2010 ident: 10.1016/j.cell.2018.08.067_bib41 article-title: Chromogens in multiple immunohistochemical staining used for visual assessment and spectral imaging: The colorful future publication-title: J. Histotechnol. doi: 10.1179/his.2010.33.1.31 – volume: 11 start-page: 367 year: 2010 ident: 10.1016/j.cell.2018.08.067_bib12 article-title: A flexible R package for nonnegative matrix factorization publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-367 – volume: 2 start-page: 175 year: 2016 ident: 10.1016/j.cell.2018.08.067_bib2 article-title: Foxl1-expressing mesenchymal cells constitute the intestinal stem cell niche publication-title: Cell. Mol. Gastroenterol. Hepatol. doi: 10.1016/j.jcmgh.2015.12.004 – volume: 8 start-page: e76871 year: 2013 ident: 10.1016/j.cell.2018.08.067_bib37 article-title: Generation of BAC transgenic epithelial organoids publication-title: PLoS ONE doi: 10.1371/journal.pone.0076871 – volume: 141 start-page: 1762 year: 2011 ident: 10.1016/j.cell.2018.08.067_bib36 article-title: Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium publication-title: Gastroenterology doi: 10.1053/j.gastro.2011.07.050 – volume: 15 start-page: 19 year: 2014 ident: 10.1016/j.cell.2018.08.067_bib4 article-title: Adult intestinal stem cells: Critical drivers of epithelial homeostasis and regeneration publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm3721 – year: 2010 ident: 10.1016/j.cell.2018.08.067_bib40 – volume: 92 start-page: 116 year: 2016 ident: 10.1016/j.cell.2018.08.067_bib33 article-title: Fibroblasts and myofibroblasts of the intestinal lamina propria in physiology and disease publication-title: Differentiation doi: 10.1016/j.diff.2016.05.002 – volume: 30 start-page: 207 year: 2002 ident: 10.1016/j.cell.2018.08.067_bib10 article-title: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository publication-title: Nucleic Acids Res. doi: 10.1093/nar/30.1.207 – volume: 558 start-page: 449 year: 2018 ident: 10.1016/j.cell.2018.08.067_bib9 article-title: GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells publication-title: Nature doi: 10.1038/s41586-018-0190-3 – volume: 17 start-page: 75 year: 2016 ident: 10.1016/j.cell.2018.08.067_bib24 article-title: Pooling across cells to normalize single-cell RNA sequencing data with many zero counts publication-title: Genome Biol. doi: 10.1186/s13059-016-0947-7 – volume: 57 start-page: 1398 year: 2008 ident: 10.1016/j.cell.2018.08.067_bib27 article-title: Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis publication-title: Gut doi: 10.1136/gut.2008.148395 – volume: 495 start-page: 65 year: 2013 ident: 10.1016/j.cell.2018.08.067_bib7 article-title: Intestinal label-retaining cells are secretory precursors expressing Lgr5 publication-title: Nature doi: 10.1038/nature11965 – volume: 12 start-page: 357 year: 2015 ident: 10.1016/j.cell.2018.08.067_bib17 article-title: HISAT: A fast spliced aligner with low memory requirements publication-title: Nat. Methods doi: 10.1038/nmeth.3317 – volume: 2 start-page: 18 year: 2002 ident: 10.1016/j.cell.2018.08.067_bib23 article-title: Classification and regression by randomForest publication-title: R News – volume: 85 start-page: 54 year: 2015 ident: 10.1016/j.cell.2018.08.067_bib38 article-title: Computational assignment of cell-cycle stage from single-cell transcriptome data publication-title: Methods doi: 10.1016/j.ymeth.2015.06.021 – volume: 113 start-page: E2162 year: 2016 ident: 10.1016/j.cell.2018.08.067_bib14 article-title: Myofibroblasts are distinguished from activated skin fibroblasts by the expression of AOC3 and other associated markers publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1603534113 – volume: 32 start-page: 896 year: 2014 ident: 10.1016/j.cell.2018.08.067_bib31 article-title: Normalization of RNA-seq data using factor analysis of control genes or samples publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2931 – volume: 33 start-page: 495 year: 2015 ident: 10.1016/j.cell.2018.08.067_bib35 article-title: Spatial reconstruction of single-cell gene expression data publication-title: Nat. Biotechnol. doi: 10.1038/nbt.3192 – volume: 557 start-page: 242 year: 2018 ident: 10.1016/j.cell.2018.08.067_bib39 article-title: Subepithelial telocytes are an important source of Wnts that supports intestinal crypts publication-title: Nature doi: 10.1038/s41586-018-0084-4 – volume: 132 start-page: 5317 year: 2005 ident: 10.1016/j.cell.2018.08.067_bib42 article-title: The serosal mesothelium is a major source of smooth muscle cells of the gut vasculature publication-title: Development doi: 10.1242/dev.02141 – volume: 117 start-page: 258 year: 2007 ident: 10.1016/j.cell.2018.08.067_bib6 article-title: Myd88-dependent positioning of Ptgs2-expressing stromal cells maintains colonic epithelial proliferation during injury publication-title: J. Clin. Invest. doi: 10.1172/JCI29159 – volume: 28 year: 2008 ident: 10.1016/j.cell.2018.08.067_bib19 article-title: Building predictive models in R using the caret package publication-title: J. Stat. Softw. – volume: 30 start-page: 923 year: 2014 ident: 10.1016/j.cell.2018.08.067_bib22 article-title: featureCounts: An efficient general purpose program for assigning sequence reads to genomic features publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt656 – volume: 304 start-page: G823 year: 2013 ident: 10.1016/j.cell.2018.08.067_bib20 article-title: A novel population of subepithelial platelet-derived growth factor receptor α-positive cells in the mouse and human colon publication-title: Am. J. Physiol. Gastrointest. Liver Physiol. doi: 10.1152/ajpgi.00001.2013 – volume: 2 start-page: 127 year: 2014 ident: 10.1016/j.cell.2018.08.067_bib34 article-title: Wnt secretion from epithelial cells and subepithelial myofibroblasts is not required in the mouse intestinal stem cell niche in vivo publication-title: Stem Cell Reports doi: 10.1016/j.stemcr.2013.12.012 – volume: 13 start-page: 392 year: 2013 ident: 10.1016/j.cell.2018.08.067_bib5 article-title: Mesenchymal stromal cells: Sensors and switchers of inflammation publication-title: Cell Stem Cell doi: 10.1016/j.stem.2013.09.006 – volume: 135 start-page: 1228 year: 2008 ident: 10.1016/j.cell.2018.08.067_bib29 article-title: PD-1 ligand expression by human colonic myofibroblasts/fibroblasts regulates CD4+ T-cell activity publication-title: Gastroenterology doi: 10.1053/j.gastro.2008.07.016 – volume: 16 start-page: 284 year: 2012 ident: 10.1016/j.cell.2018.08.067_bib43 article-title: clusterProfiler: An R package for comparing biological themes among gene clusters publication-title: OMICS doi: 10.1089/omi.2011.0118 – volume: 32 start-page: 1241 year: 2016 ident: 10.1016/j.cell.2018.08.067_bib1 article-title: destiny: Diffusion maps for large-scale single-cell data in R publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv715 – volume: 36 start-page: 421 year: 2018 ident: 10.1016/j.cell.2018.08.067_bib13 article-title: Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors publication-title: Nat. Biotechnol. doi: 10.1038/nbt.4091 – volume: 33 start-page: 1179 year: 2017 ident: 10.1016/j.cell.2018.08.067_bib25 article-title: Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw777 |
| SSID | ssj0008555 |
| Score | 2.6912644 |
| Snippet | Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity... |
| SourceID | pubmedcentral proquest pubmed crossref elsevier |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 372 |
| SubjectTerms | Animals Cell Proliferation colitis Colitis - genetics Colitis - physiopathology Colon - physiology crypt niche CyTOF disease severity epithelial cells Epithelial Cells - metabolism epithelium fibroblasts Fibroblasts - physiology genes Genetic Heterogeneity Homeostasis Humans immunity Inflammation inflammatory bowel disease Inflammatory Bowel Diseases - physiopathology Intestinal Mucosa - immunology Intestinal Mucosa - physiology intestines Intestines - immunology Intestines - physiology Mesenchymal Stem Cells - physiology mesenchyme Mesoderm - metabolism Mesoderm - physiology Mice Mice, Inbred C57BL Myofibroblasts oxidative stress Pericytes protein-lysine 6-oxidase RAW 264.7 Cells Single-Cell Analysis - methods single-cell RNA-seq SOX6 SOXD Transcription Factors - physiology stem cells stratification stromal cell target discovery Thromboplastin - physiology TNFSF14 transcription factors Tumor Necrosis Factor Ligand Superfamily Member 14 - genetics tumor necrosis factors Wnt Signaling Pathway - physiology Wnts |
| Title | Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease |
| URI | https://dx.doi.org/10.1016/j.cell.2018.08.067 https://www.ncbi.nlm.nih.gov/pubmed/30270042 https://www.proquest.com/docview/2115275708 https://www.proquest.com/docview/2221041530 https://pubmed.ncbi.nlm.nih.gov/PMC6176871 |
| Volume | 175 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1NT9wwELUQElIvqLS0LLTIlbhVEfFXHB_LAoJW7aEUaW9W4kxEKsgiAar4952xkxVbxB56TDKWnLE9fmPPvGHswJWlLlVNQe1gMm0ak7lamwzXlqiUq1wTYoDsj-LsUn-dmdkam465MBRWOdj-ZNOjtR7eHA7aPLztOsrxdbIsiH1FCVHE9GvKKqUkvtnRwhqXxqQqBg5XPkoPiTMpxosOxym8q0w0nvalzek5-Pw3hvLJpnT6mm0OaJJ_SR3eYmvQv2Ebqb7k41t2cRHZYYlZg_-EWPQGdyo-bznCPh7P7_kUZfsu8O-UhhSuHm-Adz0_71ucKjfxCp4fzf_ANT9OVznb7PL05Nf0LBuqKGQBocJ91ghB9IytbLSReROCVa5GJwtMAwpsnkOr80ZAACldW5XQoL9s0A0TgNbQKvWOrffzHnYYl9JKwhttoYS2eVsphEfKBRxYXYOpJ0yM6vNhoBinShfXfowl--1J5Z5U7qn8ZWEn7POizW0i2FgpbcZR8UvTxOMOsLLdp3EIPa4f-lz1MH-48-gAG2mNzcsVMhIdY0Q6Kp-w92nYF32le1-yfBNmlybEQoD4u5e_9N1V5PFG8Figv7r7n_-0x17RU4ws1B_YOs4o-IgI6b7eR9_g_Nt-XAh_ASGCDlk |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwEB5VrRBcEG8WChiJG4oav-L42G6pdqHtgbbS3qzEcdSgNluJItR_z4ydrFgQe-AajyXHHo-_sWe-Afhgy1KVsqag9qAzpRud2VrpDPcWr6StbONjgOxpMbtQnxd6sQXTMReGwioH259serTWw5e9YTb3brqOcnytKAtiX5GcF5R-vYNoICfVni8OVua41DqVMbC49VF8yJxJQV50O07xXWXi8TT_Op3-Rp9_BlH-diodPYKHA5xk-2nEj2Er9E_gXiowefcUzs4iPSxRa7CvIVa9waOKLVuGuI_FC3w2Rdm-8-yE8pD85d11YF3P5n2LunId3-DZwfJnuGKH6S3nGVwcfTqfzrKhjELmESvcZg3nxM_YikZpkTfeG2lr9LKCboIMJs9Dq_KGBx-EsG1VhgYdZo1-GA9oDo2Uz2G7X_bhJTAhjCDA0RaSK5O3lUR8JK3HlVV10PUE-Dh9zg8c41Tq4sqNwWTfHE25oyl3VP-yMBP4uOpzkxg2NkrrcVXcmp44PAI29ns_LqHDDUTNVR-WP7479IC1MNrk5QYZgZ4xQh2ZT-BFWvbVWOnhl0zfBMyaQqwEiMB7vaXvLiORN6LHAh3WV__5T-_g_uz85Ngdz0-_vIYH1BLDDNUubKN2hTcIl27rt3E7_AJjehCD |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Structural+Remodeling+of+the+Human+Colonic+Mesenchyme+in+Inflammatory+Bowel+Disease&rft.jtitle=Cell&rft.au=Kinchen%2C+James&rft.au=Chen%2C+Hannah+H.&rft.au=Parikh%2C+Kaushal&rft.au=Antanaviciute%2C+Agne&rft.date=2018-10-04&rft.issn=0092-8674&rft.volume=175&rft.issue=2&rft.spage=372&rft.epage=386.e17&rft_id=info:doi/10.1016%2Fj.cell.2018.08.067&rft.externalDBID=n%2Fa&rft.externalDocID=10_1016_j_cell_2018_08_067 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0092-8674&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0092-8674&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0092-8674&client=summon |