**Authors in BOLD denote Spence Lab members // Spence Lab publications in PubMed
Preprints
We deposit all of our manuscripts as preprints - check out our latest work here:
https://www.biorxiv.org/search/spence%252Bjason%252Bmichigan
Github
Our publicly available datasets can be found here:
https://github.com/jason-spence-lab
2024
Nascent matrix deposition supports alveolar organoid formation from aggregates in synthetic hydrogels. Madeline K. Eiken, Charlie J. Childs, Lindy K. Brastrom, Tristan Frum, Eleanor M. Plaster, Orren Shachaf, Suzanne Pfeiffer, Justin E. Levine, Konstantinos-Dionysios Alysandratos, Darrell N. Kotton, Jason R. Spence, Claudia Loebel. BioRxiv. doi: 10.1101/2024.03.19.585720
2023
Opposing roles for TGFβ- and BMP-signaling during nascent alveolar differentiation in the developing human lung. Frum T, Hsu PP, Hein RFC, Conchola AS, Zhang CJ, Utter OR, Anand A, Zhang Y, Clark SG, Glass I, Sexton JZ, Spence JR. NPJ Regen Med. 2023 Sep 9;8(1):48. doi: 10.1038/s41536-023-00325-z. PMID: 37689780
Regionally distinct progenitor cells in the lower airway give rise to neuroendocrine and multiciliated cells in the developing human lung. Conchola AS, Frum T, Xiao Z, Hsu PP, Kaur K, Downey MS, Hein RFC, Miller AJ, Tsai YH, Wu A, Holloway EM, Anand A, Murthy PKL, Glass I, Tata PR, Spence JR. Proc Natl Acad Sci U S A. 2023 Jun 13;120(24):e2210113120. doi: 10.1073/pnas.2210113120. Epub 2023 Jun 6. PMID: 37279279.
Transplanted human intestinal organoids: a resource for modeling human intestinal development. Singh A, Poling HM, Chaturvedi P, Thorner K, Sundaram N, Kechele DO, Childs CJ, McCauley HA, Fisher GW, Brown NE, Spence JR, Wells JM, Helmrath MA. Development. 2023 May 1;150(9):dev201416. doi: 10.1242/dev.201416. Epub 2023 May 5. PMID: 37070767.
EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids. Childs CJ, Holloway EM, Sweet CW, Tsai YH, Wu A, Vallie A, Eiken MK, Capeling MM, Zwick RK, Palikuqi B, Trentesaux C, Wu JH, Pellon-Cardenas O, Zhang CJ, Glass IA, Loebel C, Yu Q, Camp JG, Sexton JZ, Klein OD, Verzi MP, Spence JR. JCI Insight. 2023 Mar 22;8(6):e165566. doi: 10.1172/jci.insight.165566. PMID: 36821371.
A Pilot Study: Transcriptional Profiling, Functional Analysis, and Organoid Modeling of Intestinal Mucosa in Hirschsprung Disease. Lotakis DM, Dheer R, Dame MK, Cuttitta AJ, Tigani DJ, Spence JR, Young VB, Ralls MW. J Pediatr Surg. 2023 Jun;58(6):1164-1169. doi: 10.1016/j.jpedsurg.2023.02.020. Epub 2023 Feb 18. PMID: 36922279.
FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells. Danopoulos S, Belgacemi R, Hein RFC, Miller AJ, Deutsch GH, Glass I, Spence JR, Al Alam D. Am J Physiol Lung Cell Mol Physiol. 2023 Apr 1;324(4):L433-L444. doi: 10.1152/ajplung.00316.2022. Epub 2023 Feb 15. PMID: 36791060.
A human liver organoid screening platform for DILI risk prediction. Zhang CJ, Meyer SR, O'Meara MJ, Huang S, Capeling MM, Ferrer-Torres D, Childs CJ, Spence JR, Fontana RJ, Sexton JZ. J Hepatol. 2023 May;78(5):998-1006. doi: 10.1016/j.jhep.2023.01.019. Epub 2023 Feb 3. PMID: 36738840.
Transferrin Receptor-Mediated Iron Uptake Promotes Colon Tumorigenesis. Kim H, Villareal LB, Liu Z, Haneef M, Falcon DM, Martin DR, Lee HJ, Dame MK, Attili D, Chen Y, Varani J, Spence JR, Kovbasnjuk O, Colacino JA, Lyssiotis CA, Lin HC, Shah YM, Xue X. Adv Sci (Weinh). 2023 Apr;10(10):e2207693. doi: 10.1002/advs.202207693. Epub 2023 Jan 26. PMID: 36703617.
In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Bouffi C, Wikenheiser-Brokamp KA, Chaturvedi P, Sundaram N, Goddard GR, Wunderlich M, Brown NE, Staab JF, Latanich R, Zachos NC, Holloway EM, Mahe MM, Poling HM, Vales S, Fisher GW, Spence JR, Mulloy JC, Zorn AM, Wells JM, Helmrath MA. Nat Biotechnol. 2023 Jan 26. doi: 10.1038/s41587-022-01558-x. Epub ahead of print. PMID: 36702898.
2022
Mapping the adult human esophagus in vivo and in vitro. Ferrer-Torres D, Wu JH, Zhang CJ, Hammer MA, Dame MK, Wu A, Holloway EM, Karpoff K, McCarthy CL, Bohm MS, Cuttitta AJ, Tigani DJ, Huang S, Tsai YH, Miller AJ, Walker T, Bayer DE, Hogan SP, Turgeon DK, Lin J, Higgins PDR, Sexton J, Spence JR. Development. 2022 Oct 15;149(20):dev200614. doi: 10.1242/dev.200614. Epub 2022 Oct 24. PMID: 36278875; PMCID: PMC9720751.
Approaches to benchmark and characterize in vitro human model systems. Childs CJ, Eiken MK, Spence JR. Development. 2022 Oct 15;149(20):dev200641. doi: 10.1242/dev.200641. Epub 2022 Oct 10. PMID: 36214410.
Human Lung Organoid Culture in Alginate With and Without Matrigel to Model Development and Disease. Dye BR, Decker JT, Hein RFC, Miller AJ, Huang S, Spence JR, Shea LD. Tissue Eng Part A. 2022 Nov;28(21-22):893-906. doi: 10.1089/ten.TEA.2022.0054. Epub 2022 Oct 6. PMID: 36029210; PMCID: PMC9805886.
Human neutrophil IL1β directs intestinal epithelial cell extrusion during Salmonella infection. Lawrence AE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Sule GJ, Knight JS, Wobus CE, Spence JR, Young VB, O'Riordan MX, Abuaita BH. PLoS Pathog. 2022 Oct 3;18(10):e1010855. doi: 10.1371/journal.ppat.1010855. PMID: 36191054
Organoids as tools for fundamental discovery and translation-a Keystone Symposia report. Cable J, Lutolf MP, Fu J, Park SE, Apostolou A, Chen S, Song CJ, Spence JR, Liberali P, Lancaster M, Meier AB, Pek NMQ, Wells JM, Capeling MM, Uzquiano A, Musah S, Huch M, Gouti M, Hombrink P, Quadrato G, Urenda JP. Ann N Y Acad Sci. 2022 Dec;1518(1):196-208. doi: 10.1111/nyas.14874. Epub 2022 Sep 30. PMID: 36177906
Stable iPSC-derived NKX2-1+ lung bud tip progenitor organoids give rise to airway and alveolar cell types. Hein RFC, Conchola AS, Fine AS, Xiao Z, Frum T, Brastrom LK, Akinwale MA, Childs CJ, Tsai YH, Holloway EM, Huang S, Mahoney J, Heemskerk I, Spence JR. Development. 2022 Oct 15;149(20):dev200693. doi: 10.1242/dev.200693. Epub 2022 Aug 30. PMID: 36039869
R-SPONDIN2+ mesenchymal cells form the bud tip progenitor niche during human lung development. Hein RFC, Wu JH, Holloway EM, Frum T, Conchola AS, Tsai YH, Wu A, Fine AS, Miller AJ, Szenker-Ravi E, Yan KS, Kuo CJ, Glass I, Reversade B, Spence JR. Dev Cell. 2022 Jul 11;57(13):1598-1614.e8. doi: 10.1016/j.devcel.2022.05.010. Epub 2022 Jun 8. PMID: 35679862
Vertical sleeve gastrectomy induces enteroendocrine cell differentiation of intestinal stem cells through bile acid signaling. Kim KS, Peck BC, Hung YH, Koch-Laskowski K, Wood L, Dedhia PH, Spence JR, Seeley RJ, Sethupathy P, Sandoval DA. JCI Insight. 2022 Jun 8;7(11):e154302. doi: 10.1172/jci.insight.154302. PMID: 35503251
Microstructured Hydrogels to Guide Self-Assembly and Function of Lung Alveolospheres. Loebel C, Weiner AI, Eiken MK, Katzen JB, Morley MP, Bala V, Cardenas-Diaz FL, Davidson MD, Shiraishi K, Basil MC, Ferguson LT, Spence JR, Ochs M, Beers MF, Morrisey EE, Vaughan AE, Burdick JA. Adv Mater. 2022 Jul;34(28):e2202992. doi: 10.1002/adma.202202992. Epub 2022 Jun 7. PMID: 35522531; PMCID: PMC9283320.
Rapid establishment of human colonic organoid knockout lines. Gu W, Colarusso JL, Dame MK, Spence JR, Zhou Q. STAR Protoc. 2022 Apr 12;3(2):101308. doi: 10.1016/j.xpro.2022.101308. PMID: 35463469
Acquisition of NOTCH dependence is a hallmark of human intestinal stem cell maturation. Tsai YH, Wu A, Wu JH, Capeling MM, Holloway EM, Huang S, Czerwinkski M, Glass I, Higgins PDR, Spence JR. Stem Cell Reports. 2022 May 10;17(5):1138-1153. doi: 10.1016/j.stemcr.2022.03.007. Epub 2022 Apr 7. PMID: 35395175
Efficient differentiation of human primordial germ cells through geometric control reveals a key role for Nodal signaling. Jo K, Teague S, Chen B, Khan HA, Freeburne E, Li H, Li B, Ran R, Spence JR, Heemskerk I. Elife. 2022 Apr 8;11:e72811. doi: 10.7554/eLife.72811. PMID: 35394424
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor. Kadur Lakshminarasimha Murthy P, Sontake V, Tata A, Kobayashi Y, Macadlo L, Okuda K, Conchola AS, Nakano S, Gregory S, Miller LA, Spence JR, Engelhardt JF, Boucher RC, Rock JR, Randell SH, Tata PR. Nature. 2022 Apr;604(7904):111-119. doi: 10.1038/s41586-022-04541-3. Epub 2022 Mar 30. PMID: 35355018
RSV-induced changes in a 3-dimensional organoid model of human fetal lungs. Harford TJ, Rezaee F, Dye BR, Fan J, Spence JR, Piedimonte G. PLoS One. 2022 Mar 9;17(3):e0265094. doi: 10.1371/journal.pone.0265094. PMID: 35263387
Suspension culture promotes serosal mesothelial development in human intestinal organoids. Capeling MM, Huang S, Childs CJ, Wu JH, Tsai YH, Wu A, Garg N, Holloway EM, Sundaram N, Bouffi C, Helmrath M, Spence JR.Cell Rep. 2022 Feb 15;38(7):110379. doi: 10.1016/j.celrep.2022.110379.PMID: 35172130
Perfusion System for Modification of Luminal Contents of Human Intestinal Organoids and Realtime Imaging Analysis of Microbial Populations. Ginga NJ, Slyman R, Kim GA, Parigoris E, Huang S, Yadagiri VK, Young VB, Spence JR, Takayama S.Micromachines (Basel). 2022 Jan 14;13(1):131. doi: 10.3390/mi13010131.PMID: 35056297
2021
Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids. Abuaita BH, Lawrence AE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Wobus CE, Spence JR, Young VB, O'Riordan MX. PLoS Pathog. 2021 Oct 20;17(10):e1009987. doi: 10.1371/journal.ppat.1009987. eCollection 2021 Oct.PMID: 34669717
SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling. Gu W, Wang H, Huang X, Kraiczy J, Singh PNP, Ng C, Dagdeviren S, Houghton S, Pellon-Cardenas O, Lan Y, Nie Y, Zhang J, Banerjee KK, Onufer EJ, Warner BW, Spence J, Scherl E, Rafii S, Lee RT, Verzi MP, Redmond D, Longman R, Helin K, Shivdasani RA, Zhou Q. Cell Stem Cell. 2022 Jan 6;29(1):101-115.e10. doi: 10.1016/j.stem.2021.09.004. Epub 2021 Sep 27.PMID: 34582804
UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma. Ray P*, Nancarrow DJ*, Ferrer-Torres D*, Wang Z, San Martinho M, Hinton T, Wu JH, Wu A, Turgeon DK, Hammer MA, Dame MK, Lawrence TS, O'Brien PJ, Spence JR, Beer DG, Ray D.Cell Mol Gastroenterol Hepatol. 2022;13(1):129-149. doi: 10.1016/j.jcmgh.2021.08.003. Epub 2021 Aug 17.PMID: 34416429. *=co-first authors
Morphological cell profiling of SARS-CoV-2 infection identifies drug repurposing candidates for COVID-19. Mirabelli C, Wotring JW, Zhang CJ, McCarty SM, Fursmidt R, Pretto CD, Qiao Y, Zhang Y, Frum T, Kadambi NS, Amin AT, O'Meara TR, Spence JR, Huang J, Alysandratos KD, Kotton DN, Handelman SK, Wobus CE, Weatherwax KJ, Mashour GA, O'Meara MJ, Chinnaiyan AM, Sexton JZ. Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2105815118. doi: 10.1073/pnas.2105815118.PMID: 34413211
Membrane Bound Peroxiredoxin-1 Serves as a Biomarker for In Vivo Detection of Sessile Serrated Adenomas. Jaiswal S, Joshi B, Chen J, Wang F, Dame MK, Spence JR, Newsome GM, Katz EL, Shah YM, Ramakrishnan SK, Li G, Lee M, Appelman HD, Kuick R, Wang TD. Antioxid Redox Signal. 2022 Jan;36(1-3):39-56. doi: 10.1089/ars.2020.8244. Epub 2021 Dec 21.PMID: 3440985
Effect of ABT-263 on Intestinal Fibrosis in Human Myofibroblasts, Human Intestinal Organoids, and the Mouse Salmonella typhimurium Model. Johnson LA, Rodansky ES, Tran A, Collins SG, Eaton KA, Malamet B, Steiner CA, Huang S, Spence JR, Higgins PDR.Inflamm Bowel Dis. 2022 Feb 1;28(2):161-175. doi: 10.1093/ibd/izab166.PMID: 34302470
TCF21+ mesenchymal cells contribute to testis somatic cell development, homeostasis, and regeneration in mice. Shen YC, Shami AN, Moritz L, Larose H, Manske GL, Ma Q, Zheng X, Sukhwani M, Czerwinski M, Sultan C, Chen H, Gurczynski SJ, Spence JR, Orwig KE, Tallquist M, Li JZ, Hammoud SS. Nat Commun. 2021 Jun 23;12(1):3876. doi: 10.1038/s41467-021-24130-8.PMID: 34162856
Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells. Schwartz AJ, Goyert JW, Solanki S, Kerk SA, Chen B, Castillo C, Hsu PP, Do BT, Singhal R, Dame MK, Lee HJ, Spence JR, Lakhal-Littleton S, Vander Heiden MG, Lyssiotis CA, Xue X, Shah YM. Nat Metab. 2021 Jul;3(7):969-982. doi: 10.1038/s42255-021-00406-7. Epub 2021 Jun 21.PMID: 34155415
Biomarkers for the Prediction and Diagnosis of Fibrostenosing Crohn's Disease: A Systematic Review. Steiner CA, Berinstein JA, Louissaint J, Higgins PDR, Spence JR, Shannon C, Lu C, Stidham RW, Fletcher JG, Bruining DH, Feagan BG, Jairath V, Baker ME, Bettenworth D, Rieder F; Stenosis Therapy and Anti-Fibrotic Research (STAR) Consortium.Clin Gastroenterol Hepatol. 2021 Jun 2:S1542-3565(21)00593-0. doi: 10.1016/j.cgh.2021.05.054. Online ahead of print.PMID: 34089850
Charting human development using a multi-endodermal organ atlas and organoid models. Yu Q, Kilik U, Holloway EM, Tsai YH, Harmel C, Wu A, Wu JH, Czerwinski M, Childs CJ, He Z, Capeling MM, Huang S, Glass IA, Higgins PDR, Treutlein B, Spence JR#, Camp JG#. Cell. 2021 Jun 10;184(12):3281-3298.e22. doi: 10.1016/j.cell.2021.04.028. Epub 2021 May 20.PMID: 34019796. *=co-first authors #=co-corresponding authors
Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System. Lawrence AE, Abuaita BH, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Wobus CE, Spence JR, Young VB, O'Riordan MX.mBio. 2021 May 18;12(3):e00399-21. doi: 10.1128/mBio.00399-21.PMID: 34006652
NH2-terminal deletion of specific phosphorylation sites on PHOX2B disrupts the formation of enteric neurons in vivo. Chang DF, Gilliam EA, Nucho LA, Garcia J, Shevchenko Y, Zuber SM, Squillaro AI, Maselli KM, Huang S, Spence JR, Grikscheit TC.Am J Physiol Gastrointest Liver Physiol. 2021 Jun 1;320(6):G1054-G1066. doi: 10.1152/ajpgi.00073.2021. Epub 2021 Apr 21.PMID: 33881351
Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk. Howden SE, Wilson SB, Groenewegen E, Starks L, Forbes TA, Tan KS, Vanslambrouck JM, Holloway EM, Chen YH, Jain S, Spence JR, Little MH.Cell Stem Cell. 2021 Apr 1;28(4):671-684.e6. doi: 10.1016/j.stem.2020.12.001. Epub 2020 Dec 29.PMID: 33378647
Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Hung YH, Huang S, Dame MK, Yu Q, Yu QC, Zeng YA, Camp JG, Spence JR, Sethupathy P.Nucleic Acids Res. 2021 Jan 25;49(2):726-744. doi: 10.1093/nar/gkaa1204.PMID: 33406262
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. Sarvestani SK, Signs S, Hu B, Yeu Y, Feng H, Ni Y, Hill DR, Fisher RC, Ferrandon S, DeHaan RK, Stiene J, Cruise M, Hwang TH, Shen X, Spence JR, Huang EH. Nat Commun. 2021 Jan 11;12(1):262. doi: 10.1038/s41467-020-20351-5.PMID: 33431859
SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation. Yan B, Freiwald T, Chauss D, Wang L, West E, Mirabelli C, Zhang CJ, Nichols EM, Malik N, Gregory R, Bantscheff M, Ghidelli-Disse S, Kolev M, Frum T, Spence JR, Sexton JZ, Alysandratos KD, Kotton DN, Pittaluga S, Bibby J, Niyonzima N, Olson MR, Kordasti S, Portilla D, Wobus CE, Laurence A, Lionakis MS, Kemper C, Afzali B, Kazemian M.Sci Immunol. 2021 Apr 7;6(58):eabg0833. doi: 10.1126/sciimmunol.abg0833.PMID: 33827897
N-terminal deletion of specific phosphorylation sites on PHOX2B disrupts the formation of enteric neurons in vivo. Chang DF, Gilliam EA, Nucho LA, Garcia J, Shevchenko Y, Zuber SM, Squillaro AI, Maselli KM, Huang S, Spence JR, Grikscheit TC.Am J Physiol Gastrointest Liver Physiol. 2021 Apr 21. doi: 10.1152/ajpgi.00073.2021. Online ahead of print.PMID: 33881351
2020
Mapping Development of the Human Intestinal Niche at Single-Cell Resolution.Holloway EM***, Czerwinski M***, Tsai YH***, Wu JH, Wu A, Childs CJ, Walton KD, Sweet CW, Yu Q, Glass I, Treutlein B, Camp JG, Spence JR. Cell Stem Cell. 2020 Nov 25:S1934-5909(20)30546-4. doi: 10.1016/j.stem.2020.11.008. Online ahead of print.PMID: 33278341 ***denotes co-first authors
DATA: Holloway, Czersinski and Tsai et al.:
Download Human Fetal Duodenum Cell Ranger Matrix Files used in this manuscript here
Download raw data from ArrayExpress
Low-Level Mouse DNA in Conditioned Medium Generates False Positive Cross-Species Contamination Results in Human Organoid Cultures.Bohm MS, Dame MK, Boyd J, Su K, Wu A, Attili D, Chu V, Colacino JA, Spence JR. Front Cell Dev Biol. 2020 Nov 6;8:587107. doi: 10.3389/fcell.2020.587107. eCollection 2020.PMID: 33240885
Effect of Cell Spreading on Rosette Formation by Human Pluripotent Stem Cell-Derived Neural Progenitor Cells.Townshend RF, Shao Y, Wang S, Cortez CL, Esfahani SN, Spence JR, O'Shea KS, Fu J, Gumucio DL, Taniguchi K. Front Cell Dev Biol. 2020 Oct 15;8:588941. doi: 10.3389/fcell.2020.588941. eCollection 2020.PMID: 33178701
The Lumen of Human Intestinal Organoids Poses Greater Stress to Bacteria Compared to the Germ-Free Mouse Intestine: Escherichia coli Deficient in RpoS as a Colonization Probe.Barron MR, Cieza RJ, Hill DR, Huang S, Yadagiri VK, Spence JR, Young VB.mSphere. 2020 Nov 11;5(6):e00777-20. doi: 10.1128/mSphere.00777-20.PMID: 33177212
Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells. Hawkins FJ, Suzuki S, Beermann ML, Barillà C, Wang R, Villacorta-Martin C, Berical A, Jean JC, Le Suer J, Matte T, Simone-Roach C, Tang Y, Schlaeger TM, Crane AM, Matthias N, Huang SXL, Randell SH, Wu J, Spence JR, Carraro G, Stripp BR, Rab A, Sorsher EJ, Horani A, Brody SL, Davis BR, Kotton DN. Cell Stem Cell. 2020 Oct 19:S1934-5909(20)30492-6. doi: 10.1016/j.stem.2020.09.017. Online ahead of print.PMID: 33098807
RYK-mediated filopodial pathfinding facilitates midgut elongation.Wang S, Roy JP, Tomlinson AJ, Wang EB, Tsai YH, Cameron L, Underwood J, Spence JR, Walton KD, Stacker SA, Gumucio DL, Lechler T. Development. 2020 Oct 27;147(20):dev195388. doi: 10.1242/dev.195388.PMID: 32994164
Human induced pluripotent stem cell-derived lung organoids in an ex vivo model of the congenital diaphragmatic hernia fetal lung. Kunisaki SM, Jiang G, Biancotti JC, Ho KKY, Dye BR, Liu AP, Spence JR. Stem Cells Transl Med. 2020 Sep 19. doi: 10.1002/sctm.20-0199. Online ahead of print.PMID: 32949227
Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. Palikuqi B, Nguyen DT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY, Rafii S. Nature. 2020 Sep;585(7825):426-432. doi: 10.1038/s41586-020-2712-z. Epub 2020 Sep 9.PMID: 32908310
hPSC-derived organoids: models of human development and disease. Frum T, Spence JR. J Mol Med (Berl). 2020 Aug 28. doi: 10.1007/s00109-020-01969-w. Online ahead of print.PMID: 32857169 Review.
Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells. Holloway EM, Wu JH, Czerwinski M, Sweet CW, Wu A, Tsai YH, Huang S, Stoddard AE, Capeling MM, Glass I, Spence JR. Dev Cell. 2020 Aug 24;54(4):516-528.e7. doi: 10.1016/j.devcel.2020.07.023.PMID: 32841595
DATA: Holloway et al.:
Raw scRNAseq data (human fetal lung) (Miller et al., 2020) ArrayExpress: E-MTAB-8221
Raw scRNAseq data (human fetal kidney) This paper ArrayExpress: E-MTAB-9083
Raw scRNAseq data (HIO and vHIOs) This paper ArrayExpress: E-MTAB-9228
Raw scRNAseq data (human fetal intestine) (Czerwinski et al., 2020) ArrayExpress: E-MTAB-9489
Raw scRNAseq data (human fetal intestine and lung) This paper ArrayExpress: E-MTAB-9363
Raw bulk RNAseq data (human fetal ECs) This paper ArrayExpress: E-MTAB-9372
Generation of Knockout Gene-Edited Human Intestinal Organoids.Rajendra C, Wald T, Barber K, Spence JR, Fattahi F, Klein OD. Methods Mol Biol. 2020;2171:215-230. doi: 10.1007/978-1-0716-0747-3_13.PMID: 32705644
Identification and Isolation of Human LGR5+ Cells Using an Antibody-Based Strategy. Dame MK, Huang S, Attili D, Spence JR, Colacino JA. Methods Mol Biol. 2020;2171:3-23. doi: 10.1007/978-1-0716-0747-3_1.PMID: 32705632
AXL Is a Potential Target for the Treatment of Intestinal Fibrosis. Steiner CA, Rodansky ES, Johnson LA, Berinstein JA, Cushing KC, Huang S, Spence JR, Higgins PDR. Inflamm Bowel Dis. 2020 Jul 17:izaa169. doi: 10.1093/ibd/izaa169. Online ahead of print.PMID: 32676663
Gastrointestinal organoids: a next-generation tool for modeling human development. Singh A, Poling HM, Spence JR, Wells JM, Helmrath MA. Am J Physiol Gastrointest Liver Physiol. 2020 Sep 1;319(3):G375-G381. doi: 10.1152/ajpgi.00199.2020. Epub 2020 Jul 13.PMID: 32658619
Grading TESI: Crypt and villus formation in tissue-engineered small intestine alters with stem/progenitor cell source.Gilliam EA, Schlieve CR, Fowler KL, Rea JN, Schall KA, Huang S, Spence JR, Grikscheit TC. Am J Physiol Gastrointest Liver Physiol. 2020 Aug 1;319(2):G261-G279. doi: 10.1152/ajpgi.00387.2019. Epub 2020 Jun 29.PMID: 32597710
Induced pluripotent stem cell-derived enteric neural crest cells repopulate human aganglionic tissue-engineered intestine to form key components of the enteric nervous system. Chang DF, Zuber SM, Gilliam EA, Nucho LA, Levin G, Wang F, Squillaro AI, Huang S, Spence JR, Grikscheit TC. J Tissue Eng. 2020 Apr 27;11:2041731420905701. doi: 10.1177/2041731420905701. eCollection 2020 Jan-Dec.PMID: 32435442
Efficient Generation and Transcriptomic Profiling of Human iPSC-Derived Pulmonary Neuroendocrine Cells. Hor P, Punj V, Calvert BA, Castaldi A, Miller AJ, Carraro G, Stripp BR, Brody SL, Spence JR, Ichida JK, Ryan Firth AL, Borok Z. iScience. 2020 May 22;23(5):101083. doi: 10.1016/j.isci.2020.101083. Epub 2020 Apr 21.PMID: 32380423
Understanding Human Lung Development through In Vitro Model Systems. Conway RF, Frum T, Conchola AS, Spence JR. Bioessays. 2020 Apr 20:e2000006. doi: 10.1002/bies.202000006. [Epub ahead of print] PMID: 32310312
Differentiation of human colon tissue in culture: Effects of calcium on trans-epithelial electrical resistance and tissue cohesive properties. McClintock SD, Attili D, Dame MK, Richter A, Silvestri SS, Berner MM, Bohm MS, Karpoff K, McCarthy CL, Spence JR, Varani J, Aslam MN. PLoS One. 2020 Mar 5;15(3):e0222058. doi: 10.1371/journal.pone.0222058. eCollection 2020.
In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. Miller AJ, Yu Q, Czerwinski M, Tsai YH, Conway RF, Wu A, Holloway EM, Walker T, Glass IA, Treutlein B, Camp JG, Spence JR. Dev Cell. 2020 Apr 6;53(1):117-128.e6. doi: 10.1016/j.devcel.2020.01.033. Epub 2020 Feb 27.PMID: 32109386
DATA: Miller and Yu et al.:
Download Seurat Object associated with manuscript
Download Raw Data from ArrayExpress
Human lung organoids develop into adult airway-like structures directed by physico-chemical biomaterial properties. Dye BR, Youngblood RL, Oakes RS, Kasputis T, Clough DW, Spence JR, Shea LD. Biomaterials. 2020 Jan 6;234:119757. doi: 10.1016/j.biomaterials.2020.119757. [Epub ahead of print] PMID: 31951973
2019
Enteroendocrine Progenitor Cell-Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner. Singh AP, Hung YH, Shanahan MT, Kanke M, Bonfini A, Dame MK, Biraud M, Peck BCE, Oyesola OO, Freund JM, Cubitt RL, Curry EG, Gonzalez LM, Bewick GA, Tait-Wojno ED, Kurpios NA, Ding S, Spence JR, Dekaney CM, Buchon N, Sethupathy P. Cell Mol Gastroenterol Hepatol. 2019 Nov 19. pii: S2352-345X(19)30156-0. doi: 10.1016/j.jcmgh.2019.11.001. [Epub ahead of print] PMID: 31756561
Microbial Metabolite Signaling Is Required for Systemic Iron Homeostasis. Das NK, Schwartz AJ, Barthel G, Inohara N, Liu Q, Sankar A, Hill DR, Ma X, Lamberg O, Schnizlein MK, Arqués JL, Spence JR, Nunez G, Patterson AD, Sun D, Young VB, Shah YM. Cell Metab. 2020 Jan 7;31(1):115-130.e6. doi: 10.1016/j.cmet.2019.10.005. Epub 2019 Nov 7.PMID: 31708445
Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. Kolawole AO, Mirabelli C, Hill DR, Svoboda SA, Janowski AB, Passalacqua KD, Rodriguez BN, Dame MK, Freiden P, Berger RP, Vu DL, Hosmillo M, O'Riordan MXD, Schultz-Cherry S, Guix S, Spence JR, Wang D, Wobus CE. PLoS Pathog. 2019 Oct 31;15(10):e1008057. doi: 10.1371/journal.ppat.1008057. eCollection 2019 Oct. PMID: 31671153
Identification of anoctamin 1 (ANO1) as a key driver of esophageal epithelial proliferation in eosinophilic esophagitis. Vanoni S, Zeng C, Marella S, Uddin J, Wu D, Arora K, Ptaschinski C, Que J, Noah T, Waggoner L, Barski A, Kartashov A, Rochman M, Wen T, Martin L, Spence J, Collins M, Mukkada V, Putnam P, Naren A, Chehade M, Rothenberg ME, Hogan SP. J Allergy Clin Immunol. 2020 Jan;145(1):239-254.e2. doi: 10.1016/j.jaci.2019.07.049. Epub 2019 Oct 21. PMID: 31647967
Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD. Golob JL, DeMeules MM, Loeffelholz T, Quinn ZZ, Dame MK, Silvestri SS, Wu MC, Schmidt TM, Fiedler TL, Hoostal MJ, Mielcarek M, Spence J, Pergam SA, Fredricks DN. Blood Adv. 2019 Oct 8;3(19):2866-2869. doi: 10.1182/bloodadvances.2019000362. No abstract available.PMID: 31585950
HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine. Chen L, Toke NH, Luo S, Vasoya RP, Aita R, Parthasarathy A, Tsai YH, Spence JR, Verzi MP. Development. 2019 Aug 6;146(19). pii: dev179432. doi: 10.1242/dev.179432. PMID: 31345929
Citrobacter rodentium induces tissue-resident memory CD4+ T-cells. Bishu S, Hou G, El Zaatari M, Bishu SR, Popke D, Zhang M, Grasberger H, Zou W, Stidham RW, Higgins PDR, Spence JR, Kamada N, Kao JY. Infect Immun. 2019 May 6. pii: IAI.00295-19. doi: 10.1128/IAI.00295-19.
Biologically inspired approaches to enhance human organoid complexity. Holloway EM, Capeling MM, Spence JR. Development. 2019 Apr 16;146(8). pii: dev166173. doi: 10.1242/dev.166173. Review.
Single cell RNA sequencing identifies TGFβ as a key regenerative cue following LPS-induced lung injury. Riemondy KA, Jansing NL, Jiang P, Redente EF, Gillen AE, Fu R, Miller AJ, Spence JR, Gerber AN, Hesselberth JR, Zemans RL. JCI Insight. 2019 Mar 26;5. pii: 123637. doi: 10.1172/jci.insight.123637.
The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Kumar N, Tsai YH, Chen L, Zhou A, Banerjee KK, Saxena M, Huang S, Toke NH, Xing J, Shivdasani RA, Spence JR, Verzi MP. Development. 2019 Feb 11. pii: dev.172189. doi: 10.1242/dev.172189. PMID: 30745430
Generation of lung organoids from human pluripotent stem cells in vitro. Miller AJ, Dye BR, Ferrer-Torres D, Hill DR, Overeem AW, Shea LD, Spence JR. Nat Protoc. 2019 Feb;14(2):518-540. doi: 10.1038/s41596-018-0104-8. PMID: 30664680 FULL TEXT HERE
CD4+ tissue-resident memory T-cells expand and are a major source of mucosal tumor necrosis factor α in active Crohn's Disease. Bishu S, El Zaatari M, Hayashi A, Hou G, Bowers N, Kinnucan J, Manoogian B, Muza-Moons MM, Zhang M, Grasberger H, Bourque C, Zou W, Higgins PDR, Spence JR, Stidham RW, Kamada N, Kao JY. J Crohns Colitis. 2019 Feb 4. doi: 10.1093/ecco-jcc/jjz010.
Organoid single cell profiling identifies a transcriptional signature of glomerular disease. Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O'Connor C, Luo J, Nair V, Cebrian C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M; European Renal cDNA Bank (ERCB); Nephrotic Syndrome Study Network (NEPTUNE). JCI Insight. 2019 Jan 10;4(1). pii: 122697. doi: 10.1172/jci.insight.122697. [Epub ahead of print] PMID: 30626756
Nonadhesive Alginate Hydrogels Support Growth of Pluripotent Stem Cell-Derived Intestinal Organoids Capeling MM, Czerwinski M, Huang S, Tsai YH, Wu A, Nagy MS, Juliar B, Sundaram N, Song Y, Han WM, Takayama S, Alsberg E, Garcia AJ, Helmrath M, Putnam AJ, Spence JR. Stem Cell Reports. 2019 Feb 12;12(2):381-394.DOI:https://doi.org/10.1016/j.stemcr.2018.12.001
2018
PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery. Cruz-Acuña R, Quirós M, Huang S, Siuda D, Spence JR***, Nusrat A***, García AJ***. Nat Protoc. 2018 Sep;13(9):2102-2119. doi: 10.1038/s41596-018-0036-3. Erratum in: Nat Protoc. 2018 Oct 24;:. PMID: 30190557 ***co-senior/corresponding authors
Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, Chen YC, Troyanskaya O, Spence JR***, Kretzler M***, Cebrián C***. Development. 2018 Aug 30;145(16). pii: dev164038. doi: 10.1242/dev.164038. PMID:30166318 ***co-senior/corresponding authors
Lactobacillus rhamnosus GG prevents epithelial barrier dysfunction induced by interferon-gamma and fecal supernatants from irritable bowel syndrome patients in human intestinal enteroids and colonoids Han X, Lee A, Huang S, Gao J, Spence JR, Owyang C. Gut Microbes. 2018 Jul 24:1-18. doi: 10.1080/19490976.2018.1479625. PMID:30040527
A Method for Cryogenic Preservation of Human Biopsy Specimens and Subsequent Organoid Culture. Tsai YH***, Czerwinski M***, Wu A, Dame MK, Attili D, Hill E, Colacino JA, Nowacki LM, Shroyer NF, Higgins PDR, Kao JY, Spence JR. Cell Mol Gastroenterol Hepatol. 2018 May 30;6(2):218-222.e7. doi: 10.1016/j.jcmgh.2018.04.008. eCollection 2018. PMID:30105282 ***=co-first authors/equal contribution
Taming the Wild West of Organoids, Enteroids, and Mini-Guts. Spence JR. Cell Mol Gastroenterol Hepatol. 2017 Nov 28;5(2):159-160. doi: 10.1016/j.jcmgh.2017.11.003. eCollection 2018. No abstract available. PMID:29693042 *Invited Commentary
Identification, Isolation, and Characterization of Human LGR5-positive Colon Adenoma Cells Dame MK, Attili D, McClintock SD, Dedhia PH, Ouillette P, Hardt O, Chin AM, Xue X, Laliberte J, Katz EL, Newsome GM, Hill DR, Miller AJ, Tsai YH, Agorku D, Altheim CH, Bosio A, Simon B, Samuelson LC, Stoerker JA, Appelman HD, Varani J, Wicha MS, Brenner DE, Shah YM, Spence JR, Colacino JA. Development. 2018 Mar 14;145(6). pii: dev153049. doi: 10.1242/dev.153049. PMID:29467240
In Vitro Induction and In Vivo Engraftment of Lung Bud Tip Progenitor Cells Derived from Human Pluripotent Stem Cells. Miller AJ, Hill DR, Nagy MS, Aoki Y, Dye BR, Chin AM, Huang S, Zhu F, White ES, Lama V, Spence JR. Stem Cell Reports. 2017 Dec 12. pii: S2213-6711(17)30519-2. doi: 10.1016/j.stemcr.2017.11.012. [Epub ahead of print] PMID:29249664
2017
Real-time Measurement of Epithelial Barrier Permeability in Human Intestinal Organoids. Hill, D.R., Huang, S., Tsai, Y.H., Spence, J.R., Young, V.B. J. Vis. Exp. (), e56960, doi:10.3791/56960 (2017). VIDEO HERE PDF HERE
Clocking the Pace of Organoid Research. Spence JR. Cell Mol Gastroenterol Hepatol. 2017 May 13;4(1):203-204. doi: 10.1016/j.jcmgh.2017.04.006. eCollection 2017 Jul. No abstract available. PMID:29204507 *invited comentary
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. Hill DR, Huang S, Nagy MS, Yadagiri VK, Fields C, Mukherjee D, Bons B, Dedhia PH, Chin AM, Tsai YH, Thodla S, Schmidt TM, Walk S, Young VB*, Spence JR*. Elife. 2017 Nov 7;6. pii: e29132. doi: 10.7554/eLife.29132. PMID:29110754 * co-corresponding/senior authors
Synthetic hydrogels for human intestinal organoid generation and colonic wound repair. Cruz-Acuña R^, Quirós M^, Farkas AE, Dedhia PH, Huang S, Siuda D, García-Hernández V, Miller AJ, Spence JR**, Nusrat A**, García AJ**. Nature Cell Biology. 2017. published ahead of print October 23. doi: https://doi.org/10.1038/ncb3632 ^co-first authors; **co-corresponding/senior authors PDF HERE
Quantitative proteomics identifies STEAP4 as a critical regulator of mitochondrial dysfunction linking inflammation and colon cancer. Xue X, Bredell BX, Anderson ER, Martin A, Mays C, Nagao-Kitamoto H, Huang S, Győrffy B, Greenson JK, Hardiman K, Spence JR, Kamada N, Shah YM. Proceedings of the National Academy of Sciences. 2017. published ahead of print October 23, 2017, doi:10.1073/pnas.1712946114
Take a deep breath and digest the material: organoids and biomaterials of the respiratory and digestive systems. Dye BR, Kasputis T, Spence JR and Shea LD. MRS Communications. Volume 7, Issue 3 September 2017 , pp. 502-514. Review. https://doi.org/10.1557/mrc.2017.61
Macrophage-derived IL-10 mediates mucosal repair by epithelial WISP-1 signaling. Quiros M, Nishio H, Neumann PA, Siuda D, Brazil JC, Azcutia V, Hilgarth R, O'Leary MN, Garcia-Hernandez V, Leoni G, Feng M, Bernal G, Williams H, Dedhia PH, Gerner-Smidt C, Spence J, Parkos CA, Denning TL, Nusrat A. J Clin Invest. 2017 Sep 1;127(9):3510-3520. doi: 10.1172/JCI90229. Epub 2017 Aug 7. PMID:28783045
Neural Crest Cell Implantation Restores Enteric Nervous System Function and Alters the Gastrointestinal Transcriptome in Human Tissue-Engineered Small Intestine. Schlieve CR, Fowler KL, Thornton M, Huang S, Hajjali I, Hou X, Grubbs B, Spence JR, Grikscheit TC. Stem Cell Reports. 2017 Aug 9. pii: S2213-6711(17)30327-2. doi: 10.1016/j.stemcr.2017.07.017. [Epub ahead of print] PMID:28803915
In Vitro Models to Study Human Lung Development, Disease and Homeostasis. Miller AJ, Spence JR. Physiology (Bethesda). 2017 May;32(3):246-260. doi: 10.1152/physiol.00041.2016. Review. PMID:28404740
Differentiation of Human Pluripotent Stem Cells into Colonic Organoids via Transient Activation of BMP Signaling. Múnera JO, Sundaram N, Rankin SA, Hill DR, Watson C, Mahe M, Vallance JE, Shroyer NF, Sinagoga KL, Zarzoso-Lacoste A, Hudson JR, Howell JC, Chatuvedi P, Spence JR, Shannon JM, Zorn AM, Helmrath MA, Wells JM. Cell Stem Cell. 2017 Jul 6;21(1):51-64.e6. doi: 10.1016/j.stem.2017.05.020. Epub 2017 Jun 22. PMID:28648364
Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche. Shao Y, Taniguchi K, Gurdziel K, Townshend RF, Xue X, Yong KM, Sang J, Spence JR, Gumucio DL, Fu J. Nat Mater. 2017 Apr;16(4):419-425. doi: 10.1038/nmat4829. Epub 2016 Dec 12. PMID:27941807
Bioengineering for intestinal organoid cultures. Kim GA, Spence JR, Takayama S. Curr Opin Biotechnol. 2017 Jun 21;47:51-58. doi: 10.1016/j.copbio.2017.05.006. [Epub ahead of print] Review. PMID:28646678
Notch1 and Notch2 receptors regulate mouse and human gastric antral epithelial cell homoeostasis. Gifford GB, Demitrack ES, Keeley TM, Tam A, La Cunza N, Dedhia PH, Spence JR, Simeone DM, Saotome I, Louvi A, Siebel CW, Samuelson LC. Gut. 2017 Jun;66(6):1001-1011. doi: 10.1136/gutjnl-2015-310811. Epub 2016 Mar 1. PMID: 26933171
Morphogenesis and maturation of the embryonic and postnatal intestine. Chin AM, Hill DR, Aurora M, Spence JR. Semin Cell Dev Biol. 2017 Feb 1. pii: S1084-9521(17)30066-6. doi: 10.1016/j.semcdb.2017.01.011.
In vitro patterning of pluripotent stem cell-derived intestine recapitulates in vivo human development. Tsai YH* and Nattiv R*, Dedhia PH, Nagy MS, Chin AM, Thomson M, Klein OD, Spence JR. Development. 2017 Mar 15;144(6):1045-1055. doi: 10.1242/dev.138453. *equal contribution
(Re)Building a Kidney. Leif Oxburgh, Thomas J. Carroll, Ondine Cleaver, Daniel R. Gossett, Deborah K. Hoshizaki, Jeffrey A. Hubbell, Benjamin D. Humphreys, Sanjay Jain, Jan Jensen, David L. Kaplan, Carl Kesselman, Christian J. Ketchum, Melissa H. Little, Andrew P. McMahon, Stuart J. Shankland, Jason R. Spence, M. Todd Valerius, Jason A. Wertheim, Oliver Wessely, Ying Zheng, and Iain A. Drummond. J Am Soc Nephrol http://jasn.asnjournals.org/content/early/2017/01/16/ASN.2016101077.full
BRAFV600E cooperates with CDX2 inactivation to promote serrated colorectal tumorigenesis. Sakamoto N, Feng Y, Stolfi C, Kurosu Y, Green M, Lin J, Green M, Sentani K, Yasui W, McMahon M, Hardiman KM, Spence JR, Horita N, Greenson JK, Kuick R, Cho KR, Fearon ER. Elife. 2017 Jan 10;6. pii: e20331. doi: 10.7554/eLife.20331.
Hacking the Matrix. Czerwinski M, Spence JR. Cell Stem Cell. 2017 Jan 5;20(1):9-10. doi: 10.1016/j.stem.2016.12.010. *invited commentary
2016
Gastrointestinal organoids: understanding the molecular basis of the host-microbe interface Hill DR and Spence JR Cell Mol Gastroenterol Hepatol. 2016 Dec 19;3(2):138-149. doi: 10.1016/j.jcmgh.2016.11.007. Review. PMID:28275681
A Dynamic WNT/β-CATENIN Signaling Environment Leads to WNT-Independent and WNT-Dependent Proliferation of Embryonic Intestinal Progenitor Cells. Chin AM, Tsai YH, Finkbeiner SR, Nagy MS, Walker EM, Ethen NJ, Williams BO, Battle MA, Spence JR. Stem Cell Reports. 2016 Oct 6. pii: S2213-6711(16)30210-7. doi: 10.1016/j.stemcr.2016.09.004.
A bioengineered niche promotes in vivo engraftment and maturation of pluripotent stem cell derived human lung organoids. Dye BR, Dedhia PH, Miller AJ, Nagy MS, White ES, Shea LD, Spence JR. Elife. 2016 Sep 28;5. pii: e19732. doi: 10.7554/eLife.19732. [Epub ahead of print]
LGR4 and LGR5 Function Redundantly During Human Endoderm Differentiation. Tsai YH, Hill DR, Kumar N, Huang S, Chin AM, Dye BR, Nagy MS, Verzi MP, Spence JR. Cell Mol Gastroenterol Hepatol. 2016 Jun 23;2(5):648-662.e8. DOI: http://dx.doi.org/10.1016/j.jcmgh.2016.06.002
Hox6 genes modulate in vitro differentiation of mESCs to insulin-producing cells. Larsen BM, Marty-Santos L, Newman M, Lukacs DT, Spence JR, Wellik DM. In Vitro Cell Dev Biol Anim. 2016 Jul 21. [Epub ahead of print] PMID:27444630
hPSC-derived lung and intestinal organoids as models of human fetal tissue. Aurora M, Spence JR. Dev Biol. 2016 Jun 7. pii: S0012-1606(16)30188-9. doi: 10.1016/j.ydbio.2016.06.006. [Epub ahead of print] Review. PMID:27287882
How to grow a lung: Applying Principles of Developmental Biology to Generate Lung Lineages From Human Pluripotent Stem Cells. Dye BR, Miller AJ, Spence JR. Current Pathobiology Reports. June 2016, Volume 4, Issue 2, pp 47–57
Organoid Models of Human Gastrointestinal Development and Disease. Dedhia PH, Bertaux-Skeirik N, Zavros Y, Spence JR. Gastroenterology. 2016 Jan 13. doi: 10.1053/j.gastro.2015.12.042. [Epub ahead of print] Review. PMID: 26774180
2015
Lumen Formation Is an Intrinsic Property of Isolated Human Pluripotent Stem Cells. Taniguchi K, Shao Y, Townshend RF, Tsai YH, DeLong CJ, Lopez SA, Gayen S, Freddo AM, Chue DJ, Thomas DJ, Spence JR, Margolis B, Kalantry S, Fu J, O'Shea KS, Gumucio DL. Stem Cell Reports. 2015 Nov 24. pii: S2213-6711(15)00312-4. PMID:26626176
Generation of tissue-engineered small intestine using embryonic stem cell-derived human intestinal organoids. Finkbeiner SR, Freeman JJ, Wieck MM, El-Nachef W, Altheim CH, Tsai YH, Huang S, Dyal R, White ES, Grikscheit TC, Teitelbaum DH, Spence JR. Biol Open. 2015 Oct 12;4(11):1462-72. PMID:26459240 http://dx.doi.org/10.1242/bio.013235
Hox5 Genes Regulate the Wnt2/2b-Bmp4-Signaling Axis during Lung Development. Hrycaj SM, Dye BR, Baker NC, Larsen BM, Burke AC, Spence JR, Wellik DM. Cell Rep. 2015 Aug 11;12(6):903-12. PMID: 26235626
Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo. Finkbeiner SR, Hill DR, Altheim CH, Dedhia PH, Taylor MJ, Tsai YH, Chin AM, Mahe MM, Watson CL, Freeman JJ, Nattiv R, Thomson M, Klein OD, Shroyer NF, Helmrath MA, Teitelbaum DH, Dempsey PJ, Spence JR. Stem Cell Reports. 2015 Jun 3 PMID:26050928
Intestinal organoids: A model of intestinal fibrosis for evaluating anti-fibrotic drugs. Rodansky ES, Johnson LA, Huang S, Spence JR, Higgins PD. Exp Mol Pathol. 2015 Mar 28. PMID: 25828392
In vitro generation of human pluripotent stem cell derived lung organoids. Dye BR, Hill DR, Ferguson MA, Tsai YH, Nagy MS, Dyal R, Wells JM, Mayhew CN, Nattiv R, Klein OD, White ES, Deutsch GH, Spence JR. Elife. 2015 Mar 24;4. doi: 10.7554/eLife.05098. PMID:25803487 DOI: http://dx.doi.org/10.7554/eLife.05098
2014
Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Kyle W. McCracken, Emily M. Catá, Calyn M. Crawford, Katie L. Sinagoga, Michael Schumacher, Briana E. Rockich, Yu-Hwai Tsai, Christopher N. Mayhew, Jason R. Spence, Yana Zavros and James M. Wells. Nature. 2014 October 29. Advanced Online Publication.
An in vivo model of human small intestine using pluripotent stem cells. Watson CL, Mahe MM, Múnera J, Howell JC, Sundaram N, Poling HM, Schweitzer JI, Vallance JE, Mayhew CN, Sun Y, Grabowski G, Finkbeiner SR, Spence JR, Shroyer NF, Wells JM, Helmrath MA. Nature Medicine. 2014 Oct 19. PMID:25326803
Persistence and toxin production by Clostridium difficile within human intestinal organoids results in disruption of epithelial paracellular barrier function. Leslie JL**, Huang S**, Opp JS, Nagy MS, Kobayashi M, Young VB, Spence JR. Infect Immun. 2014 Oct 13. pii: IAI.02561-14. [Epub ahead of print] PMID:25312952 ** co-first authors.
Sox17 regulates insulin secretion in the normal and pathologic mouse β cell. Jonatan D, Spence JR, Method AM, Kofron M, Sinagoga K, Haataja L, Arvan P, Deutsch GH, Wells JM. PLoS One. 2014 Aug 21;9(8):e104675. doi: 10.1371/journal.pone.0104675. eCollection 2014. PMID:25144761
De Novo Formation of Insulin-Producing "Neo-β Cell Islets" from Intestinal Crypts. Chen YJ, Finkbeiner SR, Weinblatt D, Emmett MJ, Tameire F, Yousefi M, Yang C, Maehr R, Zhou Q, Shemer R, Dor Y, Li C, Spence JR, Stanger BZ. Cell Reports. 2014, Mar 5 PMID:24613355.
How to make an intestine. Wells JM, Spence JR. Development. 2014 Feb;141(4):752-60. doi: 10.1242/dev.097386. PMID:24496613
2013
Sox9 plays multiple roles in the lung epithelium during branching morphogenesis. Rockich BE, Hrycaj SM, Shih HP, Nagy MS, Ferguson MA, Kopp JL, Sander M, Wellik DM, Spence JR. Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):E4456-64. doi: 10.1073/pnas.1311847110. Epub 2013 Nov 4. PMID:24191021 [PubMed - in process]
Identification and Manipulation of Biliary Metaplasia in Pancreatic Tumors. Delgiorno KE, Hall JC, Takeuchi KK, Pan FC, Halbrook CJ, Washington MK, Olive KP, Spence JR, Sipos B, Wright CV, Wells JM, Crawford HC. Gastroenterology. 2013 Aug 30. doi:pii: S0016-5085(13)01273-0. 10.1053/j.gastro.2013.08.053. [Epub ahead of print]
Induction of intestinal stem cells by R-spondin 1 and Slit2 augments chemoradioprotection. Zhou WJ, Geng ZH, Spence JR, Geng JG. Nature. 2013 Jul 31. doi: 10.1038/nature12416. [Epub ahead of print] PMID:23903657
Endothelial PAS Domain Protein 1 Activates the Inflammatory Response in the Intestinal Epithelium to Promote Colitis in Mice. Xue X, Ramakrishnan S, Anderson E, Taylor M, Zimmermann EM, Spence JR, Huang S, Greenson JK, Shah YM. Gastroenterology. 2013 Jul 13. doi:pii: S0016-5085(13)01010-X. 10.1053/j.gastro.2013.07.010. [Epub ahead of print]
A gutsy task: generating intestinal tissue from human pluripotent stem cells. Finkbeiner SR, Spence JR. Dig Dis Sci. 2013 May;58(5):1176-84. doi: 10.1007/s10620-013-2620-2. Epub 2013 Mar 27. Review.
2012
Cancer biology: a new RING to Wnt signaling. Fearon ER, Spence JR. Curr Biol. 2012 Oct 9;22(19):R849-51. doi: 10.1016/j.cub.2012.08.002. PMID: 23058807
2011 and earlier
Generating human intestinal tissue from pluripotent stem cells in vitro. McCracken KW, Howell JC, Wells JM, Spence JR. Nat Protoc. 2011 Nov 10;6(12):1920-8. doi: 10.1038/nprot.2011.410. PMID: 22082986 [PubMed - in process]
Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Spence JR, Mayhew CN, Rankin SA, Kuhar MF, Vallance JE, Tolle K, Hoskins EE, Kalinichenko VV, Wells SI, Zorn AM, Shroyer NF, Wells JM. Nature. 2011 Feb 3;470(7332):105-9. Epub 2010 Dec 12. PMID: 21151107 [PubMed - indexed for MEDLINE] Free PMC Article
Vertebrate intestinal endoderm development. Spence JR, Lauf R, Shroyer NF. Dev Dyn. 2011 Mar;240(3):501-20. doi: 10.1002/dvdy.22540. Epub 2011 Jan 18. Review. PMID: 21246663 [PubMed - indexed for MEDLINE]
Sox17 regulates organ lineage segregation of ventral foregut progenitor cells. Spence JR, Lange AW, Lin SC, Kaestner KH, Lowy AM, Kim I, Whitsett JA, Wells JM. Dev Cell. 2009 Jul;17(1):62-74. PMID: 19619492 [PubMed - indexed for MEDLINE] Free PMC Article
Translational embryology: using embryonic principles to generate pancreatic endocrine cells from embryonic stem cells. Spence JR, Wells JM. Dev Dyn. 2007 Dec;236(12):3218-27. Review. PMID:17973329 [PubMed - indexed for MEDLINE] Free Article
