Journal Articles
- PIEZO-dependent mechano-sensing is essential for intestinal stem cell fate decision and maintenance.
Baghdadi MB#, Houtekamer RM, Perrin L, Rao-Bhatia A, Whelen M, Decker L, Bergert M, Pérez-Gonzàlez C, Bouras R, Gropplero G, Loe AKH, Afkhami-Poostchi A, Chen X, Huang X, Descroix S. Wrana JL, Diz-Munoz A, Gloerich M, Ayyaz A, Vignjevic DM#, Kim T-H# (# co-corresponding authors).
Science (2024) Nov29;386(6725):eadj7615.
(Featured in SickKids news, ScienceDaily, EurekAlert!, MedicalPress, NewsMedical and selected by Canada in Science for November 2024) - YAP targetome reveals activation of SPEM in gastric pre-neoplastic progression and regeneration.
Loe AKH*, Rao-Bhatia A*, Wei Z* , Kim JE, Guan B, Qin Y, Hog M, Kwak H, Liu X, Zhang L, Wrana JL, Guo H#, Kim T-H#. (* equal contribution, # co-corresponding authors).
Cell Reports (2023) Dec 26;42(12) 113497.
(Featured in BioMedArt) - A designer peptide against the EAG2-Kvβ2 potassium channel targets the interaction of cancer cells and neurons to treat glioblastoma.
Dong W, Fekete A, Chen X, Liu H, Beilhartz GL, Chen X, Bahrampour S, Xiong Y, Yang Q, Zhao H, Kong T, Morioka MS, Jung G, Kim JE, Schramek D, Dirks PB, Song Y, Kim T-H, He Y, Wanggou S, Li X, Melnyk RA, Wang LY, Huang X.
Nature Cancer (2023) 4;1418-1436.
(Cover Article, previewed by Nature Cancer, Featured in SickKids News, EurekAlert!, Bioengineer.org, Technology Networks, News Medical, The Daily Science, Press-News.org, Medical Xpress, Nouvelles Du Monde, Futur en Seine) Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function.
Smith RJ*, Liang M*, Loe AKH, Yung T, Kim JE, Hudson M, Wilson MD, Kim T-H (* equal contribution).
Nature Communications (2023) Jan 30;S41467-023-36338-2.- Chromatin and noncoding RNA-mediated mechanisms of gastric tumorigenesis.
Loe AKH*, Zhu L*, Kim T-H (* equal contribution).
Experimental & Molecular Medicine (2023) Jan;55(1):22-31. - The multiple roles of enteric glial cells in intestinal homeostasis and regeneration.
Baghdadi MB#, Kim T-H#(# co-corresponding authors).
Seminars in Cell & Developmental Biology (2023) Jan 17;S1084-9521(23)00005-8. - Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development.
Kim JE, Fei L, Horne R, Lee D, Loe AK, Miyake H, Ayar E, Kim DK, Surette MG, Philpott DJ, Sherman P, Guo G, Pierro A, KimT-H.
Immunity (2022)
(Featured in SickKids news, previewed by Immunity, and selected by 2022 December’s Top Science in Canada) - Single cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions.
Smith RJ*, Zhang H*, Hu SS*, Yung T, Francis F, Lee L, Onaitis MW, Dirks PB, Zhang C#, Kim T-H# (* equal contribution; # co-corresponding authors).
Nature Communications (2022) May 26;13(1):2965.
(Featured in Nature Portfolio Health Community, CBS19 news, UVA Health system news room, Bioengineer.org, EurekAlert!, ScienMag, Verve times, Phys.org, and Swift Telecast) - Analysis of mouse intestinal organoid culture with conditioned media isolated from mucosal enteric glial cells.
Baghdadi MB and Kim T-H.
STAR Protocols (2022) 10.1016/jxpro.2022.101351 Baghdadi MB, Ayyaz A, Coquenlorge S, Chu B, Kumar S, Streutker C, Wrana JL and Kim T-H.
Cell Stem Cell (2022) Jan 6;29(1):86-100.
(Featured in UofT Molecular Genetics news, “the role of gut brain cells in IBD”, recommended by Faculty Opinions, and previewed by Cell Stem Cell)- Uncovering the dosage-dependent roles of Arid1a in gastric tumorigenesis for combinatorial drug therapy.
Loe AKH*, Francis R*, Seo J, Lutao D, Wang Y, Kim JE, Hakim SW, Kim JE, He HH, Guo H#, Kim T-H# (* equal contribution; # co-corresponding authors).
Journal of Experimental Medicine (2021) Jun 7; 218(6).
(Featured in Ebiotrade) - Mesenchymal niches for digestive organ development, homeostasis and disease.
Loe AK*, Rao-Bhatia A*, Kim JE*, Kim T-H (* equal contribution).
Trends in Cell Biology (2021) Mar;31(3):152-165. - Fat4-Dchs1 and planar cell polarity pathways activated by Hedgehog mediate mesenchymal clustering and villus formation during mammalian gut development.
Rao-Bhatia A, Zhu M, Yin WC, Coquenlorge-Gallon S, Zhang X, Woo JH, Dean CH, Liu A, Hui CC, Shivdasani RA, McNeill H, Hopyan S, Kim T-H.
Developmental Cell (2020) March 9, 52(5):647-658.
(Featured in SickKids news, “Intestinal intelligence” and recommended by Faculty Opinions)
- Single cell and genetic analyses reveal conserved cell populations and signaling mechanisms of gastrointestinal stromal niches.
Kim JE, Fei L, Yin WC, Coquenlorge-Gallon S, Rao-Bhatia A, Zhang X, Shi SSW, Lee JH, Hahn NA, Rizvi W, Kim KH, Sung HK, Hui CC, Guo G, Kim T-H.
Nature Communications (2020) 11, 334. - Gastrointestinal transcription factors drive lineage-specific developmental programs in organ specification and cancer.
Francis R*, Guo H*, Ahmed M, Yung T, Dirks PB, He HH#, Kim T-H# (*equal contribution; # co-corresponding authors).
Science Advances (2019) Dec 11;Vol 5 no. 12, eaax8898.
(Featured in University Health Network news, “Cancer’s gut reaction“) - Sufu- and Spop-mediated downregulation of Hedgehog signaling promotes beta cell differentiation through organ-specific niche signals.
Yung T*, Poon F*, Liang M, Coquenlorge S, McGaugh EC, Hui CC, Wilson MD, Nostro MC#, Kim T-H#. (* equal contribution; # co-corresponding authors)
Nature Communications (2019) Oct 11;10(1):4647.
(Featured in Editors’ Highlights, University Health Network News “Making cells to treat diabetes” and recommended by Faculty of 1000) - GLI2 modulated by SUFU and SPOP induces intestinal stem cell niche signals in development and tumorigenesis.
Coquenlorge-Gallon S*, Yin WC*, Yung T, Pan J, Zhang X, Mo R, Belik J, Hui CC, Kim T-H (* equal contribution).
Cell Reports (2019) Jun 4;27(10):3006-3018. - Signaling and epigenetic mechanisms of intestinal stem cells and progenitors: insight into crypt homeostasis, plasticity and niches.
Smith RJ, Rao-Bhatia A, Kim T-H.
WIREs Developmental Biology (2017) Sep;6(5).
(Cover article and featured in Advanced Science news) - Single-cell transcript profiles reveal multilineage priming in early progenitors derived from Lgr5+ intestinal stem cells.
Kim T-H*, Saadatpour A*, Guo G, Saxena M, Cavazza A, Desai N, Jadhav U, Jiang L, Rivera MN, Orkin SH, Yuan GC#, Shivdasani RA.# (* equal contribution).
Cell Reports (2016) Aug 23;16(8):2053-60. - Stomach development, stem cells and disease.
Kim T-H# and Shivdasani RA# (# co-corresponding authors)
Development (2016) 143: 554-565. - Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.
Kim T-H, Li F, Ferreiro-Neira I, Ho L-L, Luyten A, Nalapareddy K, Liu XS, Verzi M, Shivdasani RA.
Nature (2014) 506(7489):511-5.
(Recommended by Faculty of 1000) - Intestinal stem cell niche: Famished Paneth cells, gluttonous stem cells.
Kim T-H, Shivdasani RA.
Current Biology (2012) 22(14):R579-80. - Intact function of Lgr5-expressing stem cells in the absence of Paneth cells.
Kim T-H, Escudero S, Shivdasani RA.
Proceedings of the National Academy of Science-USA (2012) 109(10):3932-7. - Phactr4 regulates directional migration of Enteric Neural Crest through PP1, integrin signaling and cofilin activity. (* equal contribution)
Zhang Y*, Kim T-H*, Niswander L.
Genes & Development (2012) 26(1):69-81.
(Cover Article, featured in perspectives Genes & Development 2012;26(1):1-5, highlighted in Nature Cell Biology 2012;14:130, and recommended by Faculty of 1000) - Endodermal Hedgehog signals modulate Notch pathway activity in the developing digestive tract mesenchyme. (* equal contribution)
Kim T-H*, Kim B-M*, Mao J, Rowan S, Shivdasani RA.
Development (2011) 138(15):3225-33. - Notch signaling in stomach epithelial stem cell homeostasis.
Kim T-H, Shivdasani RA.
Journal of Experimental Medicine (2011) 208(4):677-88.
(Cover article) - Genetic evidence that intestinal Notch functions vary regionally and operate through a common mechanism of Math1 repression.
Kim T-H, Shivdasani RA.
Journal of Biological Chemistry (2011) 286:11427-33. - Phactr4 regulates neural tube closure by controlling PP1, Rb phosphorylation and cell cycle progression.
Kim T-H, Goodman J, Anderson K, Niswander L.
Developmental Cell (2007) 13:87-102.
Book Chapters
- Animal models of congenital gastrointestinal maladies, Animal Models of Human Birth Defects. Advance in Experimental Medicine and Biology.
Smith RJ, Francis R, Kim JE, Kim T-H. In: Aimin Liu ed. (2020)
Springer Nature, United Kingdom: pp. 87-107. - The Alimentary Canal. The Atlas of Mouse Development (Kaufman)-supplement.San Roman AK, Kim T-H, Shivdasani RA. In: Baldock R, Bard J, Davidson D, Morriss-Kay G, eds. (2016)Elsevier, Netherlands; Ch. 5, pp. 77-84.
- Basic science of Stomach Development. Translational Gastroenterology: Organogenesis to Disease.Kim T-H, Shivdasani RA. In: Gumucio DL, Samuelson LC, Spence JR, eds. (2014)Wiley Blackwell, United States: pp. 43-56.