Publications | Overview
2024
Liu MY, Chen B, Borji M, Garcia de Alba Rivas C, Dost AFM, Moye AL, Movval Abdulla N, Paschini M, Rollins SD, Wang R, Schnapp LM, Khalil HA, Wu CJ, Sharma NS, Kim CF. Human Airway and Alveolar Organoids from Bronchoalveolar Lavage Fluid. Am J Respir Crit Care Med. 2024 Apr 23. doi: 10.1164/rccm.202310-1831LE. Epub ahead of print. PMID: 38652140.
2023
Adini A, Ko VH, Puder M, Louie SM, Kim CF, Baron J, Matthews BD. PR1P, a VEGF-stabilizing peptide, reduces injury and inflammation in acute lung injury and ulcerative colitis animal models. Front Immunol. 2023 Apr 28;14:1168676. doi: 10.3389/fimmu.2023.1168676. PMID: 37187742; PMCID: PMC10175756.
Rowbotham SP, Pessina P*, Garcia-de-Alba Rivas C*, Jensen J*, Nguyen Y, Yoon J, Li J, Wong IG, Nguyen Y, Fahey C, Moye AL, Chongsaritsinsuk J, Bronson R, Ho Sui SJ, Kim CF (2023). Aged-associated H3K9me2 loss alters the regenerative equilibrium between murine lung alveolar and bronchiolar progenitors. Developmental Cell. *Co-second authors
2022
Concepcion CP, Ma S, LaFave LM, Bhutkar A, Liu M, DeAngelo LP, Kim JY, Priore ID, Schoenfeld AJ, Miller M, Kartha VK, Westcott PMK, Sanchez-Rivera FJ, Meli K, Gupta M, Bronson RT, Riely GJ, Rekhtman N, Rudin CM, Kim CF, Regev A, Buenrostro JD, Jacks T. Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung. Cancer Discovery. 2022. 12(2), 562-585. doi: 10.1158/2159-8290.CD-21-0248.
Ararat E, Louie SM, Lu E, Paschini MP, Kim CF, Comparison of Transplantation of Lung Organoid Cell Types: One Size Does Not Fit All. American Journal of Respiratory Cell and Molecular Biology. American Journal of Respiratory Cell and Molecular Biology. 2022. 66(3), 340-343. doi: 10.1165/rcmb.2021-0263LE.
Abo KM, Saniz de Aja J, Lindstrom-Vautrin J, Konstantinos-Dionysios A, Richards A, Garcia de Alba Rivas C, Huang J, Hix OT, Werder RB, Bullitt E, Hinds A, Falconer I, Villacorta-Martin C, Jaenisch R, Kim CF, Kotton DN, Wilson AA. Air-liquid interface culture promotes maturation and allows environmental exposure of pluripotent stem cell-derived alveolar epithelium. JCI Insight. 2022. 7(6):e155589. doi: 10.1172/jci.insight.155589.
Louie SM, Moye AL, Wong IG, Lu E, Shehaj A, Garcia-de-Alba C, Ararat E, Raby BA, Lu B, Paschini M, Bronson RT, Kim CF. Progenitor potential of lung epithelial organoid cells in a transplantation model. Cell Rep. 2022. 39(2):110662. doi: 10.1016/j.celrep.2022.110662.
Yang S, Ha K, Song W, Fujita M, Kübler K, Polak P, Garcia-de-Alba C, Pessina P, Saniz de Aja J, Rowbotham S, Bhetariya P, Dost A, Moye A, Hiyama E, Nakagawa H, Kim CF, Kim H-G, Lee H. COOBoostR: An Extreme Gradient Boosting-Based Tool for Robust Tissue or Cell-of-Origin Prediction of Tumors. bioRxiv 2022. 10.24.513446; doi: https://doi.org/10.1101/2022.10.24.513446
Alysandratos KD, Garcia-de-Alba C, Yao C, Pessina P, Huang J, Villacorta-Martin C, Hix OT, Minakin K, Burgess CL, Bawa P, Murthy A, Konda B, Beers MF, Stripp BR, Kim CF, Kotton DN. Culture impact on the transcriptomic programs of primary and iPSC-derived human alveolar type 2 cells. JCI Insight. 2022 Dec 1:e158937. doi: 10.1172/jci.insight.158937. Epub ahead of print. PMID: 36454643. *co-corresponding authors
2021
Zhang T, Joubert P, Ansari-Pour N, Zhao W, Hoang PH, Lokanga R, Moye AL, Rosenbaum J, Gonzalez-Perez A, Martínez-Jiménez F, Castro A, Muscarella LA, Hofman P, Consonni D, Pesatori AC, Kebede M, Li M, Gould Rothberg BE, Peneva I, Schabath MB, Poeta ML, Costantini M, Hirsch D, Heselmeyer-Haddad K, Hutchinson A, Olanich M, Lawrence SM, Lenz P, Duggan M, Bhawsar PMS, Sang J, Kim J, Mendoza L, Saini N, Klimczak LJ, Islam SMA, Otlu B, Khandekar A, Cole N, Stewart DR, Choi J, Brown KM, Caporaso NE, Wilson SH, Pommier Y, Lan Q, Rothman N, Almeida JS, Carter H, Ried T, Kim CF, Lopez-Bigas N, Garcia-Closas M, Shi J, Bossé Y, Zhu B, Gordenin DA, Alexandrov LB, Chanock SJ, Wedge DC, Landi MT. Genomic and evolutionary classification of lung cancer in never smokers. Nature Genetics. 2021 Sep;53(9):1348-1359. doi: 10.1038/s41588-021-00920-0
Schneider JL, Rowe JH, Garcia-de-Alba C, Kim CF, Sharpe AH, Haigis MC. The aging lung: Physiology, disease, and immunity. Cell. 2021 Apr 15 PMID - 33811810 Review
Hynds RE, Zacharias WJ, Nikolić MZ, Königshoff M, Eickelberg O, Gosens R, de Coppi P, Janes SM, Morrisey E, Clevers H, Ryan AL, Stripp BR, Sun X, Kim CF, Lin QS. National Heart, Lung and Blood Institute and Building Respiratory Epithelium and Tissue for Health (BREATH) Consortium Workshop Report: Moving Forward in Lung Regeneration. Am J Respir Cell Mol Biol. 2021 Feb 24. PMID - 33625958 Review
Sainz de Aja J, Dost AFM, Kim CF. Alveolar progenitor cells and the origin of lung cancer. J Intern Med. 2021 May PMID - 33340175 Review
2020
Dost AFM, Moye AL, Vedaie M, Tran LM, Fung E, Heinze D, Villacorta-Martin C, Huang J, Hekman R, Kwan JH, Blum BC, Louie SM, Rowbotham SP, Sainz de Aja J, Piper ME, Bhetariya PJ, Bronson RT, Emili A, Mostoslavsky G, Fishbein GA, Wallace WD, Krysan K, Dubinett SM, Yanagawa J, Kotton DN, Kim CF. Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells. Cell Stem Cell. 2020 Oct 1 PMID - 32891189
Gupta M, Concepcion CP, Fahey CG, Keshishian H, Bhutkar A, Brainson CF, Sanchez-Rivera FJ, Pessina P, Kim JY, Simoneau A, Paschini M, Beytagh MC, Stanclift CR, Schenone M, Mani DR, Li C, Oh A, Li F, Hu H, Karatza A, Bronson RT, Shaw AT, Hata AN, Wong KK, Zou L, Carr SA, Jacks T, Kim CF. BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency. Cancer Res. 2020 Sep 15 PMID - 32690724
Sainz de Aja J, Kim CF. May the (Mechanical) Force Be With AT2. Cell. PMID - 31951518
2019
Leeman KT, Pessina P, Lee JH, Kim CF. Mesenchymal Stem Cells Increase Alveolar Differentiation in Lung Progenitor Organoid Cultures. Nature Scientific Reports. PMID - 31015509
Paschini M, Kim CF. An Airway Organoid Is Forever. EMBO J. PMID - 30718273
2018
Garcia-de-Alba C, Pessina P, Kim CF. A New "Age"r for Lung Research Arrives: Genetic Targeting of Alveolar Type 1 Epithelial Cells. Am J Respir Cell Mol Biol. PMID - 30040450
Rowbotham S, Li F, Marsh B, Pessina P, Brainson C, Tuminello S, Zhang H, Schlaeger T, Wong K, Watanabe H, Dost A, Louie S, Centura A, Aronow B, Kim CF. H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression. Nature Communications. PMID - 30455465
Sinkevicius K, Bellaria K, Barrios J, Pessina P, Gupta M, Brainson Fillmore CF, Bronson RT, Kim CF. Ecadherin loss accelerates tumor progression and metastasis in a mouse model of lung adenocarcinoma. Am J Respir Cell Mol Biol. PMID - 29447458
Tan JL, Lau SN, Leaw B, Nguyen HPT, Salamonsen LA, Saad MI, Chan ST, Zhu D, Krause M, Kim CF, Sievert W, Wallace EM, Lim R. Amnion Epithelial Cell-Derived Exosomes Restrict Lung Injury and Enhance Endogenous Lung Repair. Stem Cells Transl. Med. PMID - 29297621
2017
Zhu D, Tan J, Maleken AS, Muljadi R, Chan ST, Lau SN, Elgass K, Leaw B, Mockler J, Chambers D, Leeman KT, Kim CF, Wallace EM, Lim R. Human amnion cells reverse acute and chronic pulmonary damage in experimental neonatal lung injury. Stem Cell Res. Ther. PMID - 29126435
Lee J-H, Tammela T, Hofree M, Choi J, Marjanovic N, Han S, Canner D, Paschini M, Bhang D, Jacks T, Regev A, Kim CF. Anatomically and functionally distinct lung mesenchymal populations marked by Lgr5 and Lgr6. Cell. PMID - 28886383
Agrawal PB, Wang R, Li H, Schmitz-Abe K, Simone-Roach C, Chen J, Shi J, Louie T, Sheng S, Towne MC, Brainson CF, Matthay MA, Kim CF, Bamshad M, Emond MJ, Gerard NP, Kleyman TR, Gerard C. The Epithelial Sodium Channel Is a Modifier of the Long-Term Nonprogressive Phenotype Associated With F508del CFTR Mutations. Am J Respir Cell Mol Biol. PMID - 28708422
Lau AN, Curtis SJ, Fillmore CM, Rowbotham SP, Mohseni M, Wagner DE, Beede AM, Montoro DT, Sinkevicius KW, Walton ZE, Barrios J, Weiss DJ, Camargo FD, Wong KK, Kim CF. Tumor-propagating cells and Yap/Taz activity contribute to lung tumor progression and metastasis. EMBO J.
Lee JH, Bhang DH, Beede A, Huang TL, Stripp BR, Bloch KD, Wagers AJ, Tseng YH, Ryeom S, Kim, CF. Lung stem cell differentiation in mice directed by endothelial cells via a BMP4-NFATc1-Thrombospondin-1 axis. Cell. 2014; 156: 440-455.
Xu C, Fillmore CM, Koyama S, Wu H, Zhao Y, Chen Z, Herter-Sprie GS, Akbay EA, Tchaicha JH, Altabef A, Reibel JB, Walton Z, Ji H, Watanabe H, Jänne PA, Castrillon DH, Rustgi AK, Bass AJ, Freeman GJ, Padera RF, Dranoff G, Hammerman PS,* Kim CF,* Wong KK.* Loss of Lkb1 and Pten Leads to Lung Squamous Cell Carcinoma with Elevated PD-L1 Expression. Cancer Cell. 2014; 25:590-604. *co-corresponding authors
Fillmore CM, Xu C, Desai PT, Berry JM, Rowbotham SP, Lin YJ, Zhang H, Marquez VE, Hammerman PS, Wong KK, Kim CF. EZH2 inhibition sensitizes BRG1 and EGFR mutant lung tumors to TopoII inhibitors. Nature. 2015; 520: 239-42