Epigenetic regulation during cancer transitions across 11 tumour types
Terekhanova NV*, Karpova A*, Liang WW*, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, X L, Wyczalkowski MA, Lu RJ, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo C, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC^, Chen F^, Raphael BJ^, Ding L^ (^ CO-corresponding Authors; * Contributed equally)
Nature (2023). https://doi.org/10.1038/s41586-023-06682-5
Combining the tyrosine kinase inhibitor cabozantinib and the mTORC1/2 inhibitor sapanisertib blocks ERK pathway activity and suppresses tumor growth in renal cell carcinoma
Yige Wu1,2*, Siqi Chen1,2*, Xiaolu Yang1*, Kazuhito Sato1,2*, Preet Lal1*, Yuefan Wang3, Andrew T. Shinkle1, Michael C. Wendl1,2,4,5, Tina M. Primeau1, Yanyan Zhao1, Alanna Gould1, Hua Sun1,2, Jacqueline L. Mudd1, Jeremy Hoog1, R. Jay Mashl1,2, Matthew A. Wyczalkowski1,2, Chia-Kuei Mo1,2, Ruiyang Liu1,2, John M. Herndon6,7, Sherri R. Davies1, Di Liu1, Xi Ding1, Yvonne A. Evrard8, Bryan E. Welm9, David Lum9, Mei Yee Koh9, Alana L. Welm9, Jeffrey H. Chuang10, Jeffrey A. Moscow11, Funda Meric-Bernstam12, Ramaswamy Govindan1,4, Shunqiang Li1,4, James Hsieh1, Ryan C. Fields4, Kian-Huat Lim1,4, Cynthia X. Ma1,4, Hui Zhang3, Li Ding1,2,4,6^, Feng Chen1,4^ (^ CO-corresponding Authors; * Contributed equally)
Cancer Research (2023) In Press
Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.
Yige Wu*, Nadezhda V. Terekhanova*, Wagma Caravan*, Nataly Naser Al Deen*, Preet Lal*, Siqi Chen, Chia-Kuei Mo, Song Cao, Yize Li, Alla Karpova, Ruiyang Liu, Yanyan Zhao, Andrew Shinkle, Ilya Strunilin, Cody Weimholt, Kazuhito Sato, Lijun Yao, Mamatha Serasanambati, Xiaolu Yang, Matthew Wyczalkowski, Houxiang Zhu, Daniel Cui Zhou, Reyka G. Jayasinghe, Daniel Mendez, Michael C. Wendl, David Clark, Chelsea Newton, Yijun Ruan, Melissa A. Reimers, Russell K. Pachynski, Chris Kinsinger, Scott Jewell, Daniel W. Chan, Hui Zhang, Aadel A. Chaudhuri, Milan G. Chheda, Benjamin D. Humphreys, Mehdi Mesri, Henry Rodriguez, James J. Hsieh, Li Ding# & Feng Chen#
Nature Communications 14, Article number: 1681 (2023)
- * Co-first authors
- # Co-Corresponding Authors
SenNet Consortium (F. Chen as a member of SenNet and the writing group for this perspective)
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health
Nature Aging volume 2, pages1090–1100 (2022)
Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Yao L*, Wang JT*, Jayasinghe RG*, O’Neal J, Tsai CF, Rettig MP, Song Y, Liu R, Zhao Y, Ibrahim OM, Fiala MA, Fortier JM, Chen S, Gehrs L, Martins Rodrigues F, Wendl MC, Kohnen D, Shinkle A, Cao S, Foltz SM, Zhou DC, Storrs E, Wyczalkowski MA, Mani S, Goldsmith SR, Zhu Y, Hamilton M, Liu T, Chen F, Vij R^, Ding L^, DiPersio JF^
Cancer Res 2023 Feb 13:CAN-22-1769; [ahead of print]
Spatially Restricted Drivers and Transitional Cell Populations Cooperate With the Microenvironment in Untreated and Chemo-Resistant Pancreatic Cancer
Cui Zhou D*, Jayasinghe RG*, …, Chen F, DeNardo DG, Fields RC, Ding L
Histopathologic and Proteogenomic Heterogeneity Reveals Features of Clear Cell Renal Cell Carcinoma Aggressiveness
Li Y*, Lih TM*, Dhanasekaran SM*^, Mannan R*, Chen L*, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kolodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyo D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DWˇ, Ricketts CJ^ˇ, Nesvizhskii AIˇ, Zhang H^ˇ, Ding L^ˇ
Clinical Proteomic Tumor Analysis Consortium
Cancer Cell 2022 Dec 20:S1535-6108(22)00565-7;
Pollock: Fishing for Cell States
Storrs EP, Zhou DC, Wendl MC, Wyczalkowski MA, Karpova A, Wang LB, Li Y, Southard-Smith A, Jayasinghe RG, Yao L, Liu R, Wu Y, Terekhanova NV, Zhu H, Herndon JM, Puram S, Chen F, Gillanders WE, Fields RC, Ding L
Bioinform Adv 2022 May 13;2(1):vbac028
Pan-Cancer Studies: Evolving from Basic Research Toward the Clinic
Feng Chen, Michael C. Wendl, Matthew Wyczalkowski, Matthew H. Bailey, Yize Li, Li Ding
Sun H*, Cao S*, Mashl RJ*, Mo CK*, Zaccaria S*, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, DiPersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L
NCI PDXNet Consortium
Comprehensive Characterization of 536 Patient-Derived Xenograft Models Prioritizes Candidates For Targeted Treatment
Nat Commun 2021 Aug 24;12(1):5086
Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, …, Chen F, …, Ding L.
Proteogenomic and metabolomic characterization of human glioblastoma.
Cancer Cell. 2021 Apr 12;39(4):509-528.e20. doi: 10.1016/j.ccell.2021.01.006. Epub 2021 Feb 11. PubMed PMID: 33577785; PubMed Central PMCID: PMC8044053.
Cao S, Cui Zhou D, Oh C, Jayasinghe RG, Zhao Y, Yoon C, Wyczalkowski MA, Bailey MH, Tsou T, Gao Q,Malone A, Reynolds S, Shmulevich I,Wendl MC, Chen F* &Ding L*
Discovery of driver non-coding splice-site-creating mutations in cancer
* Co-Corresponding Authors
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
Rozenblatt-Rosen O*, Regev A*, Oberdoerffer P*, Nawy T*, Hupalowska A, Rood J, Ashenberg O, Cerami E, Coffey R, Demir E, Ding L, Esplin E, Ford J, Goecks J, Ghosh S, Gray J, Guinney J, Hanlon S, Hughes S, Hwang S, A. Iacobuzio-Donahue C, Jane-Valbuena J, …, Tan K, West RB, Williams EH
Human Tumor Atlas Network
Cell 2020 Apr 16; 181(2): 236-249
Clark DJ, Dhanasekaran SM, Petralia F, …, Chen F, …, Ding L, …, Zhang H. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
Cell. 2019 Oct 31;179(4):964-983.e31. doi: 10.1016/j.cell.2019.10.007. PubMed PMID: 31675502.
Ding L, Chen F.
Predicting Tumor Response to PD-1 Blockade.
N Engl J Med. 2019 Aug 1;381(5):477-479. doi: 10.1056/NEJMcibr1906340. PubMed PMID: 31365807.
Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies S, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyö D, Li S, Liu T, Carr SA, Ding L.
Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.
Mol Cell Proteomics. 2019 Aug;18(8):1630-1650. doi: 10.1074/mcp.RA118.001243. Epub 2019 Jun 13. PubMed PMID: 31196969; PubMed Central PMCID: PMC6682998.
Jain S*, Chen F*. Developmental pathology of congenital kidney and urinary tract anomalies. Clin Kidney J. 2019 Jun;12(3):382-399. doi: 10.1093/ckj/sfy112. eCollection 2019 Jun. PubMed PMID: 31198539; PubMed Central PMCID: PMC6543978.
* Co-Corresponding Authors
Adamovich AI, Banerjee T, Wingo M, Duncan K, Ning J, Martins Rodrigues F, Huang KL, Lee C, Chen F, Ding L, Parvin JD. Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity. PLoS Genet. 2019 Mar;15(3):e1008049. doi: 10.1371/journal.pgen.1008049. eCollection 2019 Mar. PubMed PMID: 30925164; PubMed Central PMCID: PMC6457558.
Cao S, Wylie KM, Wyczalkowski MA, Karpova A, Ley J, Sun S, Mashl RJ, Liang WW, Wang X, Johnson K, DiPersio JF, Gay H, Ratner L, Chen F, Adkins DR, Ding L. Dynamic host immune response in virus-associated cancers. Commun Biol. 2019;2:109. doi: 10.1038/s42003-019-0352-3. eCollection 2019. PubMed PMID: 30911684; PubMed Central PMCID: PMC6430765.
Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyö D, Townsend RR, Dipersio JF, Chen F*, Ding L*. Integrative omics analyses broaden treatment targets in human cancer. Genome Med. 2018 Jul 27;10(1):60. doi: 10.1186/s13073-018-0564-z. PubMed PMID: 30053901; PubMed Central PMCID: PMC6064051.
* Co-Corresponding Authors
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F*, Ding L*. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. PubMed PMID: 29625052; PubMed Central PMCID: PMC5949147.
* Co-Corresponding Authors
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033. PubMed PMID: 29625049; PubMed Central PMCID: PMC5916814.
Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. PubMed PMID: 29617662; PubMed Central PMCID: PMC5916809.
Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F*, Ding L*. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052. PubMed PMID: 29617666; PubMed Central PMCID: PMC6055527.
* Co-Corresponding Authors
Ding L, Chen F. Precancerous Clonal Expansion: A New Therapeutic Target?. J Clin Oncol. 2017 May 10;35(14):1503-1505. doi: 10.1200/JCO.2017.72.2868. Epub 2017 Mar 14. PubMed PMID: 28291387.
Ginley B, Tomaszewski JE, Yacoub R, Chen F, Sarder P. Unsupervised labeling of glomerular boundaries using Gabor filters and statistical testing in renal histology. J Med Imaging (Bellingham). 2017 Apr;4(2):021102. doi: 10.1117/1.JMI.4.2.021102. Epub 2017 Feb 28. PubMed PMID: 28331889; PubMed Central PMCID: PMC5331029.
Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F*, Ding L*. Protein-structure-guided discovery of functional mutations across 19 cancer types. Nat Genet. 2016 Aug;48(8):827-37. doi: 10.1038/ng.3586. Epub 2016 Jun 13. PubMed PMID: 27294619; PubMed Central PMCID: PMC5315576.
* Co-Corresponding Authors
Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L. Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep. 2016 Jun 24;6:28294. doi: 10.1038/srep28294. PubMed PMID: 27339696; PubMed Central PMCID: PMC4919655.
Manda KR, Tripathi P, Hsi AC, Ning J, Ruzinova MB, Liapis H, Bailey M, Zhang H, Maher CA, Humphrey PA, Andriole GL, Ding L, You Z, Chen F. NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence. Oncogene. 2016 Jun 23;35(25):3282-92. doi: 10.1038/onc.2015.389. Epub 2015 Oct 19. PubMed PMID: 26477312; PubMed Central PMCID: PMC5012433.
Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, Huang KL, Scott A, Foltz S, Niu B, Johnson KJ, Moed M, Slagboom PE, Chen F, Wendl MC, Ding L. Systematic discovery of complex insertions and deletions in human cancers. Nat Med. 2016 Jan;22(1):97-104. doi: 10.1038/nm.4002. Epub 2015 Dec 14. PubMed PMID: 26657142; PubMed Central PMCID: PMC5003782.
Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, Dipersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L. Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun. 2015 Dec 22;6:10086. doi: 10.1038/ncomms10086. PubMed PMID: 26689913; PubMed Central PMCID: PMC4703835.
Guo Q, Tripathi P, Manson SR, Austin PF, Chen F. Transcriptional dysregulation in the ureteric bud causes multicystic dysplastic kidney by branching morphogenesis defect. J Urol. 2015 May;193(5 Suppl):1784-90. doi: 10.1016/j.juro.2014.08.122. Epub 2014 Oct 6. PubMed PMID: 25301096; PubMed Central PMCID: PMC4504205.
Guo Q, Wang Y, Tripathi P, Manda KR, Mukherjee M, Chaklader M, Austin PF, Surendran K, Chen F. Adam10 mediates the choice between principal cells and intercalated cells in the kidney. J Am Soc Nephrol. 2015 Jan;26(1):149-59. doi: 10.1681/ASN.2013070764. Epub 2014 Jun 5. PubMed PMID: 24904084; PubMed Central PMCID: PMC4279728.
Xie M, Lu C, Wang J, McLellan MD, Johnson KJ, Wendl MC, McMichael JF, Schmidt HK, Yellapantula V, Miller CA, Ozenberger BA, Welch JS, Link DC, Walter MJ, Mardis ER, Dipersio JF, Chen F, Wilson RK, Ley TJ, Ding L. Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nat Med. 2014 Dec;20(12):1472-8. doi: 10.1038/nm.3733. Epub 2014 Oct 19. PubMed PMID: 25326804; PubMed Central PMCID: PMC4313872.
Brunskill EW, Park JS, Chung E, Chen F, Magella B, Potter SS. Single cell dissection of early kidney development: multilineage priming. Development. 2014 Aug;141(15):3093-101. doi: 10.1242/dev.110601. PubMed PMID: 25053437; PubMed Central PMCID: PMC4197661.
Tripathi P, Wang Y, Coussens M, Manda KR, Casey AM, Lin C, Poyo E, Pfeifer JD, Basappa N, Bates CM, Ma L, Zhang H, Pan M, Ding L, Chen F. Activation of NFAT signaling establishes a tumorigenic microenvironment through cell autonomous and non-cell autonomous mechanisms. Oncogene. 2014 Apr 3;33(14):1840-9. doi: 10.1038/onc.2013.132. Epub 2013 Apr 29. PubMed PMID: 23624921; PubMed Central PMCID: PMC3770739.
Ding L, Raphael BJ, Chen F, Wendl MC. Advances for studying clonal evolution in cancer. Cancer Lett. 2013 Nov 1;340(2):212-9. doi: 10.1016/j.canlet.2012.12.028. Epub 2013 Jan 23. Review. PubMed PMID: 23353056; PubMed Central PMCID: PMC3783624.
Pan MG, Xiong Y, Chen F. NFAT gene family in inflammation and cancer. Curr Mol Med. 2013 May;13(4):543-54. doi: 10.2174/1566524011313040007. Review. PubMed PMID: 22950383; PubMed Central PMCID: PMC3694398.
Walker KA, Sims-Lucas S, Di Giovanni VE, Schaefer C, Sunseri WM, Novitskaya T, de Caestecker MP, Chen F, Bates CM. Deletion of fibroblast growth factor receptor 2 from the peri-wolffian duct stroma leads to ureteric induction abnormalities and vesicoureteral reflux. PLoS One. 2013;8(2):e56062. doi: 10.1371/journal.pone.0056062. Epub 2013 Feb 7. PubMed PMID: 23409123; PubMed Central PMCID: PMC3567073.
Wang Y, Guo Q, Casey A, Lin C, Chen F. A new tool for conditional gene manipulation in a subset of keratin-expressing epithelia. Genesis. 2012 Dec;50(12):899-907. doi: 10.1002/dvg.22046. Epub 2012 Aug 20. PubMed PMID: 22764128; PubMed Central PMCID: PMC3681952.
Toib A, Zhang HX, Broekelmann TJ, Hyrc KL, Guo Q, Chen F, Remedi MS, Nichols CG. Cardiac specific ATP-sensitive K+ channel (KATP) overexpression results in embryonic lethality. J Mol Cell Cardiol. 2012 Sep;53(3):437-45. doi: 10.1016/j.yjmcc.2012.07.001. Epub 2012 Jul 13. PubMed PMID: 22796573; PubMed Central PMCID: PMC3423334.
Guo Q, Xia B, Zhang F, Richardson MM, Li M, Zhang JS, Chen F, Zhang XA. Tetraspanin CO-029 inhibits colorectal cancer cell movement by deregulating cell-matrix and cell-cell adhesions. PLoS One. 2012;7(6):e38464. doi: 10.1371/journal.pone.0038464. Epub 2012 Jun 5. PubMed PMID: 22679508; PubMed Central PMCID: PMC3367972.
Tripathi P, Wang Y, Casey AM, Chen F. Absence of canonical Smad signaling in ureteral and bladder mesenchyme causes ureteropelvic junction obstruction. J Am Soc Nephrol. 2012 Apr;23(4):618-28. doi: 10.1681/ASN.2011060566. Epub 2012 Jan 26. PubMed PMID: 22282597; PubMed Central PMCID: PMC3312498.
Chen F, Ding L. Co-survival of the fittest few: mosaic amplification of receptor tyrosine kinases in glioblastoma. Genome Biol. 2012 Jan 30;13(1):141. doi: 10.1186/gb-2012-13-1-141. PubMed PMID: 22289423; PubMed Central PMCID: PMC3334575.
Rogers SA, Tripathi P, Mohanakumar T, Liapis H, Chen F, Talcott MR, Faulkner C, Hammerman MR. Engraftment of cells from porcine islets of Langerhans following transplantation of pig pancreatic primordia in non-immunosuppressed diabetic rhesus macaques. Organogenesis. 2011 Jul-Sep;7(3):154-62. doi: 10.4161/org.7.3.16522. Epub 2011 Jul 1. PubMed PMID: 21654197; PubMed Central PMCID: PMC3243028.
Guo Q, Tripathi P, Poyo E, Wang Y, Austin PF, Bates CM, Chen F. Cell death serves as a single etiological cause of a wide spectrum of congenital urinary tract defects. J Urol. 2011 Jun;185(6):2320-8. doi: 10.1016/j.juro.2011.02.044. Epub 2011 Apr 21. PubMed PMID: 21511282; PubMed Central PMCID: PMC3169200.
Wang Y, Jarad G, Tripathi P, Pan M, Cunningham J, Martin DR, Liapis H, Miner JH, Chen F. Activation of NFAT signaling in podocytes causes glomerulosclerosis. J Am Soc Nephrol. 2010 Oct;21(10):1657-66. doi: 10.1681/ASN.2009121253. Epub 2010 Jul 22. PubMed PMID: 20651158; PubMed Central PMCID: PMC3013542.
Tripathi P, Guo Q, Wang Y, Coussens M, Liapis H, Jain S, Kuehn MR, Capecchi MR, Chen F. Midline signaling regulates kidney positioning but not nephrogenesis through Shh. Dev Biol. 2010 Apr 15;340(2):518-27. doi: 10.1016/j.ydbio.2010.02.007. Epub 2010 Feb 10. PubMed PMID: 20152829; PubMed Central PMCID: PMC2854326.
Chen F. Genetic and developmental basis for urinary tract obstruction. Pediatr Nephrol. 2009 Sep;24(9):1621-32. doi: 10.1007/s00467-008-1072-y. Epub 2008 Dec 16. Review. PubMed PMID: 19085015; PubMed Central PMCID: PMC2844875.
Wang Y, Tripathi P, Guo Q, Coussens M, Ma L, Chen F. Cre/lox recombination in the lower urinary tract. Genesis. 2009 Jun;47(6):409-13. doi: 10.1002/dvg.20515. PubMed PMID: 19415630; PubMed Central PMCID: PMC2848076.
Lin C, Yin Y, Chen H, Fisher AV, Chen F, Rauchman M, Ma L. Construction and characterization of a doxycycline-inducible transgenic system in Msx2 expressing cells. Genesis. 2009 May;47(5):352-9. doi: 10.1002/dvg.20506. PubMed PMID: 19370755; PubMed Central PMCID: PMC2749712.
Chen F. Plumbing the depths of urinary tract obstruction by using murine models. Organogenesis. 2009 Jan;5(1):297-305. doi: 10.4161/org.8055. PubMed PMID: 19568351; PubMed Central PMCID: PMC2659371.
Jia Q, McDill BW, Sankarapandian B, Wu S, Liapis H, Holzman LB, Capecchi MR, Miner JH, Chen F. Ablation of developing podocytes disrupts cellular interactions and nephrogenesis both inside and outside the glomerulus. Am J Physiol Renal Physiol. 2008 Dec;295(6):F1790-8. doi: 10.1152/ajprenal.90519.2008. Epub 2008 Oct 8. PubMed PMID: 18842818; PubMed Central PMCID: PMC2604822.
Hoffert JD, Fenton RA, Moeller HB, Simons B, Tchapyjnikov D, McDill BW, Yu MJ, Pisitkun T, Chen F, Knepper MA. Vasopressin-stimulated increase in phosphorylation at Ser269 potentiates plasma membrane retention of aquaporin-2. J Biol Chem. 2008 Sep 5;283(36):24617-27. doi: 10.1074/jbc.M803074200. Epub 2008 Jul 7. PubMed PMID: 18606813; PubMed Central PMCID: PMC2528999.
Rogers SA, Chen F, Talcott MR, Faulkner C, Thomas JM, Thevis M, Hammerman MR. Long-term engraftment following transplantation of pig pancreatic primordia into non-immunosuppressed diabetic rhesus macaques. Xenotransplantation. 2007 Nov;14(6):591-602. doi: 10.1111/j.1399-3089.2007.00429.x. PubMed PMID: 17991147.
Jia Q, McDill BW, Li SZ, Deng C, Chang CP, Chen F. Smad signaling in the neural crest regulates cardiac outflow tract remodeling through cell autonomous and non-cell autonomous effects. Dev Biol. 2007 Nov 1;311(1):172-84. doi: 10.1016/j.ydbio.2007.08.044. Epub 2007 Aug 31. PubMed PMID: 17916348; PubMed Central PMCID: PMC2692609.
Li SZ, McDill BW, Kovach PA, Ding L, Go WY, Ho SN, Chen F. Calcineurin-NFATc signaling pathway regulates AQP2 expression in response to calcium signals and osmotic stress. Am J Physiol Cell Physiol. 2007 May;292(5):C1606-16. doi: 10.1152/ajpcell.00588.2005. Epub 2006 Dec 13. PubMed PMID: 17166937.
Rogers SA, Chen F, Talcott M, Liapis H, Hammerman MR. Glucose tolerance normalization following transplantation of pig pancreatic primordia into non-immunosuppressed diabetic ZDF rats. Transpl Immunol. 2006 Nov;16(3-4):176-84. doi: 10.1016/j.trim.2006.08.007. Epub 2006 Sep 7. PubMed PMID: 17138051.
Zhang Y, Li SZ, Li J, Pan X, Cahoon RE, Jaworski JG, Wang X, Jez JM, Chen F, Yu O. Using unnatural protein fusions to engineer resveratrol biosynthesis in yeast and Mammalian cells. J Am Chem Soc. 2006 Oct 11;128(40):13030-1. doi: 10.1021/ja0622094. PubMed PMID: 17017764.
McDill BW, Li SZ, Kovach PA, Ding L, Chen F. Congenital progressive hydronephrosis (cph) is caused by an S256L mutation in aquaporin-2 that affects its phosphorylation and apical membrane accumulation. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6952-7. doi: 10.1073/pnas.0602087103. Epub 2006 Apr 25. PubMed PMID: 16641094; PubMed Central PMCID: PMC1459000.
Schaeffer PJ, Wende AR, Magee CJ, Neilson JR, Leone TC, Chen F, Kelly DP. Calcineurin and calcium/calmodulin-dependent protein kinase activate distinct metabolic gene regulatory programs in cardiac muscle. J Biol Chem. 2004 Sep 17;279(38):39593-603. doi: 10.1074/jbc.M403649200. Epub 2004 Jul 19. PubMed PMID: 15262994.
Rogers SA, Chen F, Talcott M, Hammerman MR. Islet cell engraftment and control of diabetes in rats after transplantation of pig pancreatic anlagen. Am J Physiol Endocrinol Metab. 2004 Apr;286(4):E502-9. doi: 10.1152/ajpendo.00445.2003. Epub 2003 Dec 16. PubMed PMID: 14678953.
Chang CP, McDill BW, Neilson JR, Joist HE, Epstein JA, Crabtree GR, Chen F. Calcineurin is required in urinary tract mesenchyme for the development of the pyeloureteral peristaltic machinery. J Clin Invest. 2004 Apr;113(7):1051-8. doi: 10.1172/JCI20049. PubMed PMID: 15057312; PubMed Central PMCID: PMC379320.
Graef IA, Chen F, Crabtree GR. NFAT signaling in vertebrate development. Curr Opin Genet Dev. 2001 Oct;11(5):505-12. doi: 10.1016/s0959-437x(00)00225-2. Review. PubMed PMID: 11532391.
Graef IA*, Chen F*, Chen L, Kuo A, Crabtree GR. Signals transduced by Ca(2+)/calcineurin and NFATc3/c4 pattern the developing vasculature. Cell. 2001 Jun 29;105(7):863-75. doi: 10.1016/s0092-8674(01)00396-8. PubMed PMID: 11439183.
*Co-first authors
Chen F, Capecchi MR. Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function together to control development of the mammary gland in response to pregnancy. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):541-6. doi: 10.1073/pnas.96.2.541. PubMed PMID: 9892669; PubMed Central PMCID: PMC15172.
Chen F, Greer J, Capecchi MR. Analysis of Hoxa7/Hoxb7 mutants suggests periodicity in the generation of the different sets of vertebrae. Mech Dev. 1998 Sep;77(1):49-57. doi: 10.1016/s0925-4773(98)00126-9. PubMed PMID: 9784603.
Chen F, Capecchi MR. Targeted mutations in hoxa-9 and hoxb-9 reveal synergistic interactions. Dev Biol. 1997 Jan 15;181(2):186-96. doi: 10.1006/dbio.1996.8440. PubMed PMID: 9013929.