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Tumor Niche Network-Defined Subtypes Predict Immunotherapy response of Esophageal Squamous Cell Cancer

Kyung-Pil Ko, Shengzhe Zhang, Yuanjian Huang, Bongjun Kim, Gengyi Zou, Sohee Jun, Jie Zhang, Cecilia Martin, Karen J. Dunbar, Gizem Efe, Anil K. Rustgi, Haiyang Zhang, Hiroshi Nakagawa, Jae-Il Park

Despite the promising outcome of immune checkpoint blockade (ICB), ICB resistance is a new challenge. Thus, selecting patients for specific ICB applications is crucial for maximizing therapeutic efficacy. Herein we curated 69 human esophageal squamous cell cancer (ESCC) patients’ tumor microenvironment (TME) single-cell transcriptomic datasets for ESCC subtyping. Notably, integrative analyses of the cellular network transcriptional signatures of T cells, myeloid cells, and fibroblasts define distinct ESCC subtypes characterized by T cell exhaustion, Interferon alpha and beta signaling, TIGIT enrichment, and specific marker genes. Furthermore, this approach classifies ESCC patients into ICB responders and non-responders, validated by liquid biopsy single-cell transcriptomics. This study stratifies ESCC patients by TME transcriptional network, which provides a novel insight into tumor niche remodeling and helps predict ICB responses of ESCC patients.

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CRACD, a gatekeeper restricting proliferation, heterogeneity, and immune evasion of small cell lung Cancer

Shengzhe Zhang, Kee-Beom Kim, Yuanjian Huang, Dong-Wook Kim, Bongjun Kim, Kyung-Pil Ko, Gengyi Zou, Jie Zhang, Sohee Jun, Nicole A. Kirk, Ye Eun Hwang, Young Ho Ban, Joseph M. Chan, Charles M. Rudin, Kwon-Sik Park, Jae-Il Park

Small cell lung carcinoma (SCLC) is a lethal neuroendocrine type of lung cancer with limited therapeutic options. Despite recent advances in cancer immunotherapy, the efficacy of immunotherapy is limited to a subset of patients with SCLC. However, the mechanisms responsible for refractoriness to immunotherapy remain elusive. CRACD (capping protein inhibiting regulator of actin dynamics; KIAA1211/CRAD) is frequently mutated and transcriptionally downregulated in SCLC. Here we show that Cracd knockout (KO) enhances transformation of preneoplastic neuroendocrine cells and significantly accelerates SCLC development initiated by loss of Rb1, Trp53, and Rbl2 in the lung epithelium of mice. Cracd KO increases tumor cell heterogeneity in SCLC tumors. Notably, the Cracd-deficient SCLC tumors display exclusion of CD8+ T cells, which coincides with epigenetic suppression of the MHC-I pathway. Single-cell transcriptomic analysis identifies SCLC patient tumors with concomitant inactivation of CRACD and impairment of tumor antigen presentation. These findings define CRACD as a novel tumor suppressor that regulates the proliferation and immune recognition of SCLC cells, providing new insight into the mechanisms by which SCLC evades immune surveillance.

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Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion

Kyung-Pil Ko, Yuanjian Huang, Shengzhe Zhang, Gengyi Zou, Bongjun Kim, Jie Zhang, Sohee Jun, Cecilia Martin, Karen J. Dunbar, Gizem Efe, Anil K. Rustgi, Hiroshi Nakagawa, and Jae-Il Park

In revision

Despite recent progress in identifying aberrant genetic and epigenetic alterations in esophageal squamous cell carcinoma (ESCC), the mechanism of ESCC initiation remain unknown. Using genetically engineered esophageal organoids (EOs), we identified the key genetic determinants that drive ESCC tumorigenesis. A single-cell transcriptomic analysis uncovered that Trp53, Cdkn2a, and Notch1 (PCN) triple knockout (KO) induces neoplastic features of ESCC by generating distinct cell lineage trajectories with multiple root cells and high cell plasticity. Although Trp53 and Notch1 (PN) double KO was sufficient to induce esophageal neoplasia and cellular heterogeneity, additional inactivation of Cdkn2a was indispensable for immune landscape remodeling for in vivo tumorigenesis. PCN KO generated immunosuppressive niche enriched with exhausted T cells and M2 macrophages via the CCL2-CCR2 axis in an autochthonous ESCC mouse model. Moreover, genetic or pharmacological blockade of the CCL2-CCR2 axis suppressed ESCC tumorigenesis. Comparative single-cell transcriptomic analyses classified ESCC patient tumors into three subgroups and identified a specific subset recapitulating PCN-type ESCC signatures, including the high expression of CCL2 and CD274/PD-L1. Our study unveils that loss of TP53, CDKN2A, and NOTCH1 induces esophageal neoplasia and immune evasion for ESCC initiation and proposes the CCL2 blockade as a viable approach to target a subset of ESCC.

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PCLAF-DREAM Drives Alveolar Cell Plasticity for Lung Regeneration

Bongjun Kim, Yuanjian Huang, Kyung-Pil Ko, Shengzhe Zhang, Ggengyi Zou, Jie Zhang, Moonjong Kim, Danielle Little, Lisandra Vila Ellis, Margherita Paschini, Sohee Jun, Kwon-Sik Park, Jichao Chen, Carla Kim, Jae-Il Park

doi: https://doi.org/10.1101/2022.10.11.511761

In revision

The spatiotemporal orchestration of stem/progenitor cells is essential for lung regeneration, the failure of which leads to lung disease, including fibrosis. However, the mechanism of alveolar cell plasticity during regeneration remains elusive. We previously found that PCLAF remodels the DREAM complex for cell quiescence exit and cell proliferation. PCLAF is expressed explicitly in pulmonary proliferative cells, along with the DREAM target genes. Pclaf expression and Pclaf-expressing cells were acutely increased upon lung injury. Intriguingly, Pclaf knock-out mice exhibited lung fibrosis resulting from alveolar type I (AT1) cell loss. The single-cell transcriptome and organoid analyses showed that Pclaf-DREAM complex–transactivated gene expression is required for alveolar type II (AT2) cell transition into AT1. Mechanistically, Clic4, transactivated by the Pclaf-DREAM complex, activates TGF-beta signaling for AT2-PPCs-AT1 cell lineage trajectory. Furthermore, pharmacological mimicking of the Pclaf-mediated transcriptome markedly increased alveolar regeneration. Our study unveils an unexpected role of the PCLAF-DREAM axis in controlling alveolar cell plasticity for lung regeneration and proposes a viable option for lung fibrosis prevention.

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Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis

Shengzhe Zhang, Sung Ho Lee, Litong Nie, Yuanjian Huang, Gengyi Zou, Youn-Sang Jung, Sohee Jun, Jie Zhang, Esther M. Lien, Junjie Chen, Jae-Il Park 

Cancer Communications 2022 Nov 6. doi: 10.1002/cac2.12382. PMID: 36336962 (PDF, SI, ST)

Accumulating evidence suggests that dysregulated lysosomal membrane proteins, including vacuolar ATPase (v-ATPase) and the mammalian target of rapamycin (mTOR), are involved in tumorigenesis. Therefore, lysosomal proteins were proposed as potential therapeutic targets in cancer. As one of the lysosome-related signaling pathways, mTOR signaling regulates cell proliferation, survival, motility, and metabolism. Since mTOR signaling activation promotes tumorigenesis, mTOR inhibitors (mTORi), AZD8055, MLN0128, and Rapalink-1 (the latest third-generation mTORi), have been applied to several cancers. However, the limitations of mTORi include drug resistance and the lack of biomarkers...

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Nuclear Actin Dynamics in Gene Expression, DNA Repair, and Cancer

Yuanjian Huang,* Shengzhe Zhang,* Jae-Il Park

In: Kloc, M., Kubiak, J.Z. (eds) Nuclear, Chromosomal, and Genomic Architecture in Biology and Medicine. Results and Problems in Cell Differentiation, vol 70. Springer, Cham.

https://doi.org/10.1007/978-3-031-06573-6_23 (PDF) PMID: 36348125 PMCID: PMC9677682

Actin is a highly conserved protein in mammals. The actin dynamics is regulated by actin-binding proteins and actin-related proteins. Nuclear actin and these regulatory proteins participate in multiple nuclear processes, including chromosome architecture organization, chromatin remodeling, transcription machinery regulation, and DNA repair. It is well known that the dysfunctions of these processes contribute to the development of cancer. Moreover, emerging evidence has shown that the deregulated actin dynamics is also related to cancer. This chapter discusses how the deregulation of nuclear actin dynamics contributes to tumorigenesis via such various nuclear events.

PubMed

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WNT5A-RHOA signaling is a driver of tumorigenesis and represents a therapeutically actionable vulnerability in small cell lung cancer

Kee-Beom Kim, Dong-Wook Kim, Youngchul Kim, Jun Tang, Nicole Kirk, Yongyu Gan, Bongjun Kim, Bingliang Fang, Jae-Il Park, Yi Zheng, Kwon-Sik Park

Cancer Research  14 Sep 2022, CAN-22-1170. doi: 10.1158/0008-5472.CAN-22-1170

PMID: 36102736 PMCID: PMC9669186

 

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WNT Signaling in Liver Regeneration, Disease, and Cancer

Gengyi Zou and Jae-Il Park

Clin Mol Hepatol 2022 Jul 4;. doi: 10.3350/cmh.2022.0058. PMID: 35785913

Full-text (PDF)

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Establishing Transgenic Murine Esophageal Organoids

Kyung-Pil Ko, Jie Zhang, Jae-Il Park

STAR Protocols  Volume 3, Issue 2, 17 June 2022, 101317, https://doi.org/10.1016/j.xpro.2022.101317

PMID: 35496812, PMCID: PMC9048136

Full-text (PDF)

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KIX domain determines a selective tumor-promoting role for EP300 and its vulnerability in small-cell lung cancer

Kee-Beom Kim, Ashish Kabra, Dong-Wook Kim, Yongming Xue, Yuanjian Huang, Pei-Chi Hou, Yunpeng Zhou, Leilani J. Miranda, Jae-Il Park, Xiaobing Shi, Timothy P. Bender, John H. Bush welder, Kwon-Sik Park

Science Advances   2022 Feb 18;8(7):eabl4618. doi: 10.1126/sciadv.abl4618. Epub 2022 Feb 16, PMID: 35171684

Full-text (PDF)

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A New Murine Esophageal Organoid Culture Method and Organoid-Based Model of Esophageal Squamous Cell Neoplasia

Biyun Zheng,* Kyung-Pil Ko,* Xuefen Fang, Xiaozhong Wang, Jie Zhang, Sohee Jun, Bong-Jun Kim, Wenyi Luo, Moon Jong Kim, Youn-Sang Jung, Christopher L. Cervantes, Jae-Il Park

iScience   2021 Nov 15; 103440, DOI:https://doi.org/10.1016/j.isci.2021.103440, PMID: 34877497, PMC8633967. 

scRNA-seq data (GSE174577)

Supplemental Information (PDF)

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Yap/Taz-Activated Tert-Expressing Acinar Cells Are Required for Pancreatic Regeneration

Han Na Suh, Moon Jong Kim, Sung Ho Lee, Sohee Jun, Jie Zhang, Randy L Johnson, and Jae-Il Park

BioRxiv   BioRxiv 2021 Sep; doi: https://doi.org/10.1101/2021.08.30.458292

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PAF Remodels the DREAM Complex to Bypass Cell Quiescence and Promote Lung Tumorigenesis 

Moon Jong Kim, Christopher Cervantes, Youn-Sang Jung, Xiaoshan Zhang, Jie Zhang, Sung Ho Lee, Sohee Jun, Larisa Litovchick, Wenqi Wang, Junjie Chen, Bingliang Fang, and Jae-Il Park

Molecular Cell   2021 Feb 17;S1097-2765(21)00087-3, doi: 10.1016/j.molcel.2021.02.001, PMID: 33626321, PMC8052288.     Supplementary Information (PDF)

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TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis

Youn-Sang Jung, Sabrina Stratton, Sung Ho Lee, Moon Jong Kim, Sohee Jun, Jie Zhang, Biyun Zheng, Michelle C. Barton, Jae-Il Park

Hepatology   2021 Feb;73(2):776-794. doi: 10.1002/hep.31305. Epub 2020 Nov 17. PMID: 32380568; PMCID: PMC7062731.     Supplementary Information (PDF)

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A Surge of DNA Damage Links Transcriptional Reprogramming and Hematopoietic Deficit in Fanconi Anemia

Xi Shen, Rui Wang, Moon Jong Kim, Qianghua Hu, Chih-Chao Hsu, Jun Yao, Naeh Klages-Mundt, Yanyan Tian, Erica Lynn, Thomas F. Brewer, Yilei Zhang, Banu Arun, Boyi Gan, Michael Andreeff, Shunichi Takeda, Junjie Chen, Jae-il Park, Xiaobing Shi, Christopher J. Chang, Sung Yun Jung, Jun Qin, Lei Li

Molecular Cell   2020 Dec 17;80(6):1013-1024.e6. doi: 10.1016/j.molcel.2020.11.040. PubMed PMID: 33338401.

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Targeting Wnt Signaling for Gastrointestinal Cancer Therapy: Present and Evolving Views

Moon Jong Kim,* YuanJian Huang,* Jae-Il Park

Cancers (Basel)   2020 Dec 4;12(12). doi: 10.3390/cancers12123638. PubMed PMID: 33291655.

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Blockers of Wnt3a, Wnt10a or β-catenin prevent chemotherapy-induced neuropathic pain in vivo

Hee Kee Kim, Jingi Bae, Sung Ho Lee, Seon-Hee Hwang, Min-Sik Kim, Moon Jong Kim, Sohee Jun, Chris L. Cervantes, Youn-Sang Jung, Seunghoon Back, Hangyeore Lee, Seung-Eun Lee, Patrick M Dougherty, Sang-Won Lee, Jae-Il Park, Salahadin Abdi

Neurotherapeutics   2020 Oct 30. PMID: 33128175; DOI: 10.1007/s13311-020-00956-w

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Wnt Signaling in Cancer: Therapeutic Targeting of Wnt Signaling beyond β-Catenin and Destruction Complex 

Youn-Sang Jung, Jae-Il Park

Experimental Molecular Medicine   2020 Feb 10;. doi: 10.1038/s12276-020-0380-6. PMID: 32037398, PMCID: PMC7062731

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LncGata6-Controlled Stemness in Regeneration and Cancer

Youn-Sang Jung,* Moon Jong Kim,* Jae-Il Park  

Non-coding RNA Investig   pii: 4. doi: 10.21037/ncri.2019.01.02., 1/2019, PMCID: PMC6377203

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TMEM9 Promotes Intestinal Tumorigenesis via v-ATPase-Activated Wnt/β-Catenin Signaling 

Youn-Sang Jung,* Sohee Jun,* Moon Jong Kim, Sung Ho Lee, Han Na Suh, Esther M. Lien, Hae-Yun Jung, Sunhye Lee, Jie Zhang, Jung-In Yang, Hong Ji, Ji Yuan Wu, Wenqi Wang, Rachel K. Miller, Junjie Chen, Pierre D. McCrea, Scott Kopetz, Jae-Il Park 

Nature Cell Biology   20, 1421-1433, 12/2018, PMCID: PMC6261670.   Supplementary Information (PDF)

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PAF-Myc-Controlled Cell Stemness Is Required for Intestinal Regeneration and Tumorigenesis

Moon Jong Kim, Xia Bo, Han Na Suh, Sung Ho Lee, Sohee Jun, Esther M. Lien, Jie Zhang, Kaifu Chen, Jae-Il Park     

Developmental Cell   44, 582-596, 3/2018  PMCID: PMC5854208.   Supplementary Information (PDF)

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Quiescence Exit of Tert+ Stem Cells by Wnt/β-Catenin Is Indispensable for Intestinal Regeneration

Han Na Suh, Moon Jong Kim, Youn-Sang Jung, Esther M. Lien, Sohee Jun, Jae-Il Park

Cell Reports   21, 2571-2584 11/2017  PMCID: PMC5726811.     Supplementary Information (PDF)

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Identification of KIAA1199 as a Biomarker for Pancreatic Intraepithelial Neoplasia

Suh HN,* Jun S,* Oh AY, Srivastava M, Lee S, Taniguchi CM, Zhang S, Lee WS, Chen J, Park BJ, Park JI

Scientific Reports  6:38273, 12/2016.  e-Pub 12/2016. PMCID: PMC5138641

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LIG4 mediates Wnt signalling-induced radioresistance  

Jun S,* Jung YS,* Suh HN, Wang W, Kim MJ, Oh YS, Lien EM, Shen X, Matsumoto Y, McCrea PD, Li L, Chen J, Park JI

Nature Communications  7:10994, 2016.  e-Pub 3/2016. PMCID: PMC4820809

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PAF-Wnt Signaling-Induced Cell Plasticity Is Required for Maintenance of Breast Cancer Cell Stemness 

Wang X,* Jung YS,* Jun S, Lee S, Wang W, Schneider A, Sun Oh Y, Lin SH, Park BJ, Chen J, Keyomarsi K, Park JI   

Nature Communications   doi:10.1038/ncomms10633:10633, 2016.  e-Pub 2/2016. PMCID: PMC4743006

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Wnt2 complements Wnt/β-catenin signaling in colorectal cancer 

Jung YS, Jun S, Lee SH, Sharma A, Park JI

Oncotarget   6(35)(35):37257-68, 11/2015. e-Pub 10/2015. PMCID: PMC4741928.

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PAF and EZH2 Induce Wnt/β-Catenin Signaling Hyperactivation 

Jung HY, Jun S, Lee M, Kim HC, Wang X, Ji H, McCrea PD, Park JI

Molecular Cell   52(2):193-205, 10/2013. e-Pub 9/2013. PMCID: PMC4040269    

Molecular Cell Preview

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PAF-Mediated MAPK Signaling Hyperactivation via LAMTOR3 Induces Pancreatic Tumorigenesis 

Jun S, Lee SH, Kim HC, Ng C, Schneider AM, Ji H, Ying H, Wang H, DePinho RA, Park JI

Cell Reports   e-Pub 10/2013. PMCID: PMC4157353

FOXKs Promote Wnt/β-Catenin Signaling by Translocating DVL into the Nucleus 

Wang W, Li X, Lee M, Jun S, Aziz KE, Feng L, Tran MK, Li N, McCrea PD, Park JI, Chen J.

Developmental Cell   32(6):707-18, 3/2015. PMCID: PMC4374128

P120-catenin regulates REST/CoREST, and modulates mouse embryonic stem cell differentiation 

Lee M, Ji H, Furuta Y, Park JI, McCrea PD.

Journal of Cell Science  127(Pt 18):4037-51, 9/2014. e-Pub 7/2014. PMCID: PMC4163646

HIV-1 Vpr Inhibits Telomerase Activity Via EDD-DDB1-VPRB3 E3 Ligase Complex 

Wang X, Singh S, Jung HY, Yang G, Jun S, Sastry KJ, Park JI.

Journal of Biological Chemistry  288(22):15474-80, 5/2013. e-Pub 4/2013. PMCID: PMC3668709

 

Dyrk2-Associated EDD-DDB1-VprBP E3 Ligase Inhibits Telomerase by TERT Degradation 

Jung HY, Wang X, Jun S, Park JI.

Journal of Biological Chemistry   288(10):7252-62, 3/2013. e-Pub 1/2013. PMCID: PMC3591633

 

Down's-syndrome-related kinase Dyrk1A modulates the p120-catenin-Kaiso trajectory of the Wnt signaling pathway 

Hong JY, Park JI, Lee M, Muñoz WA, Miller RK, Ji H, Gu D, Ezan J, Sokol SY, McCrea PD.

Journal of Cell Science   125(Pt 3):561-9, 2/2012. PMCID: PMC3367828

 

PTPN14 is required for the density-dependent control of YAP1 

Wang W, Huang J, Wang X, Yuan J, Li X, Feng L, Park JI, Chen J.

Genes and Development   26(17):1959-71, 9/2012. PMCID: PMC3435498

 

Shared molecular mechanisms regulate multiple catenin proteins: canonical Wnt signals and components modulate p120-catenin isoform-1 and additional p120 subfamily members 

Hong JY, Park JI, Cho K, Gu D, Ji H, Artandi SE, McCrea PD.

Journal of Cell Science   123(Pt 24):4351-4365, 12/2010. e-Pub 11/2010. PMCID: PMC2995616

 

Telomerase modulates Wnt signalling by association with target gene chromatin   

Park JI, Venteicher AS, Hong JY, Choi J, Jun S, Shkreli M, Chang W, Meng Z, Cheung P, Ji H, McLaughlin M, Veenstra TD, Nusse R, McCrea PD, Artandi SE.

Nature   460 (7251):66-72, 7/2009.   PMCID: PMC4349391

Nature News and Views 

Nature Reviews Genetics Highlights 

 

Requirement of Wnt/beta-catenin signaling in pronephric kidney development  

Lyons JP, Miller RK, Zhou X, Weidinger G, Deroo T, Denayer T, Park JI, Ji H, Hong JY, Li A, Moon RT, Jones EA, Vleminckx K, Vize PD, McCrea PD.

Mechanisms of Development   e-Pub 12/2008. PMCID: PMC2684468. 126(3-4):142-59, 3/2009.

 

Developmental functions of the P120-catenin sub-family

McCrea PD, Park JI.

Biochimica et Biophysica Acta   2007; 1773(1):17-33. PMID: 16942809

 

Frodo links Dishevelled to the p120-catenin/Kaiso pathway: distinct catenin subfamilies promote Wnt signals

Park JI, Ji H, Jun S, Gu D, Hikasa H, Li L, Sokol SY, McCrea PD.

Developmental Cell   11(5):683-95, 11/2006. PMID: 17084360.

 

Kaiso/p120-catenin and TCF/beta-catenin complexes coordinately regulate canonical Wnt gene targets 

Park JI, Kim SW, Lyons JP, Ji H, Nguyen TT, Cho K, Barton MC, Deroo T, Vleminckx K, Moon RT, McCrea PD.

Developmental Cell   8(6):843-54, 6/2005. PMID: 15935774.

Developmental Cell Preview

Non-canonical Wnt signals are modulated by the Kaiso transcriptional repressor and p120-catenin 

Kim SW, Park JI, Spring CM, Sater AK, Ji H, Otchere AA, Daniel JM, McCrea PD.

Nature Cell Biology    6(12):1212-20, 12/2004.  e-Pub 11/2004. PMID: 15543138.

 

 

Vertebrate development requires ARVCF and p120 catenins and their interplay with RhoA and Rac 

Fang X, Ji H, Kim SW, Park JI, Vaught TG, Anastasiadis PZ, Ciesiolka M, McCrea PD.

Journal of Cell Biology   165(1):87-98, 4/2004. e-Pub 4/2004. PMCID: PMC2172091.

 

Transforming growth factor-beta1 activates interleukin-6 expression in prostate cancer cells through the synergistic collaboration of the Smad2, p38-NF-kappaB, JNK, and Ras signaling pathways 

Park JI, Lee MG, Cho K, Park BJ, Chae KS, Byun DS, Ryu BK, Park YK, Chi SG.

Oncogene   22(28):4314-32, 7/2003. PMID: 12853969.

 

Frequent monoallelic deletion of PTEN and its reciprocal association with PIK3CA amplification in gastric carcinoma 

Byun DS, Cho K, Ryu BK, Lee MG, Park JI, Chae KS, Kim HJ, Chi SG.

International Journal of Cancer   104(3):318-27, 4/2003. PMID: 12569555.

 

Mitogenic conversion of transforming growth factor-beta1 effect by oncogenic Ha-Ras-induced activation of the mitogen-activated protein kinase signaling pathway in human prostate cancer

Park BJ, Park JI, Byun DS, Park JH, Chi SG.

Cancer Research   60(11):3031-8, 6/2000. PMID: 10850453.

 

Loss of imprinting and elevated expression of wild-type p73 in human gastric adenocarcinoma 

Kang MJ, Park BJ, Byun DS, Park JI, Kim HJ, Park JH, Chi SG.

Clinical Cancer Research   6(5):1767-71, 5/2000. PMID: 10815895.

 

 

*Equally contributed authors.

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