Xin Chen

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi Hydrodynamic transfection for generation of novel mouse models for liver cancer research
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California Liver Center, University of California, San Francisco, California Electronic address
    Am J Pathol 184:912-23. 2014
  2. pmc Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer
    Biao Fan
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e29824. 2012
  3. pmc Bmi1 is required for hepatic progenitor cell expansion and liver tumor development
    Lingling Fan
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e46472. 2012
  4. pmc New tools for functional genomic analysis
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
    Drug Discov Today 14:754-60. 2009
  5. pmc Indian hedgehog regulates intestinal stem cell fate through epithelial-mesenchymal interactions during development
    Cynthia Kosinski
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
    Gastroenterology 139:893-903. 2010
  6. pmc Inactivation of Spry2 accelerates AKT-driven hepatocarcinogenesis via activation of MAPK and PKM2 pathways
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    J Hepatol 57:577-83. 2012
  7. doi Integration of genomic analysis and in vivo transfection to identify sprouty 2 as a candidate tumor suppressor in liver cancer
    Susie A Lee
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Hepatology 47:1200-10. 2008
  8. pmc Role of cyclin D1 as a mediator of c-Met- and beta-catenin-induced hepatocarcinogenesis
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0446, USA
    Cancer Res 69:253-61. 2009
  9. pmc Bmi1 functions as an oncogene independent of Ink4A/Arf repression in hepatic carcinogenesis
    Chuan Rui Xu
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Mol Cancer Res 7:1937-45. 2009
  10. pmc Functional crosstalk between AKT/mTOR and Ras/MAPK pathways in hepatocarcinogenesis: implications for the treatment of human liver cancer
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, San Francisco, CA, USA
    Cell Cycle 12:1999-2010. 2013

Collaborators

Detail Information

Publications35

  1. ncbi Hydrodynamic transfection for generation of novel mouse models for liver cancer research
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California Liver Center, University of California, San Francisco, California Electronic address
    Am J Pathol 184:912-23. 2014
    ..Furthermore, it can be used as an in vivo transfection method to study biochemical cross talks among multiple pathways along hepatocarcinogenesis and to test the therapeutic potential of drugs against liver cancer...
  2. pmc Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer
    Biao Fan
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e29824. 2012
    ..It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level...
  3. pmc Bmi1 is required for hepatic progenitor cell expansion and liver tumor development
    Lingling Fan
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e46472. 2012
    ..Our study also provides the evidence, for the first time, that Bmi1 expression is required for liver cancer development in vivo, thus representing a promising target for innovative treatments against human liver cancer...
  4. pmc New tools for functional genomic analysis
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
    Drug Discov Today 14:754-60. 2009
    ..Using human liver cancer as an example, we provide further information of how these genomic approaches can be applied in cancer research...
  5. pmc Indian hedgehog regulates intestinal stem cell fate through epithelial-mesenchymal interactions during development
    Cynthia Kosinski
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
    Gastroenterology 139:893-903. 2010
    ..We examined the role of Indian hedgehog (Ihh) in mesenchymal organization and the mechanisms by which perturbations in epithelial-mesenchymal interactions affect ISC fate...
  6. pmc Inactivation of Spry2 accelerates AKT-driven hepatocarcinogenesis via activation of MAPK and PKM2 pathways
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    J Hepatol 57:577-83. 2012
    ..The goal of the present study was to investigate the eventual biochemical and genetic crosstalk between activated AKT and inactivation of Spry2 during liver cancer development by using in vivo and in vitro approaches...
  7. doi Integration of genomic analysis and in vivo transfection to identify sprouty 2 as a candidate tumor suppressor in liver cancer
    Susie A Lee
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Hepatology 47:1200-10. 2008
    ..In addition, we demonstrate that the integration of genomic analysis and in vivo transfection is a powerful tool to identify genes that are important during hepatic carcinogenesis...
  8. pmc Role of cyclin D1 as a mediator of c-Met- and beta-catenin-induced hepatocarcinogenesis
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0446, USA
    Cancer Res 69:253-61. 2009
    ..Moreover, our data suggest that CCND1 expression is not essential for liver tumor development induced by c-Met and beta-catenin...
  9. pmc Bmi1 functions as an oncogene independent of Ink4A/Arf repression in hepatic carcinogenesis
    Chuan Rui Xu
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Mol Cancer Res 7:1937-45. 2009
    ..In summary, our study shows that Bmi1 can cooperate with other oncogenic signals to promote hepatic carcinogenesis in vivo. Yet Bmi1 functions independent of Ink4A/Arf repression in liver cancer development...
  10. pmc Functional crosstalk between AKT/mTOR and Ras/MAPK pathways in hepatocarcinogenesis: implications for the treatment of human liver cancer
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, San Francisco, CA, USA
    Cell Cycle 12:1999-2010. 2013
    ....
  11. pmc Synergistic role of Sprouty2 inactivation and c-Met up-regulation in mouse and human hepatocarcinogenesis
    Susie A Lee
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
    Hepatology 52:506-17. 2010
    ..Coordinated deregulation of Spry2 and c-Met signaling may be a pivotal oncogenic mechanism responsible for unrestrained activation of ERK and AKT pathways in human hepatocarcinogenesis...
  12. pmc Cholangiocarcinomas can originate from hepatocytes in mice
    Biao Fan
    Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
    J Clin Invest 122:2911-5. 2012
    ..Our findings suggest a previously overlooked mechanism of human ICC formation that may be targetable for anti-ICC therapy...
  13. ncbi Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Carcinogenesis 26:2050-7. 2005
    ....
  14. pmc AKT (v-akt murine thymoma viral oncogene homolog 1) and N-Ras (neuroblastoma ras viral oncogene homolog) coactivation in the mouse liver promotes rapid carcinogenesis by way of mTOR (mammalian target of rapamycin complex 1), FOXM1 (forkhead box M1)/SKP2,
    Coral Ho
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    Hepatology 55:833-45. 2012
    ....
  15. doi Chromosomal changes in fibrolamellar hepatocellular carcinoma detected by array comparative genomic hybridization
    Sanjay Kakar
    Department of Pathology, University of California, San Francisco, CA, USA
    Mod Pathol 22:134-41. 2009
    ..The favorable outcome in some fibrolamellar carcinomas may be due to absent or low number of cytogenetic aberrations...
  16. pmc SCD1 Expression is dispensable for hepatocarcinogenesis induced by AKT and Ras oncogenes in mice
    Lei Li
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
    PLoS ONE 8:e75104. 2013
    ..Complete inhibition of stearoyl-CoA desaturase activity may be required to efficiently suppress liver tumor development...
  17. ncbi Hedgehog signaling in human hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences and Liver Center, University of California, San Francisco, California 94143 0446, USA
    Cancer Biol Ther 5:111-7. 2006
    ..The study therefore, for the first time, provides evidence that hedgehog signaling may be activated in some HCC tumors. The results also indicate that the hedgehog pathway may be a new candidate for therapeutic targeting in HCC...
  18. pmc Gene expression patterns in pancreatic tumors, cells and tissues
    Anson W Lowe
    Department of Medicine, Stanford University Medical Center, Stanford, California, United States of America
    PLoS ONE 2:e323. 2007
    ..This study provides a comprehensive assessment of gene expression for pancreatic tumors, the normal pancreas, and nonneoplastic pancreatic disease...
  19. pmc MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancer
    Lionel Lim
    Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA Department of Medicine, University of California San Francisco, San Francisco, CA
    Hepatology 59:202-15. 2014
    ..Conclusion: Our findings identify a new therapeutic target (miR-494) for the treatment of HCC...
  20. pmc Chromosomal abnormalities determined by comparative genomic hybridization are helpful in the diagnosis of atypical hepatocellular neoplasms
    Sanjay Kakar
    Department of Pathology, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
    Histopathology 55:197-205. 2009
    ..To explore the utility of cytogenetic abnormalities in the distinction of hepatic adenoma (HA) and well-differentiated hepatocellular carcinoma (HCC)...
  21. ncbi An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Oncogene 24:3737-47. 2005
    ..This approach of integrating other biological information with gene expression in the analysis helps select aberrantly expressed genes in HCC that may be further studied for their diagnostic or therapeutic utility...
  22. pmc Polycomb group genes Psc and Su(z)2 maintain somatic stem cell identity and activity in Drosophila
    Jose Rafael Morillo Prado
    Department of Developmental Biology, School of Medicine, Stanford University, Stanford, California, United States of America
    PLoS ONE 7:e52892. 2012
    ..Furthermore, we show that tumorigenesis in the CySC lineage interferes non-cell autonomously with maintenance of GSCs most likely by displacing them from their niche...
  23. pmc Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors
    Cynthia Kosinski
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:15418-23. 2007
    ..Our study also suggests that BMP antagonists are candidate signaling components that make up the intestinal epithelial stem cell niche...
  24. pmc Distinct pathways of genomic progression to benign and malignant tumors of the liver
    Aaron D Tward
    G W Hooper Foundation and Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:14771-6. 2007
    ....
  25. pmc Oncogene-specific formation of chemoresistant murine hepatic cancer stem cells
    Edward Kai Hua Chow
    Department of Microbiology and Immunology, G W Hooper Research Foundation, University of California, San Francisco, CA 94143, USA
    Hepatology 56:1331-41. 2012
    ..Accordingly, SP cells and their tumor-initiating subset were more resistant than non-SP cells to chemotherapeutics that are effluxed by MDR1...
  26. pmc S-nitrosylation from GSNOR deficiency impairs DNA repair and promotes hepatocarcinogenesis
    Wei Wei
    Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
    Sci Transl Med 2:19ra13. 2010
    ..Thus, our data suggest that GSNOR deficiency, through dysregulated S-nitrosylation, may promote HCC, possibly by inactivating a DNA repair system...
  27. doi Dynamics of MRI-Guided thermal ablation of VX2 tumor in paraspinal muscle of rabbits
    Xin Chen
    Radiation Oncology Department, University of California at San Francisco, 1600 Divisadero Street, Suite 0130, San Francisco, CA 94115, USA
    IEEE Trans Biomed Eng 55:1004-14. 2008
    ..The combined use of MR image monitoring and model simulation has the potential for improving pretreatment planning and real-time prediction of lesion-size dynamics for guidance of thermal ablation of tumors...
  28. ncbi RNA interference as therapeutics for hepatocellular carcinoma
    Chuanrui Xu
    Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA 94143, USA
    Recent Pat Anticancer Drug Discov 6:106-15. 2011
    ..Here, we summarized the progress of RNAi therapeutics in HCC treatment, relevant patents, potential challenges and prospects in the future...
  29. pmc Expression changes in the stroma of prostate cancer predict subsequent relapse
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 7:e41371. 2012
    ..This is the first general tumor microenvironment-based prognostic classifier. These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for predicting outcomes for patients...
  30. pmc The metabolic profile of tumors depends on both the responsible genetic lesion and tissue type
    Mariia O Yuneva
    G W Hooper Research Foundation, University of California, San Francisco, San Francisco, CA 94143, USA
    Cell Metab 15:157-70. 2012
    ..Our results suggest that the metabolic profiles of tumors are likely to depend on both the genotype and tissue of origin and have implications regarding the design of therapies targeting tumor metabolism...
  31. ncbi DNACompress: fast and effective DNA sequence compression
    Xin Chen
    Computer Science Department, University of California, Santa Barbara, CA 99106, USA
    Bioinformatics 18:1696-8. 2002
    ..While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs...
  32. ncbi MSOAR: a high-throughput ortholog assignment system based on genome rearrangement
    Zheng Fu
    Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
    J Comput Biol 14:1160-75. 2007
    ..These test results indicate that our approach is very promising for genome-wide ortholog assignment. Supplemental material and MSOAR program are available at http://msoar.cs.ucr.edu...
  33. ncbi Radiogenomic analysis to identify imaging phenotypes associated with drug response gene expression programs in hepatocellular carcinoma
    Michael D Kuo
    Department of Radiology, University of California, San Diego Medical Center, San Diego, CA 92103, USA
    J Vasc Interv Radiol 18:821-31. 2007
    ....
  34. ncbi Assignment of orthologous genes via genome rearrangement
    Xin Chen
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:302-15. 2005
    ..The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs...
  35. doi Optimisation-based thermal treatment planning for catheter-based ultrasound hyperthermia
    Xin Chen
    Thermal Therapy Research Group, Department of Radiation Oncology, University of California at San Francisco, San Francisco, California 94143 1708, USA
    Int J Hyperthermia 26:39-55. 2010
    ....