Howard Chang

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
    Rajnish A Gupta
    Howard Hughes Medical Institute and Program in Epithelial Biology, California 94305, USA
    Nature 464:1071-6. 2010
  2. pmc Dynamic chromatin localization of Sirt6 shapes stress- and aging-related transcriptional networks
    Tiara L A Kawahara
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 7:e1002153. 2011
  3. pmc Identification of proteins binding coding and non-coding human RNAs using protein microarrays
    Zurab Siprashvili
    The Program in Epithelial Biology, Stanford University School of Medicine, 269 Campus Drive, Room 2145, Stanford, CA 94305, USA
    BMC Genomics 13:633. 2012
  4. pmc Predicting a local recurrence after breast-conserving therapy by gene expression profiling
    Dimitry S A Nuyten
    Department of Radiation Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Breast Cancer Res 8:R62. 2006
  5. ncbi request reprint Anatomic demarcation of cells: genes to patterns
    Howard Y Chang
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 326:1206-7. 2009
  6. ncbi request reprint Patterning skin pigmentation via dickkopf
    Howard Y Chang
    Program in Epithelial Biology, Stanford University, Stanford, California 94305, USA
    J Invest Dermatol 127:994-5. 2007
  7. doi request reprint A systems biology approach to anatomic diversity of skin
    John L Rinn
    Department of Dermatology, Stanford University, Stanford, California, USA
    J Invest Dermatol 128:776-82. 2008
  8. pmc A dermal HOX transcriptional program regulates site-specific epidermal fate
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 22:303-7. 2008
  9. pmc Anatomic demarcation by positional variation in fibroblast gene expression programs
    John L Rinn
    Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Genet 2:e119. 2006
  10. pmc The histone demethylase UTX enables RB-dependent cell fate control
    Jordon K Wang
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 24:327-32. 2010

Research Grants

  1. Structural Motifs in RNA
    Howard Chang; Fiscal Year: 2009
  2. Simplified Diagnosis of a Prognostic Wound Response Signature in Breast Cancer
    Howard Chang; Fiscal Year: 2007
  3. Wound Response Genes in Cancer Progression
    Howard Chang; Fiscal Year: 2009
  4. Structural Motifs in RNA
    Howard Chang; Fiscal Year: 2007
  5. Wound Response Genes in Cancer Progression
    Howard Chang; Fiscal Year: 2007
  6. Gene Expression Programs in Fibroblast Differentiation
    Howard Chang; Fiscal Year: 2007
  7. Wound Response Genes in Cancer Progression
    Howard Y Chang; Fiscal Year: 2010

Collaborators

Detail Information

Publications39

  1. pmc Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
    Rajnish A Gupta
    Howard Hughes Medical Institute and Program in Epithelial Biology, California 94305, USA
    Nature 464:1071-6. 2010
    ..These findings indicate that lincRNAs have active roles in modulating the cancer epigenome and may be important targets for cancer diagnosis and therapy...
  2. pmc Dynamic chromatin localization of Sirt6 shapes stress- and aging-related transcriptional networks
    Tiara L A Kawahara
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 7:e1002153. 2011
    ..These data suggest dynamic chromatin relocalization of Sirt6 as a key output of NF-κB signaling in stress response and aging...
  3. pmc Identification of proteins binding coding and non-coding human RNAs using protein microarrays
    Zurab Siprashvili
    The Program in Epithelial Biology, Stanford University School of Medicine, 269 Campus Drive, Room 2145, Stanford, CA 94305, USA
    BMC Genomics 13:633. 2012
    ..To overcome these limitations, we have developed a rapid and large-scale approach to characterize binding of in vitro transcribed labeled RNA to ~9,400 human recombinant proteins spotted on protein microarrays...
  4. pmc Predicting a local recurrence after breast-conserving therapy by gene expression profiling
    Dimitry S A Nuyten
    Department of Radiation Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Breast Cancer Res 8:R62. 2006
    ..Here we have used gene expression profiling by microarray analysis to identify gene expression profiles that can help to predict local recurrence in individual patients...
  5. ncbi request reprint Anatomic demarcation of cells: genes to patterns
    Howard Y Chang
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 326:1206-7. 2009
    ..Dynamic chromatin states of key genes, notably the Hox loci, serve as the internal representation in cells of their positional identity within the animal...
  6. ncbi request reprint Patterning skin pigmentation via dickkopf
    Howard Y Chang
    Program in Epithelial Biology, Stanford University, Stanford, California 94305, USA
    J Invest Dermatol 127:994-5. 2007
    ..The results provide a plethora of candidate genes that may mediate DKK1's inhibitory effects on melanocyte function...
  7. doi request reprint A systems biology approach to anatomic diversity of skin
    John L Rinn
    Department of Dermatology, Stanford University, Stanford, California, USA
    J Invest Dermatol 128:776-82. 2008
    ..The use of gene, tiling, and tissue microarrays together gives a comprehensive view of the gene regulation involved in patterning the skin...
  8. pmc A dermal HOX transcriptional program regulates site-specific epidermal fate
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 22:303-7. 2008
    ..Thus, maintenance of appropriate HOX transcriptional program in adult fibroblasts may serve as a source of positional memory to differentially pattern the epithelia during homeostasis and regeneration...
  9. pmc Anatomic demarcation by positional variation in fibroblast gene expression programs
    John L Rinn
    Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Genet 2:e119. 2006
    ..Together, these findings suggest that site-specific variations in fibroblast gene expression programs are not idiosyncratic but rather are systematically related to their positional identities relative to major anatomic axes...
  10. pmc The histone demethylase UTX enables RB-dependent cell fate control
    Jordon K Wang
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 24:327-32. 2010
    ..Thus, UTX defines an evolutionarily conserved mechanism to enable coordinate transcription of a RB network in cell fate control...
  11. pmc Module map of stem cell genes guides creation of epithelial cancer stem cells
    David J Wong
    Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
    Cell Stem Cell 2:333-44. 2008
    ..Thus, activation of an ESC-like transcriptional program in differentiated adult cells may induce pathologic self-renewal characteristic of cancer stem cells...
  12. pmc Diversity, topographic differentiation, and positional memory in human fibroblasts
    Howard Y Chang
    Departments of Dermatology, Biochemistry, Pathology, and Genetics, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:12877-82. 2002
    ....
  13. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 129:1311-23. 2007
    ..Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states...
  14. pmc Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds
    Howard Y Chang
    Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E7. 2004
    ..Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas...
  15. pmc SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span
    Tiara L A Kawahara
    Program in Epithelial Biology, Division of Endocrinology, Gerontology, and Metabolism, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 136:62-74. 2009
    ..We propose that SIRT6 attenuates NF-kappaB signaling via H3K9 deacetylation at chromatin, and hyperactive NF-kappaB signaling may contribute to premature and normal aging...
  16. ncbi request reprint MYC can induce DNA breaks in vivo and in vitro independent of reactive oxygen species
    Suma Ray
    Division of Oncology, Department of Medicine and Pathology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA
    Cancer Res 66:6598-605. 2006
    ..Hence, MYC overexpression can induce ROS and SSBs under some conditions, but generally induces widespread DSBs in vivo and in vitro independent of ROS production...
  17. pmc Endothelial cell diversity revealed by global expression profiling
    Jen Tsan Chi
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:10623-8. 2003
    ..Tissue-specific expression patterns in different tissue microvascular ECs suggest they are distinct differentiated cell types that play roles in the local physiology of their respective organs and tissues...
  18. pmc A transcriptional program mediating entry into cellular quiescence
    Helen Liu
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 3:e91. 2007
    ..These results identify a gene expression program uniquely responsive to loss of growth factor signaling; members of SDERGs may constitute novel growth inhibitors that prevent cancer...
  19. pmc SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin
    Eriko Michishita
    Department of Medicine, Division of Endocrinology, Gerontology and Metabolism, School of Medicine, Stanford University, Stanford, California 94305, USA
    Nature 452:492-6. 2008
    ..Our findings constitute the first identification of a physiological enzymatic activity of SIRT6, and link chromatin regulation by SIRT6 to telomere maintenance and a human premature ageing syndrome...
  20. pmc Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation
    Julie B Sneddon
    Department of Biochemistry, Stanford University Medical Center, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:14842-7. 2006
    ..Our data suggest that BMP antagonists may be important constituents of tumor stroma, providing a favorable microenvironment for cancer cell survival and expansion in many cancers...
  21. pmc Molecular framework for response to imatinib mesylate in systemic sclerosis
    Lorinda Chung
    Stanford University, Stanford, California, and VA Palo Alto Health Care System, Palo Alto, California
    Arthritis Rheum 60:584-91. 2009
    ....
  22. ncbi request reprint From description to causality: mechanisms of gene expression signatures in cancer
    Adam S Adler
    Program in Epithelial Biology and Cancer Biology Program, Stanford University School of Medicine, Stanford, California 94305, USA
    Cell Cycle 5:1148-51. 2006
    ..Applying SLAMS on a poor-prognosis wound signature in human breast cancer, we identified CSN5-mediated ubiquitination of MYC as a novel mechanism to activate a biological program favoring metastasis...
  23. pmc Long noncoding RNA as modular scaffold of histone modification complexes
    Miao Chih Tsai
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 329:689-93. 2010
    ..Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes...
  24. pmc Regeneration, repair and remembering identity: the three Rs of Hox gene expression
    Kevin C Wang
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Trends Cell Biol 19:268-75. 2009
    ..Strategies to manipulate the plasticity of Hox gene expression will probably become a major focus in regenerative medicine...
  25. pmc Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells
    Tim C P Somervaille
    Department of Pathology, Stanford University, Stanford, CA 94305, USA Cancer Research UK Leukaemia Biology Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
    Cell Stem Cell 4:129-40. 2009
    ....
  26. pmc Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival
    Howard Y Chang
    Program in Epithelial Biology, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:3738-43. 2005
    ....
  27. pmc ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation
    Tiffany Hung
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Mol Cell 33:248-56. 2009
    ..Together, our results demonstrate a mechanism for brokering crosstalk between H3K4 methylation and H3 acetylation and reveal a molecular link between chromatin modulation and tumor suppressor mechanisms...
  28. ncbi request reprint Stemness, cancer and cancer stem cells
    David J Wong
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Cell Cycle 7:3622-4. 2008
    ..The ability to create induced cancer stem cells (iCSC) may provide opportunities to better define the biology of cancer stem cells in order to trace or eliminate them in human patients...
  29. ncbi request reprint Microarray analysis of stem cells and differentiation
    Howard Y Chang
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
    Methods Enzymol 420:225-54. 2006
    ..We also detail examples that apply microarray technology to address several of the main questions in stem cell biology...
  30. pmc Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3
    George L Sen
    VA Palo Alto Health Care System, Palo Alto, California 94305, USA
    Genes Dev 22:1865-70. 2008
    ..Within epidermal tissue, JMJD3 depletion blocked differentiation, while active JMJD3 dominantly induced it. These results indicate that epigenetic derepression by JMJD3 controls mammalian epidermal differentiation...
  31. ncbi request reprint Reversal of aging by NFkappaB blockade
    Adam S Adler
    Program in Epithelial Biology and Cancer Biology Program, Stanford University School of Medicine, Stanford, California 94305, USA
    Cell Cycle 7:556-9. 2008
    ....
  32. pmc Motif module map reveals enforcement of aging by continual NF-kappaB activity
    Adam S Adler
    Program in Epithelial Biology and Cancer Biology Program, Stanford University School of Medicine, Stanford, California 94305, USA
    Genes Dev 21:3244-57. 2007
    ..These results identify a conserved network of regulatory pathways underlying mammalian aging and show that NF-kappaB is continually required to enforce many features of aging in a tissue-specific manner...
  33. doi request reprint Revealing targeted therapy for human cancer by gene module maps
    David J Wong
    Programs in Epithelial Biology, Stanford University, Stanford, California 94305, USA
    Cancer Res 68:369-78. 2008
    ..Thus, gene module maps may enable rapid translation of complex genomic signatures in human disease to targeted therapeutic strategies...
  34. pmc Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs
    Henriette O'Geen
    Department of Pharmacology, University of California Davis, Davis, California, United States of America
    PLoS Genet 3:e89. 2007
    ..Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1...
  35. pmc Systematic functional characterization of cis-regulatory motifs in human core promoters
    Saurabh Sinha
    Department of Computer Science, University of Illinois Urbana Champaign, Urbana, Illinois 61801, USA
    Genome Res 18:477-88. 2008
    ..Our analysis thus provides a concrete framework for uncovering the biological function of cis-regulatory motifs genome wide...
  36. pmc Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire
    Maureen A Su
    Diabetes Center, Department of Pediatric, UCSF, San Francisco, California 94143, USA
    J Clin Invest 118:1712-26. 2008
    ..Together, these results may demonstrate a mechanism by which autoimmune predisposition to phenotypes distinct from APS 1 can be mediated in a dominant-negative fashion by Aire...
  37. pmc Deletional tolerance mediated by extrathymic Aire-expressing cells
    James M Gardner
    Diabetes Center, University of California San Francisco UCSF, San Francisco, CA 94122, USA
    Science 321:843-7. 2008
    ..We propose that such a secondary network of self-antigen-expressing stromal cells may help reinforce immune tolerance by preventing the maturation of autoreactive T cells that escape thymic negative selection...

Research Grants10

  1. Structural Motifs in RNA
    Howard Chang; Fiscal Year: 2009
    ..A deep and comprehensive understanding of the gene expression program would help to reveal the mechanisms of many human diseases exhibiting faulty gene expression, and allow their diagnosis and intervention with newfound precision. ..
  2. Simplified Diagnosis of a Prognostic Wound Response Signature in Breast Cancer
    Howard Chang; Fiscal Year: 2007
    ..Improved technology to identify the wound response genes in breast cancer will improve the risk assessment of breast cancer patients and better guide patients to appropriate therapies. ..
  3. Wound Response Genes in Cancer Progression
    Howard Chang; Fiscal Year: 2009
    ..Research on the wound response genes in breast cancer will help to improve the risk assessment of breast cancer patients and identify targets for cancer therapy. ..
  4. Structural Motifs in RNA
    Howard Chang; Fiscal Year: 2007
    ..A deep and comprehensive understanding of the gene expression program would help to reveal the mechanisms of many human diseases exhibiting faulty gene expression, and allow their diagnosis and intervention with newfound precision. ..
  5. Wound Response Genes in Cancer Progression
    Howard Chang; Fiscal Year: 2007
    ..Research on the wound response genes in breast cancer will help to improve the risk assessment of breast cancer patients and identify targets for cancer therapy. ..
  6. Gene Expression Programs in Fibroblast Differentiation
    Howard Chang; Fiscal Year: 2007
    ..abstract_text> ..
  7. Wound Response Genes in Cancer Progression
    Howard Y Chang; Fiscal Year: 2010
    ..Research on the wound response genes in breast cancer will help to improve the risk assessment of breast cancer patients and identify targets for cancer therapy. ..