Ite A Laird-Offringa

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc The role of DNA methylation in the development and progression of lung adenocarcinoma
    Keith M Kerr
    Department of Pathology, Aberdeen Royal Infirmary, Link Building, Foresterhill, Aberdeen, AB25 2ZN, UK
    Dis Markers 23:5-30. 2007
  2. pmc The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
    Michael J Law
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089 9176, USA
    Nucleic Acids Res 34:275-85. 2006
  3. pmc Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction
    Michael J Law
    Department of Biochemistry and Molecular Biology, University of Southern California Los Angeles, CA 90089 9176, USA
    Nucleic Acids Res 33:2917-28. 2005
  4. pmc Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Mol Cancer 6:70. 2007
  5. ncbi request reprint Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA
    Phinikoula S Katsamba
    Norris Cancer Center University of Southern California, Keck School of Medicine, Los Angeles, California 90089 9176, USA
    J Biol Chem 277:33267-74. 2002
  6. pmc DNA methylation profile of 28 potential marker loci in malignant mesothelioma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery, Keck School of Medicine, University of Southern California, Room NOR6420, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Lung Cancer 58:220-30. 2007
  7. pmc Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer
    Paul P Anglim
    Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089 9176, USA
    Mol Cancer 7:62. 2008
  8. ncbi request reprint Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and Biochemistry, Room NOR 6420, 1441 Eastlake Ave, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Lung Cancer 47:193-204. 2005
  9. pmc Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
    Suhaida A Selamat
    Department of Surgery, Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Genome Res 22:1197-211. 2012
  10. pmc DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma
    Suhaida A Selamat
    Department of Surgery, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 6:e21443. 2011

Research Grants

Collaborators

Detail Information

Publications32

  1. pmc The role of DNA methylation in the development and progression of lung adenocarcinoma
    Keith M Kerr
    Department of Pathology, Aberdeen Royal Infirmary, Link Building, Foresterhill, Aberdeen, AB25 2ZN, UK
    Dis Markers 23:5-30. 2007
    ....
  2. pmc The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
    Michael J Law
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089 9176, USA
    Nucleic Acids Res 34:275-85. 2006
    ..Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein-RNA complexes...
  3. pmc Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction
    Michael J Law
    Department of Biochemistry and Molecular Biology, University of Southern California Los Angeles, CA 90089 9176, USA
    Nucleic Acids Res 33:2917-28. 2005
    ..A quadruple stack, sandwiching two bases between Phe56 and Asp92, would occur last and coincide with the rearrangement of a C-terminal helix that partially occludes the RRM surface in the free protein...
  4. pmc Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Mol Cancer 6:70. 2007
    ....
  5. ncbi request reprint Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA
    Phinikoula S Katsamba
    Norris Cancer Center University of Southern California, Keck School of Medicine, Los Angeles, California 90089 9176, USA
    J Biol Chem 277:33267-74. 2002
    ..Our results indicate that one of the roles of the beta(2)-beta(3) loop is to provide a steric fit into the RNA loop, thereby stabilizing the RNA.protein complex...
  6. pmc DNA methylation profile of 28 potential marker loci in malignant mesothelioma
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery, Keck School of Medicine, University of Southern California, Room NOR6420, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Lung Cancer 58:220-30. 2007
    ....
  7. pmc Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer
    Paul P Anglim
    Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089 9176, USA
    Mol Cancer 7:62. 2008
    ....
  8. ncbi request reprint Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung
    Jeffrey A Tsou
    Norris Cancer Center and Department of Surgery and Biochemistry, Room NOR 6420, 1441 Eastlake Ave, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Lung Cancer 47:193-204. 2005
    ..Our observations support the strong potential of methylation markers as tools for accurate diagnosis of neoplasms in and around the lung...
  9. pmc Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
    Suhaida A Selamat
    Department of Surgery, Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Genome Res 22:1197-211. 2012
    ....
  10. pmc DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma
    Suhaida A Selamat
    Department of Surgery, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 6:e21443. 2011
    ..Delineating when abnormal DNA methylation arises may provide insight into the natural history of lung adenocarcinoma and the role that DNA methylation alterations play in tumor formation...
  11. ncbi request reprint A comparison of cluster analysis methods using DNA methylation data
    Kimberly D Siegmund
    Department of Preventive Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA
    Bioinformatics 20:1896-904. 2004
    ..Established tools to analyze this type of data do not exist. Here, we evaluate a variety of methods for cluster analysis to determine which is most reliable...
  12. ncbi request reprint Cross-species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-specific Genes
    Crystal N Marconett
    University of Southern California, Surgery, Los Angeles, California, United States
    Am J Respir Cell Mol Biol . 2016
    ..Utilizing GRAMD2 as a new AT1 cell-specific gene will enhance AT1 cell isolation, investigation of alveolar epithelial cell differentiation potential, and contribution of AT1 cells to distal lung diseases...
  13. pmc The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA
    Michael J Law
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 41:7092-100. 2013
    ..These data provide new insights into the mechanism whereby sequences C-terminal to an RRM can influence RNA binding. ..
  14. pmc DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation
    Yongheng Chen
    Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
    Cell Rep 2:1197-206. 2012
    ..These findings not only provide insights into the structure and function of GATA proteins but also shed light on the molecular basis of long-range gene regulation...
  15. pmc CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer
    Kit W Tam
    Hamon Center for Therapeutic Oncology Research and Division of Biostatistics, University of Texas Southwestern Medical Center, Dallas, Texas Department of Integrative Oncology, British Columbia Cancer Agency Research Centre, Vancouver, B C, Canada Texas Scottish Rite Hospital for Children, Dallas, Texas Department of Surgery, Biochemistry, and Molecular Biology, Keck School of Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, California Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington Oncology Biomarker Development, Genentech Inc, South San Francisco, California Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Dallas, Texas and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
    J Thorac Oncol 8:1378-88. 2013
    ..Although p16 promoter methylation has been linked to KRAS mutation and smoking, the associations between p16 inactivation mechanisms and other common genetic mutations and smoking status are still controversial or unknown...
  16. pmc The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA
    Michael J Law
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    RNA 12:1168-78. 2006
    ..While binding of U1A to a single stranded target is much weaker than to U1hpII, it occurs with nanomolar affinity, supporting recent evidence that binding of unstructured RNA by U1A has physiological significance...
  17. pmc Low level anti-Hu reactivity: A risk marker for small cell lung cancer?
    Jeffrey A Tsou
    Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Cancer Detect Prev 32:292-9. 2009
    ....
  18. ncbi request reprint Kinetic studies of RNA-protein interactions using surface plasmon resonance
    Phinikoula S Katsamba
    Keck School of Medicine, University of Southern California Norris Cancer Center, MC 9176, Room NOR6420, 1441 Eastlake Avenue, Los Angeles 90089 9176, USA
    Methods 26:95-104. 2002
    ..In addition, we present examples to illustrate how kinetic studies have provided us with unique insights into the interaction of the spliceosomal U1A protein and the neuronal HuD protein with their respective RNA targets...
  19. ncbi request reprint Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target
    Carina Johansson
    Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1569, USA
    J Mol Biol 337:799-816. 2004
    ..The less stable interaction of RBD12 with the natural RNA target is consistent with the proposed role of nucleolin as a chaperone that interacts transiently with pre-rRNA to prevent misfolding...
  20. pmc Classification of individual lung cancer cell lines based on DNA methylation markers: use of linear discriminant analysis and artificial neural networks
    Alberto M Marchevsky
    Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center, Los Angeles, California, USA
    J Mol Diagn 6:28-36. 2004
    ..Our work supports the promise of ANN analysis of DNA methylation data as a powerful approach for the development of automated methods for lung cancer classification...
  21. pmc Immune response in lung cancer mouse model mimics human anti-Hu reactivity
    Meleeneh Kazarian
    Departments of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California Norris Cancer Center, 1441 Eastlake Ave NOR 6420, Norris Cancer Center, Los Angeles, CA 90089, United States
    J Neuroimmunol 217:38-45. 2009
    ..This mouse model system will be useful to study SCLC-associated autoimmunity, its diagnostic value, and the potential protective role of oncoantigen-directed autoantibodies...
  22. pmc Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation
    Crystal N Marconett
    Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
    PLoS Genet 9:e1003513. 2013
    ..Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation. ..
  23. pmc Genome-scale screen for DNA methylation-based detection markers for ovarian cancer
    Mihaela Campan
    Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 6:e28141. 2011
    ..We developed a systematic multi-step biomarker discovery and verification strategy to identify candidate DNA methylation markers for the blood-based detection of ovarian cancer...
  24. pmc Conformationally restricted nucleotides as a probe of structure-function relationships in RNA
    Kristine R Julien
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
    RNA 14:1632-43. 2008
    ..Functional insights obtained in all three systems demonstrate the highly general applicability of LNA probing in analysis of the role of ribose orientation in RNA structure, dynamics, and function...
  25. pmc DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update
    Paul P Anglim
    Departments of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 9176, USA
    Mol Cancer 7:81. 2008
    ..Lastly, we look to future advancements that will be made possible with the interrogation of the epigenome...
  26. pmc The importance of detailed epigenomic profiling of different cell types within organs
    Theresa Ryan Stueve
    Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Epigenomics 8:817-29. 2016
    ..Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes. ..
  27. pmc Small-cell lung cancer-associated autoantibodies: potential applications to cancer diagnosis, early detection, and therapy
    Meleeneh Kazarian
    Department of Surgery, Norris Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NOR 6420, Los Angeles, CA 90089 9176, USA
    Mol Cancer 10:33. 2011
    ..We also discuss potential clinical applications for these autoantibodies, such as SCLC diagnosis, early detection, and therapy...
  28. ncbi request reprint Lipopolysaccharide-induced methylation of HuR, an mRNA-stabilizing protein, by CARM1. Coactivator-associated arginine methyltransferase
    Hongwei Li
    Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, California 90089 9176, USA
    J Biol Chem 277:44623-30. 2002
    ..Thus, CARM1, which plays a role in transcriptional activation through histone H3 methylation, may also play a role in post-transcriptional gene regulation by methylating HuR...
  29. ncbi request reprint DNA methylation analysis: a powerful new tool for lung cancer diagnosis
    Jeffrey A Tsou
    Department of Biochemistry, University of Southern California, School of Medicine, Norris Comprehensive Cancer Center, NOR 6420, 1441 Eastlake Ave, Los Angeles, California, CA 90089 9176, USA
    Oncogene 21:5450-61. 2002
    ..When combined with the development of non-invasive methods to detect such signatures, this may provide a viable method to screen subjects at risk for lung cancer...
  30. pmc Combinations of differentiation markers distinguish subpopulations of alveolar epithelial cells in adult lung
    Janice M Liebler
    Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, California
    Am J Physiol Lung Cell Mol Physiol 310:L114-20. 2016
    ..1 in AT1 cells. These findings suggest marked heterogeneity among cells previously identified as exclusively AT1 or AT2 cells, implying the presence of subpopulations of intermediate or transitional AEC in normal adult lung...
  31. ncbi request reprint Characterization of the interaction between neuronal RNA-binding protein HuD and AU-rich RNA
    Sungmin Park-Lee
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90089 9176, USA
    J Biol Chem 278:39801-8. 2003
    ..Many labile mRNAs contain U-tracts in or near their AREs. Individual AREs may thus differentially affect mRNA half-life by recruiting a unique complement of stabilizing and destabilizing factors...
  32. ncbi request reprint Hierarchical clustering of lung cancer cell lines using DNA methylation markers
    Arvind K Virmani
    Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 9593, USA
    Cancer Epidemiol Biomarkers Prev 11:291-7. 2002
    ..Our results show that DNA methylation patterns differ between NSCLC and SCLC cell lines and suggest that these patterns could be developed into a powerful molecular marker to achieve accurate diagnosis of lung cancer...

Research Grants3

  1. DEREGULATION BY HU PROTEINS IN LUNG CANCER
    Ite Laird Offringa; Fiscal Year: 2002
    ..The study of the role of Hu proteins in SCLC offers a unique opportunity to begin to understand the role of RNA- binding proteins in the development and progression of cancer. ..
  2. Lung Cancer Diagnosis Using DNA Methylation Signatures
    Ite Laird Offringa; Fiscal Year: 2004
    ....
  3. Development of DNA Methylation Markers for Early Detection of Lung Cancer
    Ite A Laird Offringa; Fiscal Year: 2010
    ..The development of sensitive and specific molecular markers for lung cancer is the key to early detection of this disease, and could greatly increase lung cancer patient survival. ..