Areas of Interest
We are interested in signal transduction pathways controlled by
protein complexes. Multiple signal transduction pathways are
controlled by protein complexes that collaborate together and
examples of the protein complexes have been described in cell
proliferation, cell migration, differentiation, as well as
apoptosis signaling. We utilize standard biochemical techniques
such as protein fractionation, as well newer technologies such
as nano-electrospray liquid chromatography tandem mass
spectrometry to study protein complexes, their identities,
abundance, and activities. Biological information that we
experimentally measured are stored in an interactive database
where a number of information processing and modeling are
further explored.
Lab Rotation Projects
Proteomics and Protein: Protein Interaction Networks
Students who wish to understand the basic techniques related
to proteomics and want to learn how to use proteomics to
understand biologically relevant protein : protein interaction
networks can participate in a rotation project.
#1 – Annexin I interacting proteins: We have recently
showed that Annexin I protein is crucial for the recognition and
engulfment of apoptotic cells. We have a good antibody that can
be used to immunoprecipitate Annexin I and associated protein
complexes. Students will participate in immunoprecipitation of
endogenous Annexin I from viable cells or apoptotic cells to
identify the proteins that co-precipitate with annexin I.
Students are anticipated to learn basic protein identification
technique using the liquid-chromatography and tandem mass
spectrometry.
#2 - Phosphotidylserine Receptor interacting protein
networks: We have also showed that Phosphatidylserine
Receptor (PSR) participates in the engulfment of apoptotic cells
by recognizing cell-surface exposed annexin I. Thus, we are
interested in identifying PSR associated proteins during the
engulfment of apoptotic cells. Students will participate in PSR
immunoprecipitation experiments and identification of cell
surface receptors and intracellular signaling proteins.
#3- Cancer Biology Projects: We are interested in
identifying cancer specific oncoproteins / tumor suppressor
protein from histological tissue arrays. We have recently
developed methods to dientify proteins directly from human
prostate cancer tissues. Students will participate in optimizing
the protein extraction conditions to detect low quantity of
proteins from tumor cells using very sensitive mass spectrometry
and proteomics technologies. At the end of the rotation,
students are expected to learn a number of techniques related to
proteomics and cancer biology.
Selected Publications
Taylor CM, Marta CB, Claycomb RJ, Han DK, Rasband MN, Coetzee
T, Pfeiffer SE. 2004. Proteomic mapping provides powerful
insights into functional myelin biology. Proc Natl Acad Sci U S
A. Mar 30;101(13):4643-8.
Chang SH, Liu CH, Conway R, Han DK, Nithipatikom K, Trifan OC,
Lane TF, Hla T. 2004. Role of prostaglandin E2-dependent
angiogenic switch in cyclooxygenase 2-induced breast cancer
progression. Proc Natl Acad Sci U S A. Jan 13;101(2):591-6.
Lundgren DH, Eng J, Wright ME, Han DK. 2003. PROTEOME-3D: An
Interactive Bioinformatics Tool for Large-Scale Data Exploration
and Knowledge Discovery. Mol Cell Proteomics. Nov;2(11):1164-76.
Epub 2003 Sep 07.
Arur S, Uche UE, Rezaul K, Fong M, Scranton V, Cowan AE,
Mohler W, Han DK. 2003. Annexin I is an endogenous ligand that
mediates apoptotic cell engulfment. Dev Cell. Apr;4(4):587-98.
Imanishi T, Han DK, Hofstra L, Hano T, Nishio I, Liles WC,
Gown AM, Schwartz SM, Han DK, Gorden AM. 2002. Apoptosis of
vascular smooth muscle cells is induced by Fas ligand derived
from monocytes/macrophage. Atherosclerosis. Mar;161(1):143-51.
Erratum in: Atherosclerosis. Mar;167(1):175.. Han David KM
[corrected to Han David K]; Gorden Alan M [corrected to Gown
Alan M].
Griffin TJ, Han DK, Gygi SP, Rist B, Lee H, Aebersold R,
Parker KC. 2001. Toward a high-throughput approach to
quantitative proteomic analysis:expression-dependent protein
identification by mass spectrometry. J Am Soc Mass Spectrom.
Dec;12(12):1238-46.
Han DK, Eng J, Zhou H, Aebersold R. 2001. Quantitative
profiling of differentiation-induced microsomal proteins using
isotope-coded affinity tags and mass spectrometry. Nat
Biotechnol. Oct;19(10):946-51.
Imanishi T, Hano T, Nishio I, Han DK, Schwartz SM, Karsan A.
2001. Apoptosis of vascular smooth muscle cells is induced by
Fas ligand derived from endothelial cells. Jpn Circ J.
Jun;65(6):556-60. Erratum in: Jpn Circ J 2002 Dec;66(12):1185.
Han MH, Han DK, Aebersold RH, Glomset JA. 2001. Effects of
protein kinase CK2, extracellular signal-regulated kinase 2, and
protein phosphatase 2A on a phosphatidic acid-preferring
phospholipase A1. J Biol Chem. Jul 20;276(29):27698-708. |
