Proteomics Research Group

The Clinical Proteomics Research Group in the Department of Clinical Chemistry has long standing expertise in the field of proteomics and mass spectrometry. Research interests of the group include differential protein profiling, protein-protein interactions, drug protein targets, immunoproteomics and characterization of post-translational modifications.

Our laboratory is equipped with a state of the art Q-TOF Ultima Global mass spectrometer (Micromass) coupled with a nano-flow CapLC (Waters) and a MALDI MicroMX mass spectrometer (Micromass). The Q-TOF has high resolution, high sensitivity and high mass accuracy. It is particularly suitable for de novo sequencing of proteins, differential protein profiling, identification of protein components from complex protein mixtures, detection and characterization of low-abundance compounds, identification of components in complex matrices, characterization of post-translational modifications, and identification of drug metabolites.

The MALDI MicroMx is a matrix-assisted laser desorption/ionization TOF MS with short analysis times and fully automated operation, which offers a simple, economical method for high throughput protein identification. With its innovative parallel post source decay (PSD), it also has the capability of confirming protein identification and for initial analysis of post-translational modifications. Furthermore, parallel PSD results in faster and more sensitive analysis with minimal sample consumption.

 

Current Projects

 

Interacting Partners of Mechanistic or Mammalian Target of Rapamycin Complex 1 (mTORC1) and mTORC2

 

The mTOR is a serine/threonine-specific kinase which plays a central role in the regulation of cell proliferation, growth, differentiation, migration, availability of nutrients and cellular energy supplies. mTOR integrates the input from multiple upstream pathways, including insulin, growth factors (i.e., IGF-1 and IGF-2), and mitogens. Malfunctions in the mTOR pathway are implicated as a contributing factor in several human diseases especially in a variety of cancers. Identification of interacting partners and components of the mTOR complex is crucial to understand the functional importance of mTOR complexes and in the design of new drugs. We use a functional proteomic approach for the identification of interacting partners of (raptor-binding) mTORC1 and (rictor-binding) mTORC2. Novel interacting proteins may offer new targets for therapeutic interventions in human diseases caused by perturbed mTORC1 signaling.

 

Doctoral student: Hazir Rahman

 

Studies on Aspergillus fumigatus proteome for identification of novel unknown immunogens

 

Diagnosis of aspergillosis remains difficult due to overlapping clinical and radiological features with cystic fibrosis and tuberculosis. Crude antigenic extracts of A. fumigatushave been widely used for detection of anti-Aspergillusantibodies (IgE and IgG) in sera but nonspecificity remains a problem. Several proteins which have been expressed recombinantly and tested for their immunoreactivity were found to be of limited use. A current Indo-German collaborative project is focused on the identification of novel allergens/immunogens of A. fumigatusto improve existing diagnostic methods to produce enhanced sensitivity and specificity. Using an immunoproteomics approach, we have identified a panel of novel immunoreactive proteins from A. fumigatus which could be used as diagnostic and vaccine candidate molecules. We are characterizing selective proteins to replace the present crude extract-based diagnostic tools and possibly be utilizated as immunotherapy agents for A. fumigatus infections.

 

Indo-German Collaborative Project, BMBF Nr. IND 06/040

 

Doctoral student: Bharat Singh (PuneUniversity, India)

 

Differential Proteome after Mycophenolic Acid Treatment

 

Mycophenolic acid (MPA) is a selective and reversible non-competitive inhibitor of inosine monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in the de novo pathway of purine synthesis. Along with its potent immunosuppressive effects, MPA adversely affects the gastrointestinal tract causing diarrhea in some patients. The exact molecular mechanism of this organ toxicity is unknown. Possible mechanisms of MPA toxicity include direct toxicity by its anti-proliferative effect, alteration in local immune responses, and toxicity from acyl MPA glucuronide (AcMPAG) adducts. We are investigating altered protein expression with in vitro human cell models and in vivo rat models after treatment with MPA. This research will help us better understand both the broader cellular effects of MPA in addition to its immunosuppressive activity and the cellular events responsible for the adverse effects of MPA.

 

Doctoral student: Muhammad Qasim

 

Intracellular changes induced by thiopurine treatment - role of thiopurine S-methyltransferase (TPMT)

 

Thiopurines are purine analogs which have been used in clinical practice as immunosuppressive and antileukemic agents for over a half century. These drugs have significant therapeutic effects in the treatment of childhood acute lymphocytic leukemia (ALL), inflammatory bowel disease (IBD), in prevention of graft rejection, and autoimmune diseases. Many concerns have been raised regarding the toxic effects and increased risk of various malignancies associated with thiopurine therapy. Metabolism of these drugs involves many enzymatically catalyzed steps and some of the important enzymes involved in their metabolic pathways have important polymorphisms in human populations. These include inosine monophosphate dehydrogenase (IMPDH), and thiopurine S-methyltransferase (TPMT). TPMT is a cytosolic methyltransferase and its differential activity can explain differences in therapy outcome in patients; either excessive toxicity or drug resistance. Extensive research on TPMT polymorphism and its possible effects has led to the introduction of individualized thiopurine therapy, but there are still there are still many important unanswered questions about individual responses which may be revealed by differential expression profiling during thiopurine treatment. Our group has generated TPMT knockdown cell lines using siRNA technology. These cell lines with normal and reduced TPMT expression recapitulate TPMT polymorphism in patients. We are interested in proteomic changes during thiopurine treatment of high (wild type) and low (knockdown) TPMT activity human cells. This research will provide a better understanding of the complex metabolism of thiopurines, and could be helpful in improving individual therapeutic outcomes.

 

Doctoral student: Misbah Tauseef

 

Identification of potential biomarkers of Creutzfeldt-Jakob Disease (CJD) using STrEPÔ technology and proteomics

 

The prion protein that is believed to cause CJD exhibits two isoforms, cellular prion protein PrPC and abnormal PrPSc which cause a transmissible spongiform encephalopathy. Recent findings suggest that PrPC is a multifunctional protein participating in several cellular processes. Using an affinity purification approach, we have identified cellular proteins that specifically interact with cellular prion protein PrPC and its common genetic variants. We are continuing to comparatively analyze the interacting partners of normal and variant proteins and characterize them functionally. Additionally, blood from normal and CJD patients is being investigated to ascertain the diagnostic potential of these PrPC interacting proteins.

 

Cooperation with the Dept. of Neurology, University Medical Center Goettingen, Dr. rer. nat. Saima Zafar, Prof. Dr. Inga Zerr

 

 

Ansprechpartner
Dr. Asif Abdul Rahman
Prof. Dr. Abdul Rahman Asif
Group Leader
Telefon:
+49 551 39-22945
Pieper:
919-1232
Telefax:
+49 551 39-12505
E-Mail:
asif@med.uni-goettingen.de