The Center for Precision Biomedicine connects research efforts across the university in systems biology, clinical and translational sciences, protein chemistry, genomics, metabonomics, nanomedicine, and proteomics, bringing together people to promote intellectual exchange and the the transfer of expertise in these key fields and beyond.
Multi-Departmental Collaboration of Interacting Centers
The IMM is the hub of a new alliance connecting research efforts across the university in systems biology, clinical and translational sciences, protein chemistry, genomics, and proteomics. This new multidisciplinary science will link the efforts of various centers, bringing together people to promote intellectual exchange and the transfer of expertise in these key fields and beyond.
Precision Medicine is emerging as an exciting, new area of science. While genomics has been highly successful at cataloging nucleic acid sequences, for the vast majority of genes the microRNA,lncRNA, protein products, and metabolites best describe the state of living system.
Further, proteins are the targets for essentially all of the drugs on the market today. Gene sequences give us a starting point, but most cellular proteins are extensively processed and modified. To understand cellular regulation, elucidate disease processes, and identify drug targets we need the detailed characterization of proteins that now appears achievable through mass spectrometry.
One mission of the Center for Precision Biomedicine (CPBM) will be to develop the experimental and analytical technologies that will make precision biomedicine a reality. One important area of development for the CPBM will be the identification of biomarkers for disease, and targeting agents against such biomarkers, for the prevention, diagnosis, and treatment of diseases. The CPBM will not only develop new technologies but provides a coordinated group of centers and programs for collaborative and service work to the McGovern Medical School, UTHealth, and the wider scientific community. The IMM is an ideal environment for bringing together resources and leadership in the experimental and computational programs being developed in the CPBM..
Mass Spectrometry Resources
We maintain two mass spectrometry centers within the IMM, the Clinical and Translational Proteomics Service Center and the Molecular Diagnostic Service Center. The equipment and personnel allow for a full range of proteomic and diagnostic services from discovery phase to clinical trials. Our MS resources include the following:
- Thermo LTQ Orbitrap XL-ETD Mass Spectrometer
- Thermo LTQ Orbitrap Fusion Tribrid™ Mass Spectrometer
- Agilent 6538 Ultra High Definition Accurate-mass Q-TOF
- Agilent 6430 Triple Quadrupole LC/ MS
- Perkin Elmer AxION 2 TOF
- Shimadzu LCMS-8040
The entire facility is supported by the CCTS Genologics LIMS system which is used for de-identified sample tracking from the bedside to analytical results from genomic, proteomic and immunological characterization. This instrumentation group is a state of the art mass spectroscopy core that is capable of providing routine mass spectroscopy services such as protein identification and peptide profiling, more demanding analyses such as post-translational modifications, and quantitative peptide and protein analyses in complex mixtures.
The Center for Precision Biomedicine (CPBM) maintains both local computation resources and has access to the Texas Advanced Computing Center (TACC). These computers are set up for analysis of tumor images, next-generation sequencing, multi-scale mathematical modeling, and proteomics analysis, among other things. Our local computer resources include:
- Dell Precision T7500N workstation with two quad core Intel Xeon E5603 (1.6 GHz) processors
- SUN SPARC M5000 server with eight dual cores processors
- Sun Shared Visualization/GPU server: 16 2.8GHz Proc 128GB RAM
- GPU Computing Server: 6 M2080 GPU, 12 2.4 GHz Proc 32 GB RAM
- Mac Pro: 12 2.66 GHz Proc, 32GB RAM, Dual 27in Display
- Aptamer Targeting – we have developed, and continue to develop, novel aptamers and aptamer techniques to target proteins or small molecules of interest, such as proteins highly expressed on the surface of cancers. Through our Nanochemistry Service Center, aptamers and aptamer selection technologies are made available to our faculty and to outside institutions for targeted delivery of nanoparticles and multi-stage vectors to tumors.
- Big Data – we are developing novel methods of image analysis to improve therapeutic efficacy of cancer treatments.
- Mathematical Modeling of Tumors – we are developing breakthrough methods of multi-scale modeling for predicting dosing efficacy of chemotherapeutic agents.
- Proteomics seeks to understand cellular regulation, elucidate disease processes, and identify drug targets using the detailed characterization of proteins achievable through mass spectrometry.
- Metabonomics – metabolic profiles and drug monitoring by NMR spectroscopy and by mass spectrometry.
- Molecular Diagnostics Service Center – conducts medical tests for determining vitamin levels and drug detection for therapeutic drug monitoring. Customized tests can be developed to fit collaborator and customer needs.
- Next-generation sequencing analysis – we developed Aptaligner, a software package for the analysis of NGS data arising from pseudo-random DNA X-Aptamers. The software is now being used to study antigenic variation in infectious agents with UTHealth collaborators.
- Proteomics Core Laboratory of the Center for Clinical and Translational Sciences provides proteomics analysis services such as protein identification, analysis of differential expression and post-translational modifications of protein, as well as analysis and interpretation of results.