51. Clinical Study of Personalized Therapeutics Based on Genomic/Proteomic Profiling
Authors: John Nemunaitis, Neil Senzer, Jerry Shen, Phillip Maples, Donald Rao, Alex Tong, Padmasini Kumar, Joe Kuhn, Yu-An Zhang, Jian Liao, Iya Khalil, Colin Hill, Adi Gazdar
Journal: Molecular Therapy (2006)

Our therapeutic strategy is to identify signature molecular components comprising key, highly linked, functional nodes of dominant or co-dominant oncogenic pathways. Correlative genomic and proteomic profiling of laser microdissected tissue using cDNA microarray and 2-dimensional Difference Gel Electrophoresis coupled with mass-spectrometry (MS) was used "at the bedside" to detect differential expression between malignant and 'normal' tissue. Ten cancer patients (5 melanoma; 2 breast; 1 lymphoma; 1 non-small-cell lung cancer; and 1 colon cancer) are undergoing analysis. Results of target prioritization are complete in patient 1 (melanoma) who demonstrated 45 up-regulated proteins (≥2 fold) in malignant compared to non-malignant tissue. Six key signature proteins were chosen based on (1) analysis of functions and processes associated with cancer growth and robustness as defined by Hanahan and Weinberg, H&W (self sufficiency, immortality, immune escape, apoptosis, replication, angiogenesis, and invasion), (2) conservation of coupled DNA in eukaryotic completed genomes, (3) coupled upregulation of mRNA and protein, and (4) transcriptional regulator activity. Western blot analysis with known protein antibodies was used to confirm MS results and identify similar levels of protein expression in selected NCI 60 cell lines.Using our systems biology construct, these 6 proteins underwent gene expression analysis and pathway modeling to determine inter- and intra-pathway connectivity to proteins involved with functions identified by H&W. A total of 1159 literature citations were identified involving the 6 key proteins. First order protein-protein interaction connectivity is shown below. Our therapeutic strategy is to identify signature molecular components comprising key, highly linked, functional nodes of dominant or co-dominant oncogenic pathways. Correlative genomic and proteomic profiling of laser microdissected tissue using cDNA microarray and 2-dimensional Difference Gel Electrophoresis coupled with mass-spectrometry (MS) was used "at the bedside" to detect differential expression between malignant and 'normal' tissue. Ten cancer patients (5 melanoma; 2 breast; 1 lymphoma; 1 non-small-cell lung cancer; and 1 colon cancer) are undergoing analysis. Results of target prioritization are complete in patient 1 (melanoma) who demonstrated 45 up-regulated proteins (≥2 fold) in malignant compared to non-malignant tissue. Six key signature proteins were chosen based on (1) analysis of functions and processes associated with cancer growth and robustness as defined by Hanahan and Weinberg, H&W (self sufficiency, immortality, immune escape, apoptosis, replication, angiogenesis, and invasion), (2) conservation of coupled DNA in eukaryotic completed genomes, (3) coupled upregulation of mRNA and protein, and (4) transcriptional regulator activity. Western blot analysis with known protein antibodies was used to confirm MS results and identify similar levels of protein expression in selected NCI 60 cell lines. Using our systems biology construct, these 6 proteins underwent gene expression analysis and pathway modeling to determine inter- and intra-pathway connectivity to proteins involved with functions identified by H&W. A total of 1159 literature citations were identified involving the 6 key proteins. First order protein-protein interaction connectivity is shown below.