A Serial Analysis of Gene Expression (SAGE) Database Analysis of Chemosensitivity

Abstract

Drug sensitivity and resistance has been most extensively studied in cell lines carried in tissue culture. Furthermore, cell lines have been widely used in testing new anticancer agents, despite the widely recognized observation that cell lines are more sensitive to cytotoxic drugs than are their corresponding solid tumors. We used the Serial Analysis of Gene Expression (SAGE) database to identify differences between solid tumors and cell lines, hoping to detect genes that could potentially explain differences in drug sensitivity. SAGE libraries were available for both solid tumors and cell lines from breast, colon, ovarian, pancreatic, and prostate carcinomas and from gliomas and medulloblastomas. Sixty-two genes were identified as overexpressed in tumors. The immune response and complement pathways were the significant common themes, with extracellular matrix (ECM) proteins third. For the 61 genes overexpressed in cell lines, protein synthesis was the dominant theme. We next used the SAGE database to identify genetic differences between tumor types that convey a broad range of survival to the patients that bear them as distant metastases. SAGE gene expression data were correlated with 5-year survivals documented in the SEER (Surveillance, Epidemiology and EndResults) database for patients diagnosed with "distant" or metastatic cancers. These are unlikely to be amenable to surgical resection; therefore, survival here reflects, to some extent, sensitivity to systemic therapy, i.e., chemotherapy. Using survival data as a surrogate of chemotherapy sensitivity, a spectrum can be generated, with testicular cancer at one end and pancreatic cancer at the other. Favorable 5-year survival, despite a distant presentation, correlates with expression of protein synthesis genes. Poor 5-year survival correlates with expression of cell adhesion, cytoskeletal, and ECM genes, a pattern similar to that found to distinguish solid tumors from the more cytotoxin-sensitive cancer cell lines. One interpretation is that resistance to chemotherapy may arise, in part, from the adherent, relatively inert condition (i.e., low in protein synthesis potential) of refractory cancers. Thus, attachment or ECM genes could be targets for anticancer therapy.

Activation of the α2β1 integrin‐mediated malignant phenotype on type I collagen in pancreatic cancer cells by shifts in the concentrations of extracellular Mg2+ and Ca2+

“…Together, these results indicate that the concentrations of extracellular Mg 21 and Ca 21 regulate a 2 b 1 integrin function on Type I collagen in vitro and suggest that divalent cation shifts could potentially influence the malignant phenotype of pancreatic cancer cells in the Type I collagen-rich local tumor microenvironment in vivo. [14][15][16][17]48,49 Consistent with our previous inhibition of adhesion studies using media containing normal divalent cation concentrations (1 mM Mg 21 /1.8 mM Ca 21 ), 20,26,41 the present studies demonstrate that antibodies directed against the a 2 b 1 integrin inhibit pancreatic cancer cell adhesion on Type I collagen in the presence of optimal divalent cation concentrations (3.5 mM Mg 21 /0.5 mM Ca 21 ) as well. For the first time, we also demonstrate that antibodies directed against the a 2 b 1 integrin also inhibit pancreatic cancer cell proliferation on Type I collagen.…”

“…3,4,[6][7][8][9][10][11] These cations presumably exert their effects by binding to the 3-5 putative cation-binding domains located on all integrin a subunits, 12 and possibly by interacting directly with b subunits. 13 We have recently demonstrated that a 2 b 1 integrin-mediated pancreatic cancer cell adhesion to Type I collagen, an ECM protein shown to be highly upregulated in pancreatic cancer [14][15][16][17] and to promote the malignant phenotype in vitro and in vivo, [18][19][20][21][22][23][24][25] is promoted in 1.5 mM Mg 21 and inhibited in 1.5 mM Ca 21 , 21 and that the a 2 b 1 integrin from pancreatic cancer cell lysates bound specifically to Type I collagen by affinity chromatography in 3 mM Mg 21 , can be eluted with 3 mM Ca. 2126 These data are consistent with our previous observations regarding the a 2 b 1 integrin, Type I collagen, and the various cell types involved in cutaneous wound repair, [27][28][29] of which strong parallels to the pancreatic cancer paradigm have been described.…”

The α2β1 integrin mediates the malignant phenotype on type I collagen in pancreatic cancer cell lines

“…Recent analyses using microarray and serial analysis of gene expression technology confirm those studies and point out the strong expression of many other ECM genes in pancreatic cancer as well (Iacobuzio-Donahue et al, 2003a, b;Binkley et al, 2004;Stein et al, 2004).…”

“…The previous demonstrations that type I collagen is clearly upregulated (Mollenhauer et al, 1987;Lohr et al, 1994;Shimoyama et al, 1995;Tani et al, 1997;Kuehn et al, 1999;Linder et al, 2001;Tempia-Caliera et al, 2002;Iacobuzio-Donahue et al, 2003a, b;Binkley et al, 2004;Stein et al, 2004), and mediates a malignant phenotype in pancreatic cancer in vivo (Armstrong et al, 2004;Bachem et al, 2005), correlates directly with our present in vitro observations, and are further extended by our demonstration that the a 2 b 1 integrin specifically regulates this type I collagen-mediated phenotype in multiple pancreatic cancer cell lines. These observations collectively suggest that targeting the a 2 b 1 integrin may have therapeutic value in the treatment of pancreatic cancer in vivo.…”

Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI)

“…Tumors of the testis, breast, and ovaries are normally responsive to chemotherapy, whereas tumors originating in the colon, kidney, or liver are often more resistant. The variation in chemotherapy sensitivity determined by tissue of origin is reduced in cell lines (5). Large screening programs are using cell line panels to predict the chemotherapeutic efficiency of compounds to different tumor types (6), the key assumption being that the tumor cell lines are good experimental models for the tumors they derive from.…”