Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification.

Clinically relevant biomarkers are useful to determine cancer patients' prognosis and treatments. To discover new putative biomarkers, we performed in silico analysis of a 325-gene panel previously associated with breast epithelial cell biology and clinical outcomes. Sixteen public datasets of microarray samples representing 8 cancer types and a total of 3,663 patients' samples were used for the analyses. Feature selection was used to identify the best subsets of the 325 genes for each classification, and linear discriminant analysis was used to quantify the accuracy of the classifications. A subset of 102 of the 325 genes were found to be housekeeping (HK) genes, and the classifications were repeated using only the 102 HK subset. The 325-gene panel and 102 HK subset were able to distinguish colon, gastric, lung, ovarian, pancreatic, and prostate tumors and leukemia from normal adjacent tissue, and classify disease subtypes of breast and lung cancers and leukemia with 70% or higher accuracy. HK genes have been overlooked as potential biomarkers due to their relative stability. This study describes a set of HK genes as putative biomarkers applicable to multiple cancer types worth following in subsequent validation studies.

Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification

Clinically relevant biomarkers are useful to determine cancer patients' prognosis and treatments. To discover new putative biomarkers, we performed in silico analysis of a 325-gene panel previously associated with breast epithelial cell biology and clinical outcomes. Sixteen public datasets of microarray samples representing 8 cancer types and a total of 3,663 patients' samples were used for the analyses. Feature selection was used to identify the best subsets of the 325 genes for each classification, and linear discriminant analysis was used to quantify the accuracy of the classifications. A subset of 102 of the 325 genes were found to be housekeeping (HK) genes, and the classifications were repeated using only the 102 HK subset. The 325-gene panel and 102 HK subset were able to distinguish colon, gastric, lung, ovarian, pancreatic, and prostate tumors and leukemia from normal adjacent tissue, and classify disease subtypes of breast and lung cancers and leukemia with 70% or higher accuracy. HK genes have been overlooked as potential biomarkers due to their relative stability. This study describes a set of HK genes as putative biomarkers applicable to multiple cancer types worth following in subsequent validation studies.

Use of tumor lines with selectable markers in assessing the effect on experimental metastases of combination chemotherapy with alkylating agents.

High-dose chemotherapy with a 3-day regimen of cyclophosphamide, cisplatin, and carmustine was used to treat mice bearing experimental lung metastases of mammary tumor cell lines with selectable markers (lines 66cl4 and 4TO7). Cloning of lung cells at various times after treatment revealed a rapid 3 to 4 log loss of clonogenic tumor cells, down to undetectable levels. However, after several weeks, clonogenic tumor cells reappeared in the lungs; few cures were obtained even when mice had a relatively low tumor burden when treated with chemotherapy. Splenocyte numbers and response to Concanavalin A indicated a transient immunosuppression. In one experiment, mice were treated with a second round of chemotherapy 3 weeks after the first. The number of clonogenic cells per lung again dropped, but regrowth of cells was rapid, and no cures were obtained. Inoculation of tumor-bearing mice s.c. after chemotherapy with lethally irradiated cells of the highly immunogenic tumor cell line 4TO7-IL-2 had little effect on the rate of reappearance of line 4TO7 in lungs, but subsequent growth of tumor cells in lungs was slowed. This model system can be used to test the efficacy of additional immunotherapy and chemotherapy regimens on minimal residual metastatic disease after high-dose chemotherapy, when remaining metastatic cells are apparently dormant.