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  Pharmaceutical Patents  

 

Title:  Molecular characteristics of non-small cell lung cancer
United States Patent: 
7,332,590
Issued: 
February 19, 2008

Inventors: 
Nacht; Mariana (Belmont, MA), Dracheva; Tatiana (Rockville, MD), Sidransky; David (Baltimore, MD), Madden; Stephen (Sudbury, MA), Jen; Jin (Brookeville, MD)
Assignee: 
The United States of America as Represented by the Department of Health and Human Services (Washington, DC)
N/A (Cambridge, MA), Genzyme Corporation (Baltimore, MD), The Johns Hopkins University of Medicine

Appl. No.: 
10/486,844
Filed: 
August 16, 2002
PCT Filed: 
August 16, 2002
PCT No.: 
PCT/US02/26027
371(c)(1),(2),(4) Date: 
September 09, 2004
PCT Pub. No.: 
WO03/015613
PCT Pub. Date: 
February 27, 2003


 

Patheon


Abstract

We used hierarchical clustering to examine gene expression profiles generated by serial analysis of gene expression (SAGE) in a total of nine normal lung epithelial cells and non-small cell lung cancers (NSCLC). Separation of normal and tumor samples, as well as histopathological subtypes, was evident using the 3,921 most abundant transcript tags. This distinction remained when just 115 highly differentially expressed transcript tags were used. Furthermore, these 115 transcript tags clustered into groups that were suggestive of the unique biological and pathological features of the different tissues examined. Adenocarcinomas were characterized by high-level expression of small airway-associated or immunologically related proteins, while squamous cell carcinomas overexpressed genes involved in cellular detoxification or antioxidation. The messages of two p53-regulated genes, p21.sup.WAF1/CIP1 and 14-3-3.sigma., were consistently under-expressed in the adenocarcinomas, suggesting that the p53 pathway itself might be compromised in this cancer type. Gene expression observed by SAGE were consistent with the results obtained by quantitative real-time PCR or cDNA array analyses using 43 additional lung tumor and normal samples. Thus, although derived from only a few tissue libraries, molecular signatures of non-small cell lung cancer derived from SAGE most likely represent an unbiased yet distinctive molecular signature for human lung cancer.

Description of the Invention

FIELD OF THE INVENTION

The invention relates to the field of cancer. In particular it relates to the areas of diagnostics and lung cancer.

BACKGROUND OF THE INVENTION

Lung cancer is the leading cause of cancer death worldwide and NSCLC accounts for nearly 80% of the disease (1). Based on cell morphology, adenocarcinoma and squamous are the most common types of NSCLC (2). Although the clinical courses of these tumors are similar, adenocarcinomas are characterized by peripheral location in the lung and often have activating mutations in the K-ras oncogene (3, 4). In contrast, squamous cell carcinomas are usually centrally located and more frequently carry p53 gene mutations (5). Furthermore, the etiology of squamous cell carcinoma is closely associated with tobacco smoking while the cause of adenocarcinoma remains unclear (6, 7). Although many molecular changes associated with NSCLC have been reported (8, 9), the global gene expression pattern associated with these two most common types of lung cancer has not be described. Understanding gene expression patterns in these major tumor types will uncover novel markers for disease detection as well as potential targets for rational therapy of lung cancer.

Several technologies are currently being utilized for gene expression profiling in human cancer (10). SAGE (11) is an open system that rapidly identifies any expressed transcript in a tissue of interest, including transcripts that had not been identified. This highly quantitative method can accurately identify the degree of expression for each transcript. Comparing SAGE profiles between the tumor and the corresponding normal tissues can readily identify genes differentially expressed in the two populations. Using this method, novel transcripts and molecular pathways have been discovered (12-14). In contrast, cDNA arrays represent a closed system that analyze relative expression levels of previously known genes or transcripts (15, 16). Because many thousands of genes can be placed on a single membrane or slide for rapid screening, studies have recently demonstrated molecular profiles of several human cancers (17-20).

Hierarchical clustering is a systematic method widely used in cDNA array data analysis where the difference between the expression patterns of many genes is generally within a few fold (21). We reasoned that because SAGE is highly quantitative, hierarchical clustering might be used to organize gene expression data generated by SAGE from just a few tissue libraries. To test this, SAGE tags from two of each libraries derived from primary adenocarcinomas, primary squamous cell carcinomas, normal lung small airway epithelial cells (SAEC), or normal bronchial/tracheal epithelial (NHBE) cells, and a lung adenocarcinoma cell line were used. SAGE tags showing the highest abundance were subjected to clustering analysis. Although each library was derived from a different individual, normal and tumor samples clustered in two separate branches while tissues of different cell types clustered together. Furthermore, SAGE tags clustered into biologically meaningful groups revealing the important molecular characteristics of these two most common NSCLC subtypes.

BRIEF SUMMARY OF THE INVENTION

The present invention provides a method of identifying a lung cancer as squamous cell carcinoma. According to the method an amount of a gene product of a gene in a lung cancer sample is determined. The gene is selected from the group consisting of: glutathione peroxidase (GPX; NM.sub.--002083), glutathione S-transferase M3 (GSTM3; NM.sub.--000849), aldoketoreductase family 1, member B 10 (NM.sub.--020299), peroxiredoxin 1 (PRDX1; NM.sub.--002574), small proline-rich protein 3 (SPRR3; NM.sub.--005416), and TNF receptor superfamily member 18 (TNFRSF18; NM004195). The amount of the gene product in the lung cancer sample is compared to the amount determined in a lung tissue sample which is non-pathological. An increased amount of the gene product in the lung cancer sample relative to the lung tissue sample which is non-pathological identifies the lung cancer as a squamous cell carcinoma.

The present invention provides a method of identifying a lung cancer as adenocarcinoma. According to the method an amount of a gene product of a small proline-rich protein 3 (SPRR3; NM.sub.--005416) gene in a lung cancer sample is determined. The amount of the gene product in the lung cancer sample is compared to the amount determined in a lung tissue sample which is non-pathological. A decreased amount of the gene product in the lung cancer sample relative to the lung tissue sample which is non-pathological identifies the lung cancer as adenocarcinoma.

The invention thus provides the art with a molecular diagnostic to supplement or replace histological features and/or clinical behavior.

DETAILED DESCRIPTION OF THE INVENTION

It is a discovery of the present inventors that certain molecular markers can be used to distinguish between the two most common forms of lung cancer: adenocarcinoma and squamous cell carcinoma. By assessing the expression levels of certain genes in a sample tumor tissue relative to normal, non-pathological lung tissue, one can make a determination of which of these types the cancer represents.

Expression of any gene which has been found to be up-regulated or down-regulated in one or more cancer types can be measured. According to one preferred embodiment, a lung tissue can be diagnosed, prognosed, or treatment determined by ascertaining an expression pattern of one or more cancer markers. Such markers include, but are not limited to glutathione peroxidase (GPX; NM.sub.--002083), glutathione S-transferase M3 (GSTM3; NM.sub.--000849), aldoketoreductase family 1, member B 10 (NM.sub.--020299), peroxiredoxin 1 (PRDX1; NM.sub.--002574), small proline-rich protein 3 (SPRR3; NM.sub.--005416), and TNF receptor superfamily member 18 (TNFRSF18; NM004195). The amount of the gene product determined in a suspected cancer tissue is compared to the amount of the same gene product in a lung tissue sample which is non-pathological. An increased or decreased amount of the gene product in the lung cancer sample relative to the lung tissue sample which is non-pathological identifies the lung cancer by type. Using such markers, one can distinguish between squamous cell carcinoma and adenocarcinoma of the lung, for example.

Either mRNA or protein can be measured as a means of determining up- or down-regulation of a gene. Any technique known in the art for measuring such gene products can be used. Quantitative techniques are preferred, however semi-quantitative or qualitative techniques can also be used. Suitable techniques for measuring gene products include, but are not limited to SAGE analysis, DNA microarray analysis, Northern blot, Western blot, immunocytochemical analysis, and ELISA,

Control samples which can be used according to the present invention include any non-pathological sample of lung tissue. These can be isolated from the same individual as the suspected lung sample or from a different individual, whether related or not. Suitable cell types include lung small airway epithelial cells as well as bronchial/tracheal epithelial cells.
 

Claim 1 of 23 Claims

1. A method of associating a lung cancer with squamous cell carcinoma comprising: determining an amount of a gene product of a gene in a lung cancer sample, said gene selected from the group consisting of: aldoketoreductase family 1, member B 10 (NM.sub.--020299), peroxiredoxin 1 (PRDX1; NM.sub.--002574), and TNF receptor superfamily member 18 (TNFRSF18; NM004195); comparing the amount of the gene product to the amount determined in a lung tissue sample which is non-pathological, wherein an increased amount of the gene product in the lung cancer sample relative to the lung tissue sample which is non-pathological associates the lung cancer with a squamous cell carcinoma.

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If you want to learn more about this patent, please go directly to the U.S. Patent and Trademark Office Web site to access the full patent.

 

 

     
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