Nasal epithelium gene expression signature and classifier for the prediction of lung cancer

Abstract

Disclosed herein are assays and methods for diagnosis and prognosis of lung cancer using expression analysis of one or more genes from a biological sample comprising nasal epithelial cells. The assays and methods of the invention provide non-invasive means of accurately detecting the presence or absence of lung cancer relative to, for example, more invasive techniques, such as bronchoscopy. Similarly, in certain aspects, the assays and methods disclosed herein provide non-invasive means of accurately identifying the smoking history of a subject.

What is claimed is: 
     
         1 . A method of diagnosing lung cancer in a subject comprising the steps of: (a) measuring a biological sample comprising nasal epithelial cells of the subject for expression of one or more genes; and (b) comparing the expression of the one or more genes to a control sample of those genes from individuals without cancer; wherein the one or more genes are selected from the group consisting of genes in Table 12, Table 13 or Table 21, and wherein differential expression of the subject's one or more genes relative to the control sample is indicative of the subject having lung cancer. 
     
     
         2 . The method of  claim 1 , wherein non-differential expression of the subject's one or more genes relative to the control sample is indicative of the subject not having lung cancer. 
     
     
         3 . A method of diagnosing lung cancer in a subject comprising the steps of: (a) measuring a biological sample comprising nasal epithelial cells of the subject for expression of one or more genes; and (b) comparing the expression of the one or more genes to a control sample of those genes from individuals with cancer; wherein the one or more genes are selected from the group consisting of genes in Table 12, Table 13 or Table 21, and wherein differential expression of the subject's one or more genes relative to the control sample is indicative of the subject not having lung cancer. 
     
     
         4 . The method of  claim 3 , wherein non-differential expression of the subject's one or more genes relative to the control sample is indicative of the subject having lung cancer. 
     
     
         5 . A method of determining whether a subject has quit smoking comprising the steps of: (a) measuring a biological sample comprising nasal epithelial cells of the subject for expression of one or more genes selected from the group consisting of genes in Table 5 or Table 6; and (b) comparing the expression of the one or more genes to a control sample of those genes from non-smokers; wherein altered expression of the subject's genes relative to the control sample is indicative of the subject having quit smoking. 
     
     
         6 . The method of  claim 5 , wherein non-altered expression of the subject's one or more genes relative to the control sample is indicative of the subject not having quit smoking. 
     
     
         7 . A method of determining whether a subject has quit smoking comprising the steps of: (a) measuring a biological sample comprising nasal epithelial cells of the subject for expression of one or more genes selected from the group consisting of genes in Table 5 or Table 6; and (b) comparing the expression of the one or more genes to a control sample of those genes from smokers; wherein altered expression of the subject's genes relative to the control sample is indicative of the subject not having quit smoking. 
     
     
         8 . The method of  claim 7 , wherein non-altered expression of the subject's one or more genes relative to the control sample is indicative of the subject having quit smoking. 
     
     
         9 . A method of determining the likelihood that a subject has lung cancer, the method comprising: (a) subjecting a biological sample comprising nasal epithelial cells to a gene expression analysis, wherein the gene expression analysis comprises comparing gene expression levels of one or more genes selected from the group of genes in Table 12, Table 13 or Table 21 to the expression levels of a control sample of those genes from individuals without cancer; and (b) determining the likelihood that the subject has lung cancer by determining differential expression of the subject's one or more genes relative to the group of genes in Table 12, Table 13 or Table 21, wherein differential expression of the subject's genes relative to the control sample is indicative of the subject having a high likelihood of lung cancer. 
     
     
         10 . The method of  claim 9 , wherein non-differential expression of the subject's one or more genes relative to the control sample is indicative of the subject having a low likelihood of lung cancer. 
     
     
         11 . A method of determining the likelihood that a subject has lung cancer, the method comprising: (a) subjecting a biological sample comprising nasal epithelial cells to a gene expression analysis, wherein the gene expression analysis comprises comparing gene expression levels of one or more genes selected from the group of genes in Table 12, Table 13 or Table 21 to the expression levels of a control sample of those genes from individuals with cancer; and (b) determining the likelihood that the subject has lung cancer by determining differential expression of the subject's one or more genes relative to the group of genes in Table 12, Table 13 or Table 21, wherein differential expression of the subject's genes relative to the control sample is indicative of the subject having a low likelihood of lung cancer. 
     
     
         12 . The method of  claim 11 , wherein non-differential expression of the subject's one or more genes relative to the control sample is indicative of the subject having a high likelihood of lung cancer. 
     
     
         13 . The method of  claims 1 - 12 , wherein at least two genes are measured. 
     
     
         14 . The method of  claims 1 - 12 , wherein at least five genes are measured. 
     
     
         15 . The method of  claims 1 - 12 , wherein at least ten genes are measured. 
     
     
         16 . The method of  claims 1 - 12 , wherein at least twenty genes are measured. 
     
     
         17 . The method of  claims 1 - 12 , wherein at least thirty genes are measured. 
     
     
         18 . The method of  claims 1 - 12 , wherein at least forty genes are measured. 
     
     
         19 . The method of  claims 1 - 12 , wherein at least fifty genes are measured. 
     
     
         20 . The method of  claims 1 - 4  and  9 - 19 , wherein the genes in Table 12 comprise those genes identified in cluster 1. 
     
     
         21 . The method of  claims 1 - 4  and  9 - 19 , wherein the genes in Table 12 comprise those genes identified in cluster 2. 
     
     
         22 . The method of  claims 1 - 4  and  9 - 19 , wherein the genes in Table 12 comprise those genes identified in cluster 3. 
     
     
         23 . The method of  claims 1 - 4  and  9 - 19 , wherein the genes in Table 12 comprise those genes identified in cluster 4. 
     
     
         24 . The method of  claims 1 - 23 , further comprising determining one or more of the subject's clinical risk factors affecting the subject's risk for having lung cancer. 
     
     
         25 . The method of  claim 24 , wherein the one or more clinical risk factors are selected from the group consisting of advanced age, smoking status, the presence of a lung nodule greater than 3 cm on CT scan, lesion location and time since quitting smoking. 
     
     
         26 . The method of  claim 25 , wherein the subject's positive smoking status is indicative of the subject having lung cancer. 
     
     
         27 . The method of  claim 25 , wherein the subject's advanced age is indicative of the subject having lung cancer. 
     
     
         28 . The method of  claim 25 , wherein the presence of a lung nodule greater than 3 cm on the subject's CT scan is indicative of the subject having lung cancer. 
     
     
         29 . The method of  claim 25 , wherein the subject's time since quitting smoking greater than 15 years is indicative of the subject having lung cancer. 
     
     
         30 . The method of  claims 5 - 8  and  13 - 19 , wherein the one or more genes comprise one or more genes from Table 14. 
     
     
         31 . The method of  claims 5 - 8  and  13 - 19 , wherein the one or more genes comprise one or more genes from Table 15. 
     
     
         32 . The method of  claims 1 - 4  and  9 - 29 , wherein the one or more genes comprise one or more genes from Table 13. 
     
     
         33 . The method of  claims 1 - 4  and  9 - 29 , wherein the one or more genes comprise all of the genes from Table 13. 
     
     
         34 . The method of  claims 1 - 33 , wherein the one or more genes comprise one or more leading edge genes from Table 21. 
     
     
         35 . The method of  claims 1 - 34 , wherein the one or more genes comprise the genes from Table 13. 
     
     
         36 . The method of  claims 1 - 35 , wherein the one or more genes further comprise one or more genes from Table 5. 
     
     
         37 . The method of  claims 1 - 36 , wherein the one or more genes further comprise one or more genes from Table 6. 
     
     
         38 . The method of  claims 1 - 37 , wherein the expression of the one or more genes is determined using a quantitative reverse transcription polymerase chain reaction, a bead-based nucleic acid detection assay or a oligonucleotide array assay. 
     
     
         39 . The method of  claims 1 - 4  and  9 - 38 , wherein the lung cancer is selected from the group consisting of adenocarcinoma, squamous cell carcinoma, small cell cancer or non-small cell cancer. 
     
     
         40 . The method of  claims 1 - 39 , wherein the one or more genes comprise mRNA. 
     
     
         41 . The method of  claim 1 - 40 , wherein the biological sample does not comprise bronchial epithelial cells or bronchial epithelial tissue. 
     
     
         42 . The method of  claims 1 - 41 , wherein the one or more genes is associated with DNA damage. 
     
     
         43 . The method of  claims 1 - 41 , wherein the one or more genes is associated with regulation of apoptosis. 
     
     
         44 . The method of  claims 1 - 41 , wherein the one or more genes is associated with immune system activation. 
     
     
         45 . The method of  claim 44 , wherein the one or more genes is associated with the interferon-gamma signaling pathway. 
     
     
         46 . The method of  claim 44 , wherein the one or more of the genes is associated with antigen presentation. 
     
     
         47 . The method of  claims 1 - 4  and  9 - 46 , wherein the method is indicative of the subject having lung cancer or of being at risk of developing lung cancer, wherein the method further comprises administering a treatment to the subject. 
     
     
         48 . The method of  claim 47 , wherein the treatment comprises chemotherapy. 
     
     
         49 . The method of  claim 47 , wherein the treatment comprises radiation therapy. 
     
     
         50 . The method of  claim 47 , wherein the method comprises immunotherapy. 
     
     
         51 . The method of  claim 47 , wherein the method comprises surgical intervention. 
     
     
         52 . A composition comprising one or more nucleic acid probes, wherein each of the one or more nucleic acids probes specifically hybridizes with an mRNA expressed from five or more genes selected from the group of genes in Table 5, Table 6, Table 12, Table 13 or Table 21. 
     
     
         53 . The composition of  claim 52 , wherein at least ten or more genes are measured. 
     
     
         54 . The composition of  claims 52 - 53 , wherein at least fifteen genes are measured. 
     
     
         55 . The composition of  claims 52 - 54 , wherein at least twenty genes are measured. 
     
     
         56 . The composition of  claims 52 - 55 , wherein at least thirty genes are measured. 
     
     
         57 . The composition of  claims 52 - 56 , wherein at least forty genes are measured. 
     
     
         58 . The composition of  claims 52 - 57 , wherein at least fifty genes are measured. 
     
     
         59 . The composition of  claims 52 - 58 , wherein at least one hundred genes are measured. 
     
     
         60 . The composition of  claims 52 - 59 , wherein the genes in Table 12 comprise those genes identified in cluster 1. 
     
     
         61 . The composition of  claims 52 - 60 , wherein the genes in Table 12 comprise those genes identified in cluster 2. 
     
     
         62 . The composition of  claims 52 - 61 , wherein the genes in Table 12 comprise those genes identified in cluster 3. 
     
     
         63 . The composition of  claims 52 - 62 , wherein the genes in Table 12 comprise those genes identified in cluster 4. 
     
     
         64 . The composition of  claims 52 - 59 , wherein one or more genes in Table 12 comprise at least one gene from each of clusters 1, 2, 3 and 4. 
     
     
         65 . The composition of  claims 52 - 64 , wherein the one or more genes is associated with DNA damage. 
     
     
         66 . The composition of  claims 52 - 64 , wherein the one or more genes is associated with regulation of apoptosis. 
     
     
         67 . The composition of  claims 52 - 64 , wherein the one or more genes is associated with immune system activation. 
     
     
         68 . The composition of  claim 67 , wherein the one or more genes is associated with the interferon-gamma signaling pathway. 
     
     
         69 . The composition of  claim 67 , wherein the one or more of the genes is associated with antigen presentation. 
     
     
         70 . The composition of  claims 52 - 69 , wherein the one or more of the genes comprise one or more of the leading edge genes identified in Table 21. 
     
     
         71 . A minimally-invasive method of determining the likelihood that a subject does not have lung cancer, the method comprising:
 (a) detecting, by quantitative reverse transcription polymerase chain reaction, a bead-based nucleic acid detection assay or a oligonucleotide array assay, mRNA or cDNA expression levels in a sample comprising nasal epithelial cells from a subject;   (b) determining mRNA or cDNA expression levels in the sample of nasal epithelial cells of two or more gene selected from the group consisting of the genes in Table 12, Table 13 or Table 21; and   (c) based on the expression levels determined in (b), determining a lung cancer risk-score that is indicative of the likelihood that the subject does not have lung cancer.   
     
     
         72 . The method of  claim 71 , wherein the subject has undergone an indeterminate or non-diagnostic bronchoscopy procedure. 
     
     
         73 . The method of  claims 71 - 72 , wherein the genes comprise at least 5 genes from Table 13. 
     
     
         74 . The method of  claims 71 - 72 , wherein the genes comprise at least 10 genes from Table 13. 
     
     
         75 . The method of  claims 71 - 72 , wherein the genes comprise at least 15 genes from Table 13. 
     
     
         76 . The method of  claims 71 - 72 , wherein the genes comprise at least 20 genes from Table 13. 
     
     
         77 . The method of  claims 71 - 72 , wherein the genes comprise at least 25 genes from Table 13. 
     
     
         78 . The method of  claims 71 - 72 , wherein the genes comprise all of the genes from Table 13. 
     
     
         79 . The method of  claims 71 - 78 , further comprising determining one or more of the subject's clinical risk factors affecting the subject's risk for having lung cancer. 
     
     
         80 . The method of  claim 79 , wherein the one or more clinical risk factors are selected from the group consisting of advanced age, smoking status, the presence of a lung nodule greater than 3 cm on CT scan, lesion location and time since quitting smoking. 
     
     
         81 . The method of  claim 80 , wherein the subject's positive smoking status is indicative of the subject having lung cancer. 
     
     
         82 . The method of  claim 80 , wherein the subject's advanced age is indicative of the subject having lung cancer. 
     
     
         83 . The method of  claim 80 , wherein the presence of a lung nodule greater than 3 cm on the subject's CT scan is indicative of the subject having lung cancer. 
     
     
         84 . The method of  claim 80 , wherein the subject's time since quitting smoking greater than 15 years is indicative of the subject having lung cancer. 
     
     
         85 . The method of  claim 80 , wherein the genes comprise at least 5 genes from Table 13, and further comprising determining one or more of the subject's clinical risk factors affecting the subject's risk for having lung cancer, wherein the one or more clinical risk factors are selected from the group consisting of advanced age, smoking status, the presence of a lung nodule greater than 3 cm on CT scan, lesion location and time since quitting smoking 
     
     
         86 . The method of  claim 80 , wherein the subject's smoking status is determined by measuring the expression of one or more genes selected from the group consisting of genes in Table 5 or Table 6 in the epithelial cells of the subject. 
     
     
         87 . The method of  claim 80 , wherein the subject's time since quitting smoking is determined by measuring the expression of one or more genes selected from the group consisting of genes in Table 5 or Table 6 in the epithelial cells of the subject.