Compositions, Methods and Kits for Diagnosis of Lung Cancer

Abstract

The present invention provides methods for identifying biomarker proteins that exhibit differential expression in subjects with a first lung condition versus healthy subjects or subjects with a second lung condition. The present invention also provides compositions comprising these biomarker proteins and methods of using these biomarker proteins or panels thereof to diagnose, classify, and monitor various lung conditions. The methods and compositions provided herein may be used to diagnose or classify a subject as having lung cancer or a non-cancerous condition, and to distinguish between different types of cancer (e.g., malignant versus benign, SCLC versus NSCLC).

What is claimed is: 
     
         1 . A method of determining that a lung condition in a subject is cancer comprising:
 (a) assessing the expression of a plurality of proteins comprising determining the protein expression level of at least each of ALDOA_HUMAN, FRIL_HUMAN, LG3BP_HUMAN, TSP1_HUMAN and COIA1_HUMAN from a biological sample obtained from the subject;   (b) calculating a score from the protein expression of at least each of ALDOA_HUMAN, FRIL_HUMAN, LG3BP_HUMAN, TSP1_HUMAN and COIA1_HUMAN from the biological sample determined in step (a); and   (c) comparing the score from the biological sample to a plurality of scores obtained from a reference population, wherein the comparison provides a determination that the lung condition is not cancer.   
     
     
         2 . The method of  claim 1 , wherein the subject has a pulmonary nodule. 
     
     
         3 . The method of  claim 2 , wherein the pulmonary nodule is 30 mm or less. 
     
     
         4 . The method of  claim 3 , wherein the pulmonary nodule is between 8-30 mm. 
     
     
         5 . The method of  claim 1 , wherein said lung condition is cancer or a non-cancerous lung condition. 
     
     
         6 . The method of  claim 1 , wherein said cancer is non-small cell lung cancer. 
     
     
         7 . The method of  claim 1 , wherein said non-cancerous lung condition is chronic obstructive pulmonary disease, hamartoma, fibroma, neurofibroma, granuloma, sarcoidosis, bacterial infection or fungal infection. 
     
     
         8 . The method of  claim 1 , wherein the subject is a human. 
     
     
         9 . The method of  claim 1 , wherein said biological sample is tissue, blood, plasma, serum, whole blood, urine, saliva, genital secretions, cerebrospinal fluid, sweat, excreta, or bronchoalveolar lavage. 
     
     
         10 . The method of  claim 1 , wherein assessing the expression of a plurality of proteins further comprises determining the protein expression level of at least one of PEDF_HUMAN, MASP1_HUMAN, GELS_HUMAN, LUM_HUMAN, C163A_HUMAN and PTPRJ_HUMAN. 
     
     
         11 . The method of  claim 1 , wherein determining the protein expression level of at least each of ALDOA_HUMAN, FRIL_HUMAN, LG3BP_HUMAN, TSP1_HUMAN and COIA1_HUMAN comprises fragmenting each protein to generate at least one peptide. 
     
     
         12 . The method of  claim 11 , wherein the proteins are fragmented by trypsin digestion. 
     
     
         13 . The method of  claim 12 , further comprising providing a synthetic, modified, heavy peptides corresponding to each peptide generated from each of ALDOA_HUMAN, FRIL_HUMAN, LG3BP_HUMAN, TSP1_HUMAN and COIA1_HUMAN. 
     
     
         14 . The method of  claim 13 , wherein at least one of the synthetic peptides has an isotopic label attached. 
     
     
         15 . The method of  claim 1 , wherein assessing the expression of a plurality of proteins is performed by mass spectrometry (MS), liquid chromatography-selected reaction monitoring/mass spectrometry (LC-SRM-MS), reverse transcriptase-polymerase chain reaction (RT-PCR), microarray, serial analysis of gene expression (SAGE), gene expression analysis by massively parallel signature sequencing (MPSS), immunoassays, immunohistochemistry (IHC), transcriptomics, or proteomics. 
     
     
         16 . The method of  claim 15 , wherein the expression of a plurality of proteins is performed by liquid chromatography-selected reaction monitoring/mass spectrometry (LC-SRM-MS). 
     
     
         17 . The method of  claim 11 , wherein a transition for each peptide is determined by liquid chromatography-selected reaction monitoring/mass spectrometry (LC-SRM-MS). 
     
     
         18 . The method of  claim 17 , wherein the peptide transitions comprise at least ALQASALK (401.25, 617.4), AVGLAGTFR (446.26, 721.4), GFLLLASLR (495.31, 559.4), LGGPEAGLGEYLFER (804.4, 1083.6), and VEIFYR (413.73, 598.3). 
     
     
         19 . The method of  claim 1 , wherein said score is determined as P s =1/[1+exp(−α−Σ i=1   5 β i *I i,s −γ*I COIA1 *I FRIL ], where {hacek over (I)} is Box-Cox transformed and normalized intensity of transition i in said sample (s), β i  is the corresponding logistic regression coefficient, α is a panel-specific constant, and γ is a coefficient for the interaction term.