# Patent

## Title
Method of classifying gene expression strength in lung cancer tissues

## Abstract

The present invention provides a method of confirming the gene expression, useful in the decision of a five year survival rate of a patient with lung cancer and the use of a DNA probe kit in the method. A method useful in the decision of a survival rate of a patient with non-small cell lung cancer comprising confirming the expression strength of at least one gene in lung cancer tissues isolated from the patient.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This is a divisional of U.S. patent application Ser. No. 11/008,265, filed Dec. 10, 2004 (presently allowed). The entire disclosure of the prior application is considered part of the disclosure and is hereby incorporated by reference.


TECHNICAL FIELD
The present invention relates to a method of confirming the expression of a specific gene in lung cancer tissues, used in a technique of predicting a five year survival rate of a patient with lung cancer with high accuracy.
BACKGROUND OF THE INVENTION
When various therapies are applied to patients with cancer (carcinoma), a five year survival rate is often used as a measure of cure. That is, a five year survival rate is a probability that a patient who underwent a cancer diagnosis or therapy will be survival over five years thereafter. By this probability, a progressive level (stage) of cancer, a therapeutic effect and the like are represented.
Until now, the TNM classification comprising the combination of the size of tumor (tumor meter, represented by T), the range where metastasis to lymphonodi are observed (represented by N) and the presence or absence of distant metastasis (represented by M), each of which is determined by clinical method, has been mainly used (“Cancer of the lung,” written by Robert Ginsberg et al., 5th edition, pp. 858 to 910, Lippincott-Raven (1997)). For example, patients judged to be in stage I under the TNM classification means those having a progressive level such that a little over 60% of the patients could be survival for five years if cancer is resected by surgery. Patients judged to be in stage III means those having a progressive level such that at most 20% the patients could be survival even under the same condition.
Recently, focusing on one or two genes specifically expressed in cancer patients or cancer tissues, a therapeutic effect is often predicted by determining the difference in the expression of said gene(s) between patients showing superior therapeutic effect and patients showing poor therapeutic effect (Horio et al, Cancer Research, Vol. 54, pp. 1 to 4, Jan. 1, 1993).
SUMMARY OF THE INVENTION
However, the TNM classification cannot be applied unless outcomes of many clinical tests are accumulated. Thus, this classification is not be said to be simple and its accuracy is not satisfactory at all. And, in a method of predicting a therapeutic effect by confirming the expression of a specific gene, the correlation between the gene expression in patients with lung cancer and a five year survival rate of the patients has not been reported.
An object of the present invention is to accurately decide a survival rate of patients especially with lung cancer. In the present invention, the expression of a specific gene in lung Cancer tissues is confirmed.
Accordingly, the present invention relates to a method useful in the decision of a survival rate of a patient with non-small cell lung cancer comprising confirming the expression strength of at least one gene selected from the group consisting of WEE1 (AA039640), MYC (AA464600), TITF1 (T60168), FOSL1 (T82817), LYPLA1 (H00817), SSBP1 (R05693), SFTPC (AA487571), THBD (H59861), NICE-4 (AA054954), PTN (AA001449), SNRPB (AA599116), NAP1L1 (R93829) CTNND1 (AA024656), CCT3 (R60933), DSC2 (AA074677), SPRR1B (AA447835), COPB (AA598868), ARG1 (AA453673), ARCN1 (AA598401), MST1 (T47813), SERPINE1 (N75719), SERPINB1 (AA486275), EST fragment (N73201), ACTR3 (N34974), PTP4A3 (AA039851), ISLR (H62387), ANXA1 (H63077), GJA1 (AA487623), HSPE1 (AA448396) and PSMA5 (AA598815) in lung cancer tissues isolated from the patient.
And, the present invention provides a method useful in the decision of a survival rate of a patient with squamous cell lung cancer comprising confirming the expression strength of at least one gene selected from the group consisting of FLJ20619 (R74480), SPC12 (R19183), EST fragment (R96358), KRT5 (AA160507), PTP4A3 (AA039851), SPRR1B (AA947835), LOC339324 (W23522), MYST4 (AA057313), SPARCL1 (AA990694), IGJ (T70057), EIF4A2 (H05919), EST fragment (AA115121), ID2 (H82706), THBD (H59861), MGC15476 (W72525), ZFP (H53499), COPB (AA598868), ZYG (AA453289) CACNA1I (N52765), FLJ4623 (N71473), CSTB (H22919), EPB41L1 (R71689), MGC4549 (AA455267), EST fragment (T64878), DSC2 (AA074677), EST fragment (H79007), EST fragment (W84776), IFI30 (AA630800), EST fragment (T81155) and IL1RN(T72877) in lung cancer tissues isolated from the patient.
Further, the present invention provides a method useful in the decision of the survival rate of a patient with non-squamous cell lung cancer comprising confirming the expression strength of at least one gene selected from the group Consisting of NICE-4 (AA054954), WEE1 (AA039640) SSBP1 (R05693), WFDC2 (AA451904), ACTA2 (AA634006), G22P1 (AA486311), MST1 (T47813), PHB (R60946), DRPLA (H08642), SNRBP (AA599116), GJA1 (AA487623), SFTPC (AA487571), ACTR1A(R40850), MYC (AA464600), RAD23B (A2489678), CCT3(R60933), SERPINE1 (N75719), LAMP1 (H29077), IRAK1 (AA683550), BIRC2 (R19628), LMAN1 (H73420), HSPE1 (AA448396), TMSB4X (AA634103), EEF1G (R43973), EST fragment (H05820), LYPLA1 (H00817), SOD1 (R52548), ARG1 (AA453673), KRT25A (W73634) and FOSL1 (T82817) in lung cancer tissues isolated from the patient.
Another aspect of the present invention relates to the use in the above method of a DNA probe comprising a nucleic acid sequence specifically hybridizing to at least one gene targeted in this method.
All genes which expression is to be confirmed in the present invention are known genes. The nucleotide sequence of each gene is registered in “UniGene”, one of the public databases provided by NCBI, with its abbreviated name and its accession number represented by the combination of alphabet (such as AA) and numeral. In the present specification including claims, all of the genes to be confirmed in the method of the present invention are represented with the abbreviated names and the accession numbers registered in “UniGene” on Nov. 19, 2003. Since a gene can be specified with the abbreviated name and the accession number registered in “UniGene”, those skilled in the art easily confirm a gene in question and its detailed nucleotide sequence by referring to “UniGene” and conduct the present invention. Similarly, as to a nucleic acid sequence of a DNA prove specific for each gene used in the method of the present invention, those skilled in the art can easily determine some candidate sequences for each gene based on the nucleic acid sequence registered in the above database using a homology searching program or the like. Especially, the nucleic acid sequence of the probe of the present invention is not limited unless it is selected such that the probe can be specifically hybridized to a gene corresponding therefor. It is not necessarily to restrict or limit to one nucleic acid sequence. Such a procedure can be made by those skilled in the art without having a need of any specific effort.
The present inventors studied to search for genes specifically expressed in lung cancer tissues of patients who were underwent non-small cell lung cancer diagnosis or therapy and who were dead within five years thereafter or survival over five or more years thereafter. As the result, they found that there is a specific tendency between a five year survival rate and a gene expression pattern.
Focusing on genes whose expression amounts were specifically increased or decreased in cancer tissues of the group of patients who were dead within five years after operation or diagnosis as compared with the group of patients who were survival over five years after operation or diagnosis, the present inventors selected predictive genes capable of distinguishing both groups efficiently using a signal-to-noise metrics (Golub et al., Science, Vol. 286, pp. 531 to 537 (1999)). Briefly, if a prognosis favorable patient and a prognosis fatal patient are defined to belong to class 0 and class 1 respectively, a signal-to-noise statistic (Sx) for gene x is calculated as follows:

Sx=(μclass 0−μclass 1/δclass 0+δclass 1)

As to each gene, μclass 0 means an average of data on total expression strength of patients belonging to class 0 (a group of prognosis favorable patients) and δclass 0 means a standard deviation of data on total expression strength of patients belonging to class 0 (a group of prognosis favorable patients). Using the thus-calculated absolute value of Sx, genes ranked higher, i.e. genes showing a significant difference in expression strength between the group of prognosis favorable patients and the group of prognosis fatal patients, were selected.

In order to assay a statistical significance of a marker gene specific for a different type of cancer, a temple level (prognosis favorable or fatal) of each patient used in the analysis in association with a set of data on gene expression strength were randomly labeled and then the signal-to-noise value (Sx value) was recalculated in accordance with the labels after randomizing. This procedure was repeated 10,000 times. P values were assigned to every genes based on the extent so that Sx value obtained by randomizing the labels was better than Sx value obtained actually.
When genes to be judged that they are significantly related to a survival rate of patients with a different type of lung cancer, i.e. predictive genes, were searched for among genes expressed in cancer tissues of the patients, the following correlation became clear.
Thus, an expression pattern such that in many lung cancer tissues of patients who were underwent non-small cell lung cancer diagnosis or therapy and dead within five years thereafter, the expression of each of WEE1 (AA039640), MYC (AA464600), FOSL1 (T82817), LYPLA1 (H00817), SSBP1 (R05693), THEM (H59861), NICE-4 (AA054954), PTN (AA001449), SNRPB (AA599116), NAP1L1 (R93829), CTNND1 (AA024656), CCT3 (R60933), DSC2 (AA074677), SPRR1B (AA447835), COPB (AA598868), ARG1 (AA453673), ARCN1 (AA598401), MST1 (T47813), SERPINE1 (N75719), SERPINB1 (AA486275), ACTR3 (N34974), PTP4A3 (AA039851), ISLR (H62387), ANXA1 (1163077), GJA1 (AA487623), HSPE1 (AA448396) and PSMA5 (AA598815) was significantly increased and the expression of each of TITF1 (T60168), SFTPC (AA487571) and EST fragment (N73201) was significantly lowered was observed. Hereinafter, the group comprising the above genes is referred to be a gene group 1.
Accordingly, by extracting total RNAs from cancer tissues of a patient who was underwent a non-small cell lung cancer diagnosis and confirming the expression strength of at least one gene belonging to the gene group 1, it is possible to predict a five year survival rate of the patient whether the patient would be dead within five years or survival over five or more years.
For example, when PTP4A3 (AA039851, fatal) is selected as a gene and a five year survival rate is predicted based on the outcome obtained by confirming the expression strength of this gene, an accuracy of 64% can be expected. When WEE1 (AA039640, fatal) or ACTR3 (N34974, fatal) is selected as a gene in addition to PTP4A3 (AA039851, fatal) and a five year survival rate is predicted based on the outcomes obtained by confirming the expression strength of these genes, an accuracy will be 66% or 7.4%. And, based on the outcomes obtained by confirming the expression strength of all genes constituting the gene group 1, an accuracy will reach 82%. The above outcomes have reliability higher than that of the prior method.
Although non-small cell lung cancer is further classified squamous cell cancer (SQ) and non-squamous cell cancer (non-SQ), the gene group 1 is useful as a gene group selected when a five year survival rate is decided without subdividing the type of lung cancer cells.
On the other-hand, the present inventors confirmed the gene expression strength for squamous cell cancer (SQ) and non-squamous cell cancer (non-SQ) and as the result, they found that a five year survival rate can be decided more accurately by using a gene group different from the gene group 1 as targets.
Thus, an expression pattern such that in many lung cancer tissues of patients who were underwent squamous cell cancer diagnosis of therapy and dead within five years thereafter, the expression of each of KRT5 (AA160507), PTP4A3 (AA039851), SPRR1B (AA447835), MYST4 (AA057313), SPARCL1 (AA490694), IGJ (T70057), EST fragment (M115121), 102 (H82706), THBD (H59861), MGC15476 (W72525), COPB (AA598868), ZYG (AA453289), CACNA1I (N52765), CSTB (1122919), EPB41L1 (R71689), MGC4549 (AA455267), DSC2 (AA074677), IFI30 (AA630800), EST fragment (T81155) and IL1RN(T72877) was significantly increased and the expression of each of FLJ20619 (R74480), SPC12 (R19183), EST fragment (R96358), LOC339324 (W23522), EIF4A2 (H05919), ZFP (H53499), FLJ4623 (N71473), EST fragment (T64878), EST fragment (H79007) and EST fragment (W84776) was significantly lowered was observed. Hereinafter, the group comprising the above genes is referred to be a gene group 2.
Accordingly, by extracting total RNAs from cancer tissues of a patient who was underwent a squamous cell cancer diagnosis and confirming the expression strength of at least one gene belonging to the gene group 2, it is possible to predict a five year survival rate of the patient whether the patient would be dead within five years or survival over five or more years.
For example, when CACNAII (N52765, fatal) is selected as a gene and a five year survival rate is predicted based on the outcome obtained by confirming the expression strength of this gene, an accuracy of 81% can be expected. When FLJ20619 (R74480, favorable) is selected as a gene in addition to CACNAII (N52765, fatal) and a five year survival rate is predicted based on the outcomes obtained by confirming the expression strength of these genes, an accuracy will be 75% or 81%. And, based on the outcomes obtained by confirming the expression strength of all genes constituting the gene group 2, an accuracy will reach 100%.
And, an expression pattern such that in many lung cancer tissues of patients who were underwent non-squamous cell cancer diagnosis or therapy and dead within five years thereafter, the expression of each of NICE-4 (AA054954), WEE1 (AA039640), SSBP1 (R05693), G22P1 (AA486311), MST1 (T47813) PHB (R60946), DRPLA (H08642), SNRBP (AA599116), GJA1 (AA487623), ACTR1A (R40850), MYC (AA464600), RAD23B (AA489678), CCT3 (R60933), SERPINE1 (N75719), BIRC2 (R19628), LMAN1 (H73420) HSPE1 (AA448396), EEF1G (R43973), EST fragment (1405820), LYPLA1 (H00817), SOD1 (R52548), ARG1 (AA453673), KRT25A (W73634) and FOSL1 (T82817) was significantly increased and the expression of each of WFDC2 (AA451904), ACTA2 (AA634006), SFTPC (AA487571), LAMP1 (H29077), IRAK1 (AA683550) and TMSB4X (AA634103) was significantly lowered was observed. Hereinafter, the group comprising the above genes is referred to be a gene group 3.
Accordingly, by extracting total RNAs from cancer tissues of a patient who was underwent a non-squamous cell cancer and confirming the expression strength of at least one gene belonging to the gene group 3, it is possible to predict a five year survival rate of the patient whether the patient would be dead within five years or survival over five or more years.
For example, when SFTPC (AA487571, favorable) is selected as a gene and a five year survival rate is predicted based on the outcome obtained by confirming the expression strength of this gene, an accuracy of 56% can be expected. When NICE-4 (AA054954, fatal) or GJA1 (AA487623, fatal) is selected as a gene in addition to SFTPC (AA487571, favorable) and a five year survival rate is predicted based on the outcomes obtained by the expression strength of these genes, an accuracy will be 79% or 76%. And, based on the outcomes obtained by the expression strength of all genes constituting the gene group 3, an accuracy will reach 91%.
As mentioned above, it is preferable to select two or more genes, more preferably all genes belonging to each gene group as targets although only one gene may be freely selected from each gene group and used it.
Further, the present invention provides information about samples γobtained from cancer tissues of new patients for deciding whether the patients will be survival or dead based on the above correlation.
In order to decide whether new patients with lung cancer (test samples γ) will be prognostic favorable or fatal after five years, Vx may be calculated for each gene contained in a set of predictive genes from the equation: Vx=Sx(Gxγ−bx) wherein Sx is the above-mentioned signal-to-noise statistic; Gxγ represents the expression strength of each gene x contained in the set of predictive genes; and bx is calculated from the equation: bx=(μclass 0+μclass 1)/2. When the sum of Vx (ΣVx) for the genes contained in the set of predictive genes is calculated to be plus (+), the patient in question is decided to be “prognosis favorable”. When ΣVx is calculated to be minus (−), the patient in question is decided to be “prognosis fatal”.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 represents the outcomes obtained by predicting patients with non-squamous cell lung cancer using 25 predictive genes in a weighted-voting model.
FIG. 2 is a survival curve showing the prognosis “favorable” or “fatal” of patients with non-small cell lung cancer.
FIG. 3 represents the outcomes obtained by predicting patients with non-squamous cell lung cancer using 12 predictive genes in a weighted-voting model.
FIG. 4 represents the outcomes obtained by predicting patients with squamous cell lung cancer using 19 predictive genes in a weighted-voting model.
FIG. 5 is a survival curve showing the prognosis “favorable” or “fatal” of patients with non-squamous cell lung cancer.
FIG. 6 is a survival curve showing the prognosis “favorable” or “fatal” of patients with squamous cell lung cancer.



EFFECT OF THE INVENTION
By using the method of the present invention, a five year survival rate of patients with lung cancer can be predicted with high accuracy. Therefore, it is possible according to the present invention to predict whether or not a patient with a different type of lung cancer could be survival over five or more years with high accuracy by Confirming that a specified gene group is expressed in cancer tissues of the patient.
DISCLOSURE OF THE INVENTION
Expression strength of each gene belonging to the gene group specified in the present invention can be confirmed by providing a specific probe every nucleotide sequence and conducting PCR or hybridization. The nucleotide sequence of each gene can be easily confirmed from the database “UniGene”. And, conditions such as the design of a probe specifically hybridizing to each gene, its synthesis, hybridization and the like can be suitably determined by those skilled in the art without having a need of any specific effort.
The probe can be synthesized as a set of probes capable of subjecting to PCR reaction for each gene, i.e. PCR primers. The expression strength may be confirmed by conducting PCR reaction using these primers.
Upon practice of the present method, the expression of a gene is preferably confirmed in the so-called microarray. As an microarray, a glass substrate on which probe DNAs are spotted; a membrane on which probe DNAs are spotted; beads on which probe DNAs are spotted; a glass substrate on which probes are directly synthesized; and the like have been developed. Examples of the microarray include a membrane microarray available from Invitrogen (GeneFiltersTM, Mammalian Microarrays; Catalog #GF200 or GF201). This membrane microarray contains 11168 spots in total of probe DNA corresponding to 8644 independent genes. It is confirmed by Blast search that the sequence of each probe does not occur the so-called cross hybridization even when gene (s) closely related to each sequence is (are) present, otherwise the expression of such gene (s) is detected erroneously.
Examples of the microarray available in the present invention include cDNA or oligo-arrays available from Affimetrix, Agilent and other companies, in addition to the membrane microarray available from Invitrogen.
It is desirable in the present invention to immediately frozen cancer tissues isolated from a patient with lung cancer during thoractomy or by biopsy with an endoscope or the like to prepare a slice, prepare a tissue section by hollowing out minutely regions rich in cancer cells in the slice, extract RNAs from the tissue section according to any standard method and transform all mRNAs expressed in the tissue into a cDNA by acting a reverse transcriptase thereto. In this case, the targeted gene group can be labeled by adding to the cDNA a suitable radioisotope such as 33P and the like or a fluorochrome such as Cy3, Cy5 and the like during the preparation of the cDNA via the reaction with a reverse transcriptase.
According to the present invention, based on the information about the nucleotide sequence of the gene contained in each gene group, the expression strength of the gene to be detected can be confirmed by hybridization or real time PCR using an oligoDNA specific for each gene to be detected. Preferably the expression of each gene group to be detected is confirmed more easily by combining cDNAs prepared with a reverse transcriptase and a suitable label with a microarray.
The expression strength of a gene group targeted in the present invention can be confirmed easily by hybridizing a labeled cDNA and a microarray under suitable conditions and then confirming the expression of the genes and their amounts as an index of the label. The expression strength is confirmed by quantifying the strength of a signal produced from the label by a suitable method.
For example, when a radioactive label is used, a signal strength can be quantified by exposing a hybridized array to an imaging plate (Fuji Photo Film), scanning and imaging using a bioimaging analyzer BAS 5000 (Fuji Photo Film), processing images of the hybridized array using L Process (Fuji Photo Film) and then analyzing using an analytical soft Array Gauge (Fuji Photo Film). Alternatively, the strength of a radioactive label can be quantified using a phospho-imager (Amersham). And, the strength of a fluorescent label can be quantified using a microarray reader (Agilent) or the like.
The thus-obtained data on label strength are converted to data on hybridization strength, respectively by using, for example, the method of Tseng et al. (Nucleic Acids Res., Vol., 29, pp. 2549 to 2557). Thereafter, a reproducibility in expression is evaluated after normalization, preparation of scatter plots for each gene and the like. Thus, a significant increase or decrease in expression amount of a targeted gene may be evaluated.
EXAMPLES
The present invention will be described in more detail by referring to the following examples which are not to be construed as limiting the scope of the invention.
Example 1
In the following example, all procedures using commercially available kits were conducted under conditions as recommended by the manufactures unless otherwise stated.
1) Extraction of Total RNAs from Lung Cancer Tissue
From each of 50 patients (15 females and 35 males; between the ages of 43 and 76, average age of 63) with non-small cell lung cancer, specifically 30 patients with glandular lung cancer, 16 patients with squamous cell lung cancer and 4 patients with large cell lung cancer (23 patients with stage I, 11 patients with stage II and 16 patients with stage III), lung cancer tissues (0.5 g in average) were isolated. The tissues were embedded in OCT compound and frozen at −80° C., thereby a frozen sample of 7 μm in thickness was prepared. Then, a region rich in cancer cells was carefully excised from the sample to obtain a section having cancer cells accounted for 75.4% in average of cells contained therein. From this section, total RNAs (12 μg in average) were extracted using RNAeasy (Quiagen) and a purity thereof was confirmed using RNA 600 nanoassay kit and 2100 Bioanalyzer (Agilent).
2) Hybridization to Microarray
5 micrograms of the total RNAs as prepared in the above 1) was transformed into cDNA using oligo-dT primer (Invitrogen) and Superscript II reverse transcriptase (Invitrogen) by adding 10 μCi of [32P] dCTP. GeneFilters (Invitrogen) was prehybridized in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham) containing 0.5 μg/ml of poly-dA (Invitrogen) and 0.5 μg/ml of Cot-1 DNA (Invitrogen) at 51° C. for 2 hours and then hybridized with a modified radiolabeled probe cDNA for 17 hours.
After hybridizing, the microarray was washed with a solution containing 2M urea, 0.1% SDS, 50 mM sodium phosphate buffer solution (pH 7.0), 150 mM NaCl, 1 mM MgCl2 and 0.2% AlkPhos DIRECT blocking reagent (Amersham) twice, a solution containing 2 mM MgCl2, 50 mM Tris and 100 mM NaCl twice ands solution containing 2 mM MgCl2, 50 mM Tris and 15 mM NaCl twice successively. The microarray was exposed to an imaging plate (Fuji Photo Film) for 2 hours and then the imaging plate was scanned and imaged using a bioimaging analyzer BAS 5000 (Fuji Photo Film) with resolution of 25 μm. The image of the hybridized array was processed with L Process (Fuji Photo Film) and then a signal strength was quantified using an analytical soft Array Gauge (Fuji Photo Film).
3) Data Processing
The data on signal strength obtained in the above 2) was converted to data on hybridization strength, respectively. First, the method of Tseng et al. (Nucleic Acids Res., Vol. 29, pp. 2549 to 2557) was employed for selecting genes used in the fitting of a non-linear nomralization curve. After normalization, scatter plots of 50 sets of replication data on each gene were prepared and a reproducibility of expression between replication pairs was evaluated. Genes showing a Pearson correlation coefficient of 0.85 or higher were selected. An average of the first hybridization and the second hybridization was used for further analysis. In addition, genes not showing a double or half change at least an expression level were excluded. Genes having a median intensity of less than 0.3 were excluded from the following analysis.
4) Isolation of Gene for Five Year Survival
Predictive genes distinguishing patients who would be dead within five years after operation or diagnosis (prognosis fatal patients) and patients who would be survival over five years after operation or diagnosis (prognosis favorable patients) most efficiently were selected using a signal-to noise metrics (Golub et al., Science, Vol. 286, pp. 531 to 537 (1999)). Briefly, if a prognosis favorable patient and a prognosis fatal patient are defined to belong to class 0 and class 1 respectively, a signal-to-noise statistic (Sx) is calculated as follows:

Sx=(μclass 0−μclass 1/δclass 0+δclass 1)

As to each gene, μclass 0 means an average of data on total expression strength of patients belonging to class 0 (the group of prognosis favorable patients) and δclass 0 means a standard deviation of data on total expression strength of patients belonging to class 0 (the group of prognosis favorable patients).

Genes ranked higher based on the absolute value of Sx were selected. In order to predict the outcomes using the thus-selected genes, a weighted-voting Classification algorithm was employed. The thus-obtained outcome classifiers were tested using a leave-one-out cross validation. In this scheme, the algorithm can be employed to find decision boundaries between class average and bx=(μclass 0+μclass 1)/2 for each gene, in addition to the calculation of Sx.
5) Permutation Test
In order to assay a statistical significance of a marker gene specific for a different type of cancer, a sample level (survival or dead) of each patient used in the analysis together with a set of data on gene expression strength were labeled randomly and then the signal-to-noise value (Sx value) for each gene was recalculated in accordance with the labels after randomizing. This procedure was repeated 10,000 times. P values were assigned to every genes based on the extent so that Sx value obtained by randomizing the labels was better than Sx value obtained actually.
6) Construction of Model Predicting Survival Rate of Patients with Non-Small Cell Cancer
In order to develop an outcome prediction classifier of each patient, a signal-to-noise metrics was employed for selecting a gene distinguishing prognosis favorable patients from prognosis fatal patients most clearly. As the outcomes of a non-supervised hierarchical clustering algorithm using spots ranked top 100 corresponding to unique 98 genes, two major branches representing prognosis favorable patients and prognosis fatal patients were obtained. Among 21 patients with non-small cell cancer, 19 patients (left frame), i.e. the favorable branch, were survival over five years after operation. On the other hand, among 29 patients with non-small cell cancer, 15 patients (right frame),i.e. the fatal branch, were dead within five years after operation. The Kaplan-Meier survival curve reveals statistically significant difference.
Since our final goal was to develop outcome classifiers at patient level, a supervised learning method was employed. Thus, weighted-voting outcome classifiers were constructed based on the predictive genes preselected using the signal-to-noise metrics. A learning error against each model while increasing the number of predictive genes used was calculated by a leave-one-out cross validation. Among 30 genes constituting the outcome classifiers for non-small cell cancer (Table 1), the weighted-voting model using 25 predictive genes ranked top 25 revealed the highest accuracy such that 41 patients (82%) of 50 patients revealed the outcomes as predicted individually (FIG. 1).







TABLE 1







Non-small cell cancer



















expression in






Rank
Gene
Description
accession No.
lung cancer
P
bx
Sx
SEQ ID NO.


















1
WEE1
WEE1 homolog
AA039640
Up
0.0027
0.483
0.483
SEQ ID NO: 1


2
MYC
v-myc viral oncogene homolog
AA464600
Up
0.0057
0.479
0.441
SEQ ID NO: 2


3
TITF1
thyroid transcription factor 1
T60168
Down
0.0085
0.452
0.416
SEQ ID NO: 3


4
FOSL1
FOS-like antigen 1 (Fra-1)
T82817
Up
0.0062
0.330
0.411
SEQ ID NO: 4


5
LYPLA1
lysophospholipase I
H00817
Up
0.0081
0.460
0.408
SEQ ID NO: 5


6
SSBP1
single-stranded DNA binding protein
R05693
Up
0.0199
0.495
0.406
SEQ ID NO: 6


7
SFTPC
surfactant, pulmonary-associated protein C
AA487571
Down
0.0113
0.322
0.405
SEQ ID NO: 7


8
THBD
thrombomodulin
H59861
Up
0.0099
0.466
0.403
SEQ ID NO: 8


9
NICE-4
NICE-4 protein
AA054954
Up
0.0099
0.514
0.403
SEQ ID NO: 9


10
PTN
pleiotrophin (heparin binding growth factor 8)
AA001449
Up
0.0100
0.500
0.401
SEQ ID NO: 10


11
SNRPB
small nuclear ribonucleoprotein polypeptides
AA599116
Up
0.0115
0.657
0.394
SEQ ID NO: 11




B and B1


13
CTNND1
catenin delta 1
R93829
Up
0.0120
0.513
0.393
SEQ ID NO: 12


12
NAP1L1
nucleosome assembly protein 1-like 1
AA024656
Up
0.0131
0.483
0.384
SEQ ID NO: 13


14
CCT3
chaperonin containing TCP1, subunit 3
R60933
Up
0.0186
0.566
0.378
SEQ ID NO: 14


15
DSC2
desmocollin 2
AA074677
Up
0.0160
0.533
0.374
SEQ ID NO: 15


16
SPRR1B
small proline-rich protein 1B (cornifin)
AA447835
Up
0.0209
0.421
0.370
SEQ ID NO: 16


17
COPB
coatomer protein complex, subunit beta
AA598868
Up
0.0195
0.466
0.369
SEQ ID NO: 17


18
ARG1
arginase type I (liver)
AA453673
Up
0.0193
0.581
0.369
SEQ ID NO: 18


19
ARCN1
archain 1 (coatomer protein complex,
AA598401
Up
0.0169
0.412
0.367
SEQ ID NO: 19




subunit delta)


20
MST1
macrophage stimulating 1
T47813
Up
0.0193
0.462
0.366
SEQ ID NO: 20


21
SERPINE1
serine (or cysteine) proteinase inhibitor,
N75719
Up
0.0194
0.495
0.366
SEQ ID NO: 21




clade E member 1


22
SERPINB1
serine (or cysteine) proteinase inhibitor,
AA486275
Up
0.0205
0.556
0.362
SEQ ID NO: 22




clade B member 1


23
ESTs

N73201
Down
0.0205
0.494
0.360
SEQ ID NO: 23


24
ACTR3
actin-related protein 3 homolog (ARP3)
N34974
Up
0.0229
0.496
0.358
SEQ ID NO: 24


25
PTP4A3
protein tyrosine phosphatase type 4A,
AA039851
Up
0.0199
0.478
0.357
SEQ ID NO: 25




member 3


26
ISLR
immunoglobulin superfamily containing
H62387
Up
0.0228
0.478
0.356
SEQ ID NO: 26




leucine-rich repeat


27
ANXA1
annexin A1
H63077
Up
0.0262
0.367
0.354
SEQ ID NO: 27


28
GJA1
gap junction protein, alpha 1
AA487623
Up
0.0230
0.406
0.354
SEQ ID NO: 28


29
HSPE1
heat shock 10 kD protein 1
AA448396
Up
0.0273
0.444
0.352
SEQ ID NO: 29


30
PSMA5
proteasome (prosome, macropain) subunit,
AA598815
Up
0.0265
0.545
0.346
SEQ ID NO: 30




alpha type, 5









As to these classifiers, 27 patients of 33 patients (82%) practically survival over five or more years after operation were decided to be “prognosis favorable” and 14 patients of 17 patients (82%) practically dead within five years after operation were decided to be “prognosis fatal”. A survival curve of patients for the prediction of “prognosis favorable” or “prognosis fatal” is shown in FIG. 2. This figure reveals the difference between two groups (P=6.0×10−6).
With the increase in the number of the above genes, another supervised learning algorithm including Support vector machine and k-nearest neighbors was employed. The accuracy of the model is comparable with that of the weighted-voting outcome classifiers, but the latter showed the highest accuracy.
In order to decide whether new patients with lung cancer (test samples γ) could be prognosis favorable or fatal after five years, Vx may be calculated for each gene contained in the set of predictive genes from the equation: Vx=Sx (Gxγ−bx) wherein Sx is the above-mentioned signal-to-noise statistic; GXγ represents an expression strength of each gene x contained in the set of predictive genes; and bx is calculated from bx=(μclass 0+μclass 1)/2. When the sum of VX (ΣVx) for genes contained in the set of predictive genes is calculated to be plus (+), the patient in question is decided to be “prognosis favorable”. When ΣVx is calculated to be minus (−), the patient in question is decided to be “prognosis fatal”.
With the increase in the number of the above genes, another supervised learning algorithm including Support vector machine and k-nearest neighbors was employed. The accuracy of the model is comparable with that of the weighted-voting outcome classifiers, but the latter showed the highest accuracy.
7) Construction of Model Predicting Survival Rate Specific for Each of Squamous Cell Cancer and Non-Squamous Cell Cancer
Squamous cell cancer and non-squamous cell cancer are recognized as diseases distinguishable clinicopathologically each other. Thus, using predictive genes for each subtype selected with the weighted-voting algorithm and the signal-to-noise metrics, outcome prediction classifiers for a different type of cancer were constructed.
Among 30 genes constituting the outcome classifiers for a different type of cancer (Tables 2 and 3), 12 genes (Table 2) for non-squamous cell cancer and 19 genes (Table 3) for squamous cell cancer revealed the highest accuracy by a leave-one-out cross validation including the increase in the number of predictive genes ranked higher.







TABLE 2







Non-squamous cell cancer



















expression in






Rank
Gene
Description
accession No.
lung cancer
P
bx
Sx
SEQ ID NO.


















1
NICE-4
NICE-4 protein
AA054954
Up
0.0036
0.567
0.604
SEQ ID NO: 9


2
WEE1
WEE1 homolog
AA039640
Up
0.0039
0.485
0.567
SEQ ID NO: 1


3
SSBP1
single-stranded DNA binding protein
R05693
Up
0.0122
0.466
0.500
SEQ ID NO: 6


4
WFDC2
WAP four-disulfide core domain 2
AA451904
Down
0.0155
0.544
0.489
SEQ ID NO: 56


5
ACTA2
actin, alpha 2, smooth muscle, aorta
AA634006
Down
0.0149
0.684
0.487
SEQ ID NO: 57


6
G22P1
thyroid autoantigen 70 kDa (Ku70)
AA486311
Up
0.0176
0.519
0.482
SEQ ID NO: 58


7
MST1
macrophage stimulating 1
T47813
Up
0.0153
0.462
0.481
SEQ ID NO: 20


8
PHB
prohibitin
R60946
Up
0.0219
0.419
0.472
SEQ ID NO: 59


9
DRPLA
dentatorubral-pallidoluysian atrophy
H08642
Up
0.0238
0.478
0.455
SEQ ID NO: 60


10
SNRPB
small nuclear ribonucleoprotein polypeptides
AA599116
Up
0.0192
0.615
0.455
SEQ ID NO: 11




B and B1


11
GJA1
gap junction protein, alpha 1
AA487623
Up
0.0268
0.332
0.446
SEQ ID NO: 61


12
SFTPC
surfactant, pulmonary-associated protein C
AA487571
Down
0.0313
0.350
0.445
SEQ ID NO: 7


13
ACTR1A
actin-related protein 1 homolog A
R40850
Up
0.0256
0.626
0.444
SEQ ID NO: 62


14
MYC
v-myc viral oncogene homolog
AA464600
Up
0.0294
0.385
0.434
SEQ ID NO: 2


15
RAD23B
RAD23 homolog B
AA489678
Up
0.0276
0.495
0.434
SEQ ID NO: 63


16
CCT3
chaperonin containing TCP1, subunit 3
R60933
Up
0.0305
0.548
0.431
SEQ ID NO: 14


17
SERPINE1
serine (or cysteine) proteinase inhibitor,
N75719
Up
0.0338
0.473
0.424
SEQ ID NO: 21




clade E member 1


18
LAMP1
lysosomal-associated membrane protein 1
H29077
Down
0.0374
0.382
0.418
SEQ ID NO: 64


19
IRAK1
interleukin-1 receptor-associated kinase 1
AA683550
Down
0.0355
0.199
0.414
SEQ ID NO: 65


20
BIRC2
baculoviral IAP repeat-containing 2
R19628
Up
0.0362
0.359
0.411
SEQ ID NO: 66


21
LMAN1
lectin, mannose-binding, 1
H73420
Up
0.0339
0.409
0.411
SEQ ID NO: 67


22
HSPE1
heat shock 10 kD protein 1
AA448396
Up
0.0411
0.406
0.410
SEQ ID NO: 68


23
TMSB4X
thymosin, beta 4, X chromosome
AA634103
Down
0.0440
0.585
0.404
SEQ ID NO: 69


24
EEF1G
eukaryotic translation elongation factor
R43973
Up
0.0450
0.638
0.404
SEQ ID NO: 70




1 gamma


25
ESTs

H05820
Up
0.0492
0.570
0.403
SEQ ID NO: 71


26
LYPLA1
lysophospholipase I
H00817
Up
0.0488
0.456
0.401
SEQ ID NO: 5


27
SOD1
superoxide dismutase 1
R52548
Up
0.0477
0.609
0.397
SEQ ID NO: 72


28
ARG1
arginase type I (liver)
AA453673
Up
0.0454
0.541
0.396
SEQ ID NO: 18


29
KRT25A
type I inner root sheath specific keratin
W73634
Up
0.0534
0.584
0.394
SEQ ID NO: 75




25 irs1


30
FOSL1
FOS-like antigen 1 (Fra-1)
T82817
Up
0.0366
0.309
0.391
SEQ ID NO: 4
















TABLE 3







Squamous cell cancer



















expression in






Rank
Gene
Description
accession No.
lung cancer
P
bx
Sx
SEQ ID NO.


















1
FLJ20619
hypothetical protein
R74480
Down
0.0068
0.507
0.882
SEQ ID NO: 31


2
SPC12
signal peptidase 12 kDa
R19183
Down
0.0087
0.521
0.859
SEQ ID NO: 32


3
ESTs

R96358
Down
0.0034
0.448
0.835
SEQ ID NO: 33


4
KRT5
keratin 5
AA160507
Up
0.0046
0.841
0.789
SEQ ID NO: 34


5
PTP4A3
protein tyrosine phosphatase type 4A, member 3
AA039851
Up
0.0104
0.438
0.753
SEQ ID NO: 25


6
SPRR1B
small proline-rich protein 1B
AA447835
Up
0.0147
0.695
0.730
SEQ ID NO: 16


7
LOC339324
hypothetical protein LOC339324
W23522
Down
0.0171
0.536
0.693
SEO ID NO: 35


8
MYST4
MYST histone acetyltransferase 4
AA057313
Up
0.0188
0.573
0.691
SEQ ID NO: 36


9
SPARCL1
SPARC-like 1
AA490694
Up
0.0210
0.454
0.682
SEQ ID NO: 37


10
IGJ
immunoglobulin J polypeptide
T70057
Up
0.0143
0.385
0.681
SEQ ID NO: 38


11
EIF4A2
eukaryotic translation initiation factor 4A, isoform 2
H05919
Down
0.0233
0.750
0.679
SEQ ID NO: 39


12
ESTs

AA115121
Up
0.0226
0.412
0.672
SEQ ID NO: 40


13
ID2
inhibitor of DNA binding 2
H82706
Up
0.0214
0.608
0.670
SEQ ID NO: 41


14
THBD
thrombomodulin
H59861
Up
0.0077
0.636
0.669
SEQ ID NO: 8


15
MGC15476
Thymus expressed gene 3-like
W72525
Up
0.0231
0.412
0.665
SEQ ID NO: 42


16
ZFP
zinc finger protein
H53499
Down
0.0217
0.632
0.659
SEQ ID NO: 43


17
COPB
coatomer protein complex, subunit beta
AA598868
Up
0.0272
0.527
0.648
SEQ ID NO: 17


18
ZYG
ZYG homolog
AA453289
Up
0.0237
0.349
0.647
SEQ ID NO: 44


19
CACNA1I
calcium channel, voltage-dependent, alpha 1I subunit
N52765
Up
0.0312
0.495
0.636
SEQ ID NO: 45


20
FLJ4623
hypothetical protein
N71473
Down
0.0309
0.457
0.632
SEQ ID NO: 46


21
CSTB
cystatin B
H22919
Up
0.0286
0.762
0.631
SEQ ID NO: 47


22
EPB41L1
erythrocyte membrane protein band 4.1-like 1
R71689
Up
0.0482
0.690
0.613
SEQ ID NO: 48


23
MGC4549
hypothetical protein
AA455267
Up
0.0327
0.410
0.606
SEQ ID NO: 49


24
ESTs

T64878
Down
0.0406
0.457
0.600
SEQ ID NO: 50


25
DSC2
desmocollin 2
AA074677
Up
0.0407
0.656
0.592
SEQ ID NO: 15


26
ESTs

H79007
Down
0.0415
0.363
0.590
SEQ ID NO: 51


27
ESTs

W84776
Down
0.0364
0.665
0.587
SEQ ID NO: 52


28
IFI30
interferon, gamma-inducible protein 30
AA630800
Up
0.0415
0.336
0.587
SEQ ID NO: 53


29
ESTs

T81155
Up
0.0552
0.633
0.583
SEQ ID NO: 54


30
IL1RN
interleukin 1 receptor antagonist
T72877
Up
0.0431
0.573
0.578
SEQ ID NO: 55









These outcomes show that among 34 patients with non-squamous cell cancer, a five year survival rate after operation of 31 patients (91%) was accurately predicted (FIG. 3). Specifically, among 25 patients who were predicted to be “prognosis favorable”, 23 patients (92%) were actually survival over five years after operation. Among 9 patients who were decided to be “prognosis fatal”, only one patient was survival over five years. The difference between the survival curve of 25 patients who were decided to be “prognosis favorable” and that of 9 patients who were predicted to be “prognosis fatal” was very significant.

## Claims

1. A method for predicting a survival rate of a patient with squamous cell lung cancer, said method comprising the steps of:
(a) isolating a cancer tissue section or a plurality of tissue sections from said patient;
(b) extracting mRNAs from said tissue section or plurality of tissue sections;
(c) transforming said mRNAs from step (b) into cDNAs, wherein said cDNAs are Labeled;
(d) determining the expression strengths of all sequences from Group A, consisting of SEQ ID NO: 34, SEQ ID NO: 25, SEQ ID NO: 16, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 8, SEQ ID NO: 42, SEQ ID NO: 17, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49), SEQ ID NO: 15, SEQ ID NO: 53, SEQ ID NO: 54 and SEQ ID NO: 55 and Group B consisting of SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 39, SEQ ID NO: 43, SEQ ID NO: 46, SEQ ID NO: 50, SEQ ID NO: 51, and SEQ ID NO: 52, and
(e) predicting a favorable prognosis when the expression of the sequences of Group A are collectively increased while the expression of the sequences of Group B are collectively decreased, or predicting a fatal prognosis when the expressions of the sequences of Group A are collectively decreased while the expressions of the sequences of Group B are collectively increased.