WO2012023286A1 - Lrrc42 as a target gene for cancer therapy and diagnosis - Google Patents

Abstract

Objective methods for diagnosing or detecting cancer, or determining a predisposition to developing cancer is described herein. In one embodiment, the present invention provides a diagnostic method that utilizes the expression level of LRRC42 as an index of cancer. The present invention further provides methods of screening for therapeutic substances useful in the treatment of LRRC42-associated disease, such as cancer, e.g. lung cancer. The invention further provides methods of inhibiting the cell growth and thus treating or alleviating one or more symptoms of LRRC42-associated diseases. The invention also features double-stranded molecules that inhibit the expression of LRRC42 gene, vectors encoding thereof and compositions containing them.

Description

LRRC42 AS A TARGET GENE FOR CANCER THERAPY AND DIAGNOSIS

The present invention relates to methods of detecting and diagnosing cancer as well as methods of treating and preventing cancer, particularly cancers associated with the overexpression of LRRC42 such as lung cancer. The present invention also relates to methods of screening for a candidate substance for treating and preventing an LRRC42-associated cancer. Moreover, the present invention relates to double-stranded molecules that reduce LRRC42 gene expression and uses thereof.

Priority
The present application claims the benefit of U.S. Provisional Application No. 61/401,869, filed on August 19, 2010, the entire contents of which are incorporated by reference herein.

Lung cancer is the most common form of cancer, accounting for 1.35 million of the 10.9 million new cases of cancer per year. It is also the leading cause of death from cancer-associated disease, accounting for 1.18 million of the 6.7 million cancer-related deaths worldwide (NPL1). Over the last decade, newly developed cytotoxic agents such as paclitaxel, docetaxel, gemcitabine, and vinorelbine have emerged to offer multiple therapeutic choices for patients with advanced NSCLC (non-small cell lung cancer); however, each of the new regimens can provide only modest survival benefits as compared with cisplatin-based therapies (NPL 2).

Recently, molecular-targeted agents, including anti-EGFR or anti-VEGF monoclonal antibody, cetuximab (Erbitux) or Bevacizumab (Avastin), and small molecule inhibitors of EGFR tyrosine kinase, such as gefitinib (Iressa) and erlotinib (Tarceva), have been examined and/or approved for clinical use (NPL 3, 4). These agents display activity against recurrent NSCLC to a certain extent, but the number of patients who could receive a survival benefit is still limited. Meanwhile patients with SCLC (small cell lung cancer) respond favorably to the 1^st line multi-agent chemotherapy, though they often relapse in a short time. Only 20% of patients with limited-stage disease (LD) can be cured with combined modality therapy and less than 5% of those with extensive-disease (ED) can achieve 5-year survival after the initial diagnosis (NPL 5). Hence, new therapeutic strategies, such as development of more selective and effective molecular-targeted agents against lung cancer, are eagerly awaited.

Systematic analysis of expression levels of thousands of genes using a cDNA microarray technology has been shown to be an effective means to identify target molecules associated with carcinogenic pathways that can serve as candidates for development of novel therapeutics and diagnostics. To isolate potential novel molecular targets for diagnosis, treatment and prevention of human cancers, genome-wide expression profiles of 120 cases of lung cancers were analyzed using a cDNA microarray containing 27,648 genes or expressed sequence tags (ESTs), coupled with laser microdissection; in the course of this study, several candidate molecular targets and biomarkers for lung cancer treatment were found (PTLs 1-2, NPLs 6-9). Among the transactivated genes, LRRC42 (Leucine rich repeat containing 42) is of particular note.

Leucine rich repeats (LRRs) are widespread strucutual motifs comprising 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucine residues. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. LRR containing proteins participate in many important biological processes, including plant and animal immunity, hormone-receptor interactions, cell adhesion, signal transduction, regulation of gene expression, and apoptosis (NPLs 10-13). However, the pathophysiological role and the biological functions of LRRC42 in cancer cells have not been reported.

[PTL1] WO2004/031413
[PTL2] WO2007/013665

Non-Patent Literature

[NPL 1] Jemal A, Siegel R, Ward E, et al. CA Cancer J Clin. 2008;58:71-96.
[NPL 2] Schiller JH, Harrington D, Belani CP, et al. Eastern Cooperative Oncology Group. N Engl J Med 2002; 346:92-8.
[NPL 3] Dowell J, Minna JD, Kirkpatrick P. Nat Rev Drug Discov 2005;4:13-4.
[NPL 4] Pal SK, Pegram M. Anticancer Drugs 2005; 16:483-94.
[NPL 5] Chute JP, Chen T, Feigal E, Simon R, Johnson BE: J Clin Oncol 1999; 17:1794-801.
[NPL6] Daigo Y, Nakamura Y. Gen Thorac Cardiovasc Surg 2008; 56:43-53.
[NPL7] Kikuchi T, Daigo Y, Katagiri T, et al. Oncogene 2003;22:2192-205.
[NPL8] Kakiuchi S, Daigo Y, Tsunoda T, Yano S, Sone S, Nakamura Y. Mol Cancer Res 2003;1:485-99.
[NPL9] Taniwaki M, Daigo Y, Ishikawa N, et al. Int J Oncol 2006;29:567-75.
[NPL10] Bella J, et al. Cell Mol Life Sci 2008; 65:2307-33.
[NPL11] Limin C, et al. Biochem Biophys Res Commun 2009;388:543-8.
[NPL12] Kajava AV. J Mol Biol 1998;277:519-27.
[NPL13] Pancer Z et al. Annu Rev Immunol 2006;24:497-518.

Central to the present invention is the discovery, through microarray analysis and RT-PCR, that LRRC42(Leucine rich repeat containing 42) is overexpressed in clinical lung cancer tissues. Furthermore, as demonstrated herein, functional knockdown of endogenous LRRC42 by siRNA in cancer cell lines results in drastic suppression of cancer cell growth, suggesting its essential role in maintaining viability of cancer cells. Since it is only scarcely expressed in adult normal organs, LRRC42 gene a particularly useful molecular target for a therapeutic approach and promising molecular target for a novel therapeutic approach with minimal adverse effect.

Accordingly, it is an object of the present invention to provide a method of detecting or diagnosing cancer, or determining a presence of or predisposition to cancer, particularly lung cancer in a subject by determining an expression level of LRRC42 gene in a subject-derived biological sample. An increase in the level of expression of LRRC42 as compared to a normal control level indicates that the subject suffers from or is at risk of developing cancer, particularly lung cancer. In the methods of the present invention, the mRNA of LRRC42 gene can be detected by appropriate probes or, primer set or, alternatively, the LRRC42 protein can be detected by anti-LRRC42 antibody.
It is another object of the present invention to provide a kit that includes a reagent for detecting a transcription or translation product of the LRRC42 gene.
It is yet another object of the present invention to provide a reagent for the diagnosis or detection of cancer that includes a nucleic acid that binds to a transcriptional product of the LRRC42 gene, or an antibody that binds to a translational product of the LRRC42 gene.
It is yet another object of the present invention to provide use of a nucleic acid that binds to a transcriptional product of the LRRC42 gene, or an antibody that binds to a translational product of the LRRC42 gene for the manufacture of a reagent for diagnosis or detection of cancer.

It is a further object of the present invention to provide methods for identifying a candidate substance that inhibits the growth of cells over-expressing the LRRC42 gene, such substances finding utility in either or both of the treatment and prevention of LRRC42- associated diseases, such as cancer. The methods of the present invention can be carried out in vitro or in vivo and use as an index the binding activity to an LRRC42 polypeptide, or an expression level of an LRRC42 gene, a biological activity of an LRRC42 polypeptide, an expression level of a reporter gene or an activity of a reporter gene controlled under a transcriptional regulatory region of the LRRC42 gene, or a binding between an LRRC42 polypeptide and a GATAD2B (GATA zinc finger domain containing 2B) polypeptide. Substances that bind to an LRRC42 polypeptide, or suppress an LRRC42 expression or activity, or a reporter gene expression or activity, or inhibit the binding between an LRRC42 polypeptide and a GATAD2B polypeptide can be identified as candidate substances for either or both of treating and preventing cancer, or inhibiting cancer cell growth. The biological activity of the LRRC42 protein to be detected is preferably cell proliferative activity (cell proliferation enhancing activity). A decrease in the biological activity of the LRRC42 protein as compared to a control level in the absence of the test substance indicates that the test substance may be used to reduce symptoms of lung cancer, or either or both of treating and preventing lung cancer.

It is yet a further object of the present invention to provide a method for either or both of the treatment and prevention of cancer, including a post-operative recurrence thereof , or inhibiting the growth of a cancerous cell over-expressing LRRC42, by administering an agent that inhibits the expression of an LRRC42 gene and/or a function of the LRRC42 protein. Preferably, the agent is an inhibitory nucleic acid (e.g., an antisense, ribozyme, double stranded molecule, aptamer). The agent may take the form a nucleic acid molecule or vector for providing double stranded molecule. Expression of the gene may be inhibited by introduction of a double stranded molecule into the target cell in an amount sufficient to inhibit expression of the LRRC42 gene. Thus, in a particularly preferred embodiment of the present invention, the method includes the step of administering to a subject a pharmaceutically effective amount of a double-stranded molecule against an LRRC42 gene or a vector encoding such a molecule, wherein the double-stranded molecule inhibits an expression of an LRRC42 gene as well as cell proliferation when introduced into a cell expression an LRRC42 gene.

It is yet a further object of the present invention to provide a pharmaceutical composition suitable for either or both of the treatment and prevention of an LRRC42-associated cancer that includes a pharmaceutically acceptable carrier and an active agent including one or more double-stranded molecules against an LRRC42 gene or a vector encoding such a molecule. In the context of the present invention, a double-stranded molecule against LRRC42 is capable of inhibiting the expression of an LRRC42 gene as well as inhibiting the cell proliferation induced thereby when introduced into a cell expressing an LRRC42 gene. In the preferred embodiment, the cancer to be treated and/or prevented is lung cancer, including NSCLCs and SCLCs. Examples of NSCLCs include lung adenocarcinoma (ADC), and lung squamous cell carcinoma (SCC).

The double-stranded molecules of the present invention are preferably composed of a sense strand and an antisense strand, wherein the sense strand includes a nucleotide sequence corresponding to a target sequence selected from among SEQ ID NOs: 7 and 8 and the antisense strand includes a sequence that is complementary to the sense strand. The sense and the antisense strands of the molecule hybridize to each other to form a double-stranded molecule. When introduced into a cell expressing an LRRC42 gene, the double-stranded molecule of the present invention inhibits an expression of the LRRC42 gene as well as cell proliferation.
The methods and materials of the present invention are capable of identifying cancer prior to detection of overt clinical symptoms thereof and may be used in the context of cancer therapy without adverse effect.

More specifically, the present invention provides the following [1] to [29]:
[1] A method of detecting or diagnosing cancer or a predisposition for developing the cancer in a subject, comprising a step of determining an expression level of an LRRC42 gene in a subject-derived biological sample, wherein an increase of said LRRC42 level as compared to a normal control level of said gene indicates that said subject suffers from or is at risk of developing cancer, wherein the expression level is determined by any one of method selected from the group consisting of:
(a) detecting an mRNA of an LRRC42 gene;
(b) detecting a protein encoded by an LRRC42 gene; and
(c) detecting a biological activity of a protein encoded by an LRRC42 gene.
[2] The method of [1], wherein said LRRC42 gene expression level is at least 10% greater than said normal control level.
[3] The method of [1], wherein the subject-derived biological sample is a biopsy specimen.
[4] The method of [1] wherein the cancer is lung cancer.
[5] A kit for diagnosing cancer or a predisposition therefore, which comprises a reagent selected from the group consisting of:
(a) a reagent for detecting an mRNA of an LRRC42 gene;
(b) a reagent for detecting a protein encoded by an LRRC42 gene; and
(c) a reagent for detecting a biological activity of a protein encoded by an LRRC42 gene.
[6] The kit of [5] wherein the reagent is a probe or a primer set to the mRNA of the LRRC42 gene, or an antibody against the protein encoded by the LRRC42 gene.
[7] A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
(a) contacting a test substance with an LRRC42 polypeptide or a fragment thereof;
(b) detecting the binding activity between the polypeptide or the fragment and the test substance; and
(c) selecting the test substance that binds to the polypeptide or the fragment as a candidate substance for either or both of treating and preventing cancer.
[8] A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
(a) contacting a test substance with a cell expressing an LRRC42 gene;
(b) detecting an expression level of the LRRC42 gene in the cell of the step (a); and
(c) selecting the test substance that reduces the expression level detected in the step (b) in comparison with the expression level of an LRRC42 gene detected in the absence of the test substance.
[9] A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
(a) contacting a test substance with an LRRC42 polypeptide or a fragment thereof;
(b) detecting a biological activity of the polypeptide or the fragment of the step (a); and
(c) selecting the test substance that suppresses the biological activity of the polypeptide or the fragment detected in the step (b) in comparison with the biological activity detected in the absence of the test substance.
[10] The method of [9], wherein the biological activity is a cell proliferative activity.
[11] A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
a) contacting a test substance with a cell into which a vector comprising the transcriptional regulatory region of LRRC42 genes and a reporter gene that is expressed under the control of the transcriptional regulatory region has been introduced,
b) measuring the expression and/or activity levels of said reporter gene in the step (a); and
c) selecting a substance that reduces the expression and/or activity levels of said reporter gene detected in the step (b) in comparison with the expression and/or activity levels in the absence of the test substance.
[12] A method of screening for a candidate substance for either or both of treating and preventing cancer, inhibiting cancer cell growth or the binding between an LRRC42 polypeptide and a GATAD2B polypeptide, wherein the method comprises the steps of:
a) contacting an LRRC42 polypeptide or a functional equivalent thereof with a GATAD2B polypeptide or a functional equivalent thereof, in the presence of a test substance;
b) detecting the binding between the polypeptides; and
c) selecting the test substance that inhibits the binding between the polypeptides.
[13] The method of [12], wherein the functional equivalent of the LRRC42 polypeptide comprises a GATAD2B-binding domain of the LRRC42 polypeptide.
[14] The method of [12] or [13], wherein the functional equivalent of the GATAD2B polypeptide comprises an LRRC42-binding domain of the GATAD2B polypeptide.
[15] The method of any one of [7] to [12], wherein the cancer is lung cancer.
[16] An isolated double-stranded molecule comprising a sense strand and an antisense strand complementary thereto, wherein the strands hybridize to each other to form the double-stranded molecule, wherein the sense strand comprises a nucleotide sequence corresponding to a target sequence selected from the group consisting of SEQ ID NOs: 7 and 8, and wherein said double-stranded molecule, when introduced into a cell expressing an LRRC42 gene, inhibits an expression of said gene as well as cell proliferation.
[17] The double-stranded molecule of [16], wherein the sense strand hybridizes with antisense strand at the target sequence to form the double-stranded molecule having between 19 and 25 nucleotide pair in length.
[18] The double-stranded molecule of [17], wherein the double-stranded molecule has one or two 3' overhangs at the 3' ends of the sense strand and/or the antisense strand.
[19] The double-stranded molecule of any one of [16] to [18], wherein said double-stranded molecule is a single polynucleotide comprising the sense strand and the antisense strand linked via a single-stranded nucleotide sequence.
[20] The double-stranded molecule of [19], wherein said polynucleotide has the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is a sense strand comprising a nucleotide sequence corresponding to a target sequence selected from the group consisting of SEQ ID NOs: 7 and 8; [B] is a nucleotide sequence consisting of about 3 to about 23 nucleotides; and [A'] is an antisense strand comprising a sequence complementary to [A].
[21] A vector encoding the double-stranded molecule of any one of [16] to [20].
[22] A method of either or both of treating and preventing a cancer in a subject, said method comprising the step of administering to said subject a pharmaceutically effective amount of a double-stranded molecule against an LRRC42 gene or a vector encoding thereof, wherein the double-stranded molecule inhibits an expression of an LRRC42 gene as well as cell proliferation when introduced into a cell expressing LRRC42 gene.
[23] The method of [22], wherein the double-stranded molecule is that of any one of [16] to [20].
[24] The method of [22], wherein the vector is that of [21].
[25] The method of any one of [22] to [24], wherein the cancer is lung cancer.
[26] A composition for either or both of treating and preventing a cancer, said composition comprising a pharmaceutically effective amount of a double-stranded molecule against an LRRC42 gene or a vector encoding thereof, and a pharmaceutically acceptable carrier, wherein the double-stranded molecule inhibits an expression of an LRRC42 gene as well as cell proliferation when introduced into a cell expressing LRRC42 gene.
[27] The composition of [26], wherein the double-stranded molecule is that of any one of [16] to [20].
[28] The composition of [26], wherein the vector is that of [21].
[29] The composition of any one of [26] to [28], wherein the cancer is lung cancer.

It will be understood by those skilled in the art that one or more aspects of this invention can meet certain objectives, while one or more other aspects can meet certain other objectives. Each objective may not apply equally, in all its respects, to every aspect of this invention. As such, the preceding objects can be viewed in the alternative with respect to any one aspect of this invention.
It will also be understood that both the foregoing summary of the present invention and the following detailed description are of exemplified embodiments, and not restrictive of the present invention or other alternate embodiments of the present invention. Other objects and features of the invention will become more fully apparent when the following detailed description is read in conjunction with the accompanying figures and examples. In particular, while the invention is described herein with reference to a number of specific embodiments, it will be appreciated that the description is illustrative of the invention and is not constructed as limiting of the invention. Various modifications and applications may occur to those who are skilled in the art, without departing from the spirit and the scope of the invention, as described by the appended claims. Likewise, other objects, features, benefits and advantages of the present invention will be apparent from this summary and certain embodiments described below, and will be readily apparent to those skilled in the art. Such objects, features, benefits and advantages will be apparent from the above in conjunction with the accompanying examples, data, figures and all reasonable inferences to be drawn therefrom, alone or with consideration of the references incorporated herein.

Various aspects and applications of the present invention will become apparent to the skilled artisan upon consideration of the brief description of the figures and the detailed description of the present invention and its preferred embodiments that follows:
Figure 1 demonstrates the LRRC42 expression in lung cancers and normal tissues. Part A depicts the results of semiquantitative RT-PCR validating the over-expression of LRRC42 in clinical samples of NSCLC (ADC and SCC) and SCLC as compared to normal lung tissues. Appropriate dilutions of each single-stranded cDNA prepared from mRNAs of lung cancer samples were prepared, using the level of beta-actin (ACTB) expression as a quantitative control. Part B depicts the results of semiquantitative RT-PCR validating the expression of LRRC42 in lung cancer cell lines. Part C depicts the results of Northern blot analysis for LRRC42, demonstrating that most normal human tissues do not. Part D depicts the subcellular localization of exogenous LRRC42 protein in COS-7 cells detected by anti-Flag, which were co-stained with DAPI.

Figure 2 demonstrates the effect of siRNA against LRRC42 on the growth of lung cancer cells that overexpress LRRC42. Part A depicts the results of semiquantitative RT-PCR analysis confirming the knockdown effect on LRRC42 expression in SBC-3 and LC319 cells in response to si-LRRC42 (si-#A or si-#B) but not control siRNAs (LUC or EGFP). Part B depicts the results of colony formation assays of SBC-5 cells transfected with specific siRNAs or control plasmids. Part C depicts the results of MTT assays of SBC-3 and LC319 cells in response to si-LRRC42 (si-#1 or si-#2), si-LUC, or si-EGFP. All assays were performed three times, and in triplicate wells.

Figure 3 demonstrates the enhancement of cell growth by LRRC42 introduction into COS-7 cells and DMS114 cells. Part A depicts the results of Western blot analysis confirming the transient expression of LRRC42 in COS-7 cells and DMS114 cells. Part B depicts the growth promoting effect in transient expression of LRRC42 in COS-7 cells and DMS114 cells. Assays were performed three times and in triplicate wells.

Figure 4 demonstrates the interaction of LRRC42 with GATAD2B. Part A depicts the results of immunoprecipitation and Western blot analysis confirming the interaction between exogenous LRRC42 and endogenous GATAD2B in SBC-3 cells transfected with LRRC42 expression vector. Part B depicts the results of immunocytochemical staining confirming the colocalization of LRRC42 and GATAD2B in nucleus of SBC-3 cells transfected with LRRC42 expression vector. Part C depicts the level of LRRC42 and GATAD2B proteins (upper) and transcripts (lower), detected by western blot and semiquantitative RT-PCR analysis in LC319 and SBC-3 cells transfected with si-LRRC42.

Part D and E depict the level of LRRC42 and GATAD2B gene expression in human lung cancer samples and cell lines, detected by semiquantitative RT-PCR analysis.

Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present invention, the preferred methods, devices, and materials are now described. However, before the present materials and methods are described, it is to be understood that the present invention is not limited to the particular sizes, shapes, dimensions, materials, methodologies, protocols, etc. described herein, as these may vary in accordance with routine experimentation and optimization. It is also to be understood that the terminology used in the description is for the purpose of describing the particular versions or embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.
The disclosure of each publication, patent or patent application mentioned in this specification is specifically incorporated by reference herein in its entirety. However, nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the present invention belongs. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Definition:
The words "a", "an", and "the" as used herein mean "at least one" unless otherwise specifically indicated.
As used herein, the phrase "biological sample" encompasses both a whole organism and a subset of its tissues, cells or component parts (e.g., body fluids, including but not limited to blood, mucus, lymphatic fluid, synovial fluid, cerebrospinal fluid, saliva, amniotic fluid, amniotic cord blood, urine, vaginal fluid and semen). Thus, the phrase "biological sample" is used herein to refer to a homogenate, lysate, extract, cell culture or tissue culture prepared from a whole organism or a subset of its cells, tissues or component parts, or a fraction or portion thereof. Likewise, the phrase "biological sample" may refer to a medium, such as a nutrient broth or gel in which an organism has been propagated, that contains cellular components, such as proteins or polynucleotides.

The terms "isolated" and "purified" when used herein in relation to a substance (e.g., polypeptide, antibody, polynucleotide, etc.) indicate that the substance is substantially free from at least one substance that may else be included in the natural source. Thus, an isolated or purified antibody refers to an antibody that is substantially free of cellular material such as carbohydrate, lipid, or other contaminating proteins from the cell or tissue source from which the protein (antibody) is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized. The term "substantially free of cellular material" includes preparations of a polypeptide in which the polypeptide is separated from cellular components of the cells from which it is isolated or recombinantly produced. Thus, a polypeptide that is substantially free of cellular material includes preparations of polypeptide having less than about 30%, 20%, 10%, or 5% (by dry weight) of heterologous protein (also referred to herein as a "contaminating protein"). When the polypeptide is recombinantly produced, it is also preferably substantially free of culture medium, which includes preparations of polypeptide with culture medium less than about 20%, 10%, or 5% of the volume of the protein preparation. When the polypeptide is produced by chemical synthesis, it is preferably substantially free of chemical precursors or other chemicals, which includes preparations of polypeptide with chemical precursors or other chemicals involved in the synthesis of the protein less than about 30%, 20%, 10%, 5% (by dry weight) of the volume of the protein preparation. That a particular protein preparation contains an isolated or purified polypeptide can be shown, for example, by the appearance of a single band following sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis of the protein preparation and Coomassie Brilliant Blue staining or the like of the gel. In a preferred embodiment, antibodies of the present invention are also isolated or purified.

An "isolated" or "purified" nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
The terms "polypeptide", "peptide", and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is a modified residue, or a non-naturally occurring residue, such as an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers.

The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that similarly functions to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those modified after translation in cells (e.g., hydroxyproline, gamma-carboxyglutamate, and O-phosphoserine). The phrase "amino acid analog" refers to compounds that have the same basic chemical structure (an alpha carbon bound to a hydrogen, a carboxy group, an amino group, and an R group) as a naturally occurring amino acid but have a modified R group or modified backbones (e.g., homoserine, norleucine, methionine, sulfoxide, methionine methyl sulfonium). The phrase "amino acid mimetic" refers to chemical compounds that have different structures but similar functions to general amino acids.
Amino acids may be referred to herein by their commonly known three letter symbols or the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.

The terms "gene", "polynucleotide", "oligonucleotide", "nucleic acid", and "nucleic acid molecule" are used interchangeably unless otherwise specifically indicated and, similarly to the amino acids, are referred to by their commonly accepted single-letter codes. Similar to the amino acids, they encompass both naturally-occurring and non-naturally occurring nucleic acid polymers. The polynucleotide, oligonucleotide, nucleotides, nucleic acids, or nucleic acid molecules may be composed of DNA, RNA or a combination thereof.

In the context of the present invention, the phrase "LRRC42 gene" encompasses polynucleotides that encode the human LRRC42 or any of the functional equivalents of the human LRRC42 gene. Likewise, the phrase "GATAD2B gene" encompasses polynucleotides that encode the human GATAD2B or any of the functional equivalents of the human GATAD2B gene. The LRRC42 gene and the GATAD2B gene can be obtained from nature as naturally occurring proteins via conventional cloning methods or through chemical synthesis based on the selected nucleotide sequence. Methods for cloning genes using cDNA libraries and such are well known in the art.
Unless otherwise defined, the term "cancer" refers to cancer over-expressing the LRRC42 gene. Examples of cancers over-expressing LRRC42 gene include, but are not limited to, lung cancers including SCLC and, NSCLC that includes adenocarcinoma (ADC) and squamous-cell carcinoma (SCC).

As used herein, the term "double-stranded molecule" refers to a nucleic acid molecule that inhibits expression of a target gene, including, for example, short interfering RNA (siRNA; e.g., double-stranded ribonucleic acid (dsRNA) or small hairpin RNA (shRNA)) and short interfering DNA/RNA (siD/R-NA; e.g., double-stranded chimera of DNA and RNA (dsD/R-NA) or small hairpin chimera of DNA and RNA (shD/R-NA)). Herein, "double-stranded molecule" is also referred to as "double-stranded nucleic acid", "double-stranded nucleic acid molecule", "double-stranded polynucleotide" and "double-stranded polynucleotide molecule".

In the context of the present invention, the term "composition" is used to refer to a product including that include the specified ingredients in the specified amounts, as well as any product that results, directly or indirectly, from combination of the specified ingredients in the specified amounts. Such terms, when used in relation to the modifier "pharmaceutical" (as in "pharmaceutical composition"), are intended to encompass products including a product that includes the active ingredient(s), and any inert ingredient(s) that make up the carrier, as well as any product that results, directly or indirectly, from combination, complexation or aggregation of any two or more of the ingredients, or from dissociation of one or more of the ingredients, or from other types of reactions or interactions of one or more of the ingredients. Accordingly, in the context of the present invention, the term "pharmaceutical composition" refers to any product made by admixing a molecule or compound of the present invention and a pharmaceutically or physiologically acceptable carrier.
The phrase "pharmaceutically acceptable carrier" or "physiologically acceptable carrier", as used herein, means a pharmaceutically or physiologically acceptable material, composition, substance or vehicle, including but not limited to, a liquid or solid filler, diluent, excipient, solvent or encapsulating material.

The term "active ingredient" herein refers to a substance in composition that is biologically or physiologically active. Particularly, in the context of pharmaceutical composition, the term "active ingredient" refers to a substance that shows an objective pharmacological effect. For example, in case of pharmaceutical compositions for use in the treatment or prevention of cancer, active ingredients in the agents or compositions may lead to at least one biological or physiologically action on cancer cells and/or tissues directly or indirectly. Preferably, such action may include reducing or inhibiting cancer cell growth, damaging or killing cancer cells and/or tissues, and so on. Typically, indirect effect of active ingredients is inductions of CTLs recognizing or killing cancer cells. Before being formulated, the "active ingredient" may also be referred to as "bulk", "drug substance" or "technical product".

To the extent that the methods and compositions of the present invention find utility in the context of "prevention" and "prophylaxis", such terms are interchangeably used herein to refer to any activity that reduces the burden of mortality or morbidity from disease. Prevention and prophylaxis can occur "at primary, secondary and tertiary prevention levels". While primary prevention and prophylaxis avoid the development of a disease, secondary and tertiary levels of prevention and prophylaxis encompass activities aimed at the prevention and prophylaxis of the progression of a disease and the emergence of symptoms as well as reducing the negative impact of an already established disease by restoring function and reducing disease-related complications. Alternatively, prevention and prophylaxis can include a wide range of prophylactic therapies aimed at alleviating the severity of the particular disorder, e.g. reducing the proliferation and metastasis of tumors.

To the extent that certain embodiments of the present invention encompass the treatment and/or prophylaxis of cancer and/or the prevention of postoperative recurrence, such methods may include any of the following steps: the surgical removal of cancer cells, the inhibition of the growth of cancerous cells, the involution or regression of a tumor, the induction of remission and suppression of occurrence of cancer, the tumor regression, and the reduction or inhibition of metastasis. Effective treatment and/or the prophylaxis of cancer decreases mortality and improves the prognosis of individuals having cancer, decreases the levels of tumor markers in the blood, and alleviates detectable symptoms accompanying cancer. A treatment may also deemed "efficacious" if it leads to clinical benefit such as, reduction in expression of the LRRC42 gene, or a decrease in size, prevalence, or metastatic potential of the cancer in the subject. When the treatment is applied prophylactically, "efficacious" means that it retards or prevents cancers from forming or prevents or alleviates a clinical symptom of cancer. Efficaciousness is determined in association with any known method for diagnosing or treating the particular tumor type.

Genes and Proteins:
The present invention is based in part on the discovery that the gene encoding LRRC42 is over-expressed in cancer as compared to non-cancerous tissue.
LRRC42 (Leucine rich repeat containing 42) contains two Leucine rich repeats (LRRs) which are widespread structural motifs comprising 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucine residues. Leucine rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions.

The present invention is further based on the discovery that LRRC42 interacts with GATAD2B.
GATAD2B (GATA zinc finger domain containing 2B) is a constituent of MeCP1 complex that is capable of repressing transcription of methylated DNA. DNA methylation of tumor suppressor gene, like Rb, p14, p15, p16 and so on, is a common feature of various human cancer including lung cancer (Lewandowska J,et al. Mutagenesis 2011, Vaissiere T, et al. Cancer Res 2009;69:243-52). MBD2 (Methyl-CpG-binding domain 2), also a component of MeCP1 complex, is capable of binding specifically to methylated DNA and known to be interacted with GATAD2B (Zhang Y, et al. Genes Dev 1999;13:1924-35, Brackertz M, et al. J Biol Chem 2002;277:40958-66). It was reported that MBD2 is involved in silencing of p16/p14 locus in human colon carcinomas cell line.

Nucleotide sequences of LRRC42 and GATAD2B polynucleotide and amino acid sequences of LRRC42 and GATAD2B polypeptide are known to those skilled in the art, and obtained, for example, from gene databases on the web site such as GenBank^TM. An exemplified nucleotide sequence of LRRC42 polynucleotide is shown in SEQ ID NO: 1, and an exemplified amino acid sequence of LRRC42 polypeptide is shown in SEQ ID NO: 2. The sequence data are also available, for example, via GenBank accession No. NM_052940. Also, an exemplified nucleic sequence of GATAD2B polynucleotide is shown in SEQ ID NO:15 , and an exemplified amino acid sequence of GATAD2B polypeptide is shown in SEQ ID NO:16. The sequence data are also available, for example, via GenBank accession No. NM_020699.2. One of skill will recognize that LRRC42 or GATAD2B sequences need not be limited to these sequences and that variants (e.g., functional equivalents and allelic variants) can be used in the present invention as described below.

The present invention contemplates "functional equivalents" and deems such to be "LRRC42 polypeptides" or "GATAD2B polypeptides" in context. Herein, a "functional equivalent" of a protein (e.g., an LRRC42 polypeptide or a GATAD2B polypeptide) is a polypeptide that has a biological activity equivalent to that of the original protein. Namely, any polypeptide that retains the biological ability of the LRRC42 protein or the GATAD2B protein may be used as such a functional equivalent in the present invention. Such functional equivalents include those wherein one or more amino acids are substituted, deleted, added, or inserted to the natural occurring amino acid sequence of the LRRC42 protein or the GATAD2B protein. Alternatively, the polypeptide may be composed an amino acid sequence having at least about 80% homology (also referred to as sequence identity) to the sequence of the respective protein, more preferably at least about 90% to 95% homology, often about 96%, 97%, 98% or 99% homology. In other embodiments, the polypeptide can be encoded by a polynucleotide that hybridizes under stringent conditions to the natural occurring nucleotide sequence of the LRRC42 gene or the GATAD2B gene.

Percent sequence identity and sequence similarity can be readily determined using conventional techniques such as the BLAST and BLAST 2.0 algorithms, which are described (Altschul SF, et al., J Mol Biol. 1990 Oct 5; 215 (3):403-10; Nucleic Acids Res. 1997 Sep 1;25(17):3389-402). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (on the worldwide web at ncbi.nlm.nih.gov/). Such algorithms involve first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them.

The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.

The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word size (W) of 28, an expectation (E) of 10, M=1, N=-2, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (Henikoff S & Henikoff JG. Proc Natl Acad Sci U S A. 1992 Nov 15; 89(22):10915-9).
A polypeptide of the present invention may also have variations in amino acid sequence, molecular weight, isoelectric point, the presence or absence of sugar chains, or form, depending on the cell or host used to produce it or the purification method utilized. Nevertheless, so long as it has a function equivalent to that of the human LRRC42 protein or the human GATAD2B protein, it is within the scope of the present invention.

In other embodiments, functional equivalents of the above polypeptides can be encoded by a polynucleotide that hybridizes under stringent conditions to the natural occurring nucleotide sequence of the LRRC42 or GATAD2B gene. The phrase "stringent (hybridization) conditions" refers to conditions under which a nucleic acid molecule will hybridize to its target sequence, typically in a complex mixture of nucleic acids, but not detectably to other sequences. Stringent conditions are sequence-dependent and will vary in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Probes, "Overview of principles of hybridization and the strategy of nucleic acid assays" (1993). Generally, stringent conditions are selected to be about 5-10 degrees C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times of background, preferably 10 times of background hybridization. Exemplary stringent hybridization conditions include the following: 50% formamide, 5x SSC, and 1% SDS, incubating at 42 degrees C, or, 5x SSC, 1% SDS, incubating at 65 degrees C, with wash in 0.2x SSC, and 0.1% SDS at 50 degrees C.

In the context of the present invention, the optimal condition of hybridization for isolating a DNA encoding a polypeptide functionally equivalent to the human LRRC42 protein or the human GATAD2B protein can be routinely selected by a person skilled in the art. For example, hybridization may be performed by conducting pre-hybridization at 68 degrees C for 30 min or longer using "Rapid-hyb buffer" (Amersham LIFE SCIENCE), adding a labeled probe, and warming at 68 degrees C for 1 hour or longer. The following washing step can be conducted, for example, in a low stringent condition. An exemplary low stringent condition may include 42 degrees C, 2x SSC, 0.1% SDS, preferably 50 degrees C, 2x SSC, 0.1% SDS. High stringency conditions are often preferably used. An exemplary high stringency condition may include washing 3 times in 2x SSC, 0.01% SDS at room temperature for 20 min, then washing 3 times in 1x SSC, 0.1% SDS at 37 degrees C for 20 min, and washing twice in 1x SSC, 0.1% SDS at 50 degrees C for 20 min. However, several factors, such as temperature and salt concentration, can influence the stringency of hybridization and one skilled in the art can routinely adjust these and other factors to arrive at the desired stringency.

It is generally known that a modification of one, two or more amino acids in a protein will not influence the function of the protein; in some cases, it may even enhance the desired function of the original protein. In fact, mutated or modified proteins (i.e., peptides composed of an amino acid sequence in which one, two, or several amino acid residues have been modified through substitution, deletion, insertion and/or addition) have been known to retain the original biological activity (Mark et al., Proc Natl Acad Sci USA 81: 5662-6 (1984); Zoller and Smith, Nucleic Acids Res 10:6487-500 (1982); Dalbadie-McFarland et al., Proc Natl Acad Sci USA 79: 6409-13 (1982)).

Accordingly, one of skill in the art will recognize that individual additions, deletions, insertions, or substitutions to an amino acid sequence which alter a single amino acid or a small percentage of amino acids (i.e., less than 5%, more preferably less than 3%, even more preferably less than 1%) or those considered to be a "conservative modifications", wherein the alteration of a protein results in a protein with similar functions, are acceptable in the context of the instant invention. Thus, functional equivalents of the LRRC42 protein or the GATAD2B protein may have an amino acid sequence wherein one, two or even more amino acids are added, inserted, deleted, and/or substituted in the original reference LRRC42 sequence or the GATAD2B sequence.

So long as the activity of the protein is maintained, the number of amino acid mutations or modifications is not particularly limited. However, it is generally preferred to alter 5% or less of the amino acid sequence, more preferably less than 3%, even more preferably less than 1%. Accordingly, in a preferred embodiment, the number of amino acids to be mutated in such a mutant is generally 30 amino acids or fewer, preferably 20 amino acids or fewer, more preferably 10 amino acids or fewer, more preferably 5 or 6 amino acids or fewer, and even more preferably 3 or 4 amino acids or fewer.

An amino acid residue to be mutated is preferably mutated into a different amino acid in which the properties of the amino acid side-chain are conserved (a process known as conservative amino acid substitution). Examples of properties of amino acid side chains are hydrophobic amino acids (A, I, L, M, F, P, W, Y, V), hydrophilic amino acids (R, D, N, C, E, Q, G, H, K, S, T), and side chains having the following functional groups or characteristics in common: an aliphatic side-chain (G, A, V, L, I, P); a hydroxyl group containing side-chain (S, T, Y); a sulfur atom containing side-chain (C, M); a carboxylic acid and amide containing side-chain (D, N, E, Q); a base containing side-chain (R, K, H); and an aromatic containing side-chain (H, F, Y, W). Conservative substitution tables providing functionally similar amino acids are well known in the art. For example, the following eight groups each contain amino acids that are conservative substitutions for one another:
1) Alanine (A), Glycine (G);
2) Aspartic acid (D), Glutamic acid (E);
3) Asparagine (N), Glutamine (Q);
4) Arginine (R), Lysine (K);
5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);
6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);
7) Serine (S), Threonine (T); and
8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins 1984).

Such conservatively modified polypeptides are included in the present LRRC42 protein or the present GATAD2B protein. However, the present invention is not restricted thereto and the LRRC42 protein or the GATAD2B protein includes non-conservative modifications, so long as the resulting modified peptide retains at least one biological activity of the original LRRC42 protein or the GATAD2B protein. In the context of the present invention, the modified proteins do not exclude polymorphic variants, interspecies homologues, and those encoded by alleles of these proteins.

In addition to above-described peptides and proteins, the present invention encompasses genes and polynucleotides that encode such functional equivalents of the LRRC42 protein or the GATAD2B protein. In addition to hybridization, a gene amplification method, for example, the polymerase chain reaction (PCR) method, can be utilized to isolate a polynucleotide encoding a polypeptide functionally equivalent to the LRRC42 protein or the GATAD2B protein, using a primer synthesized based on the sequence information of the protein encoding DNA (SEQ ID NO: 1 for LRRC42 and SEQ ID NO: 15 for GATAD2B). Polynucleotides and polypeptides that are functionally equivalent to the human LRRC42 gene and protein, respectively, normally have a high homology to the originating nucleotide or amino acid sequence thereof. "High homology" typically refers to a homology of 40% or higher, preferably 60% or higher, more preferably 80% or higher, even more preferably 90% to 95% or higher, even more preferably 96%, 97%, 98%, 99% or higher. The homology of a particular polynucleotide or polypeptide can be determined by following the algorithm in "Wilbur and Lipman, Proc Natl Acad Sci USA 80: 726-30 (1983)".

The present invention also encompasses partial peptides and fragments of the LRRC42 and GATAD2B proteins and their use in screening methods. A partial peptide having an amino acid sequence specific to the LRRC42 or GATAD2B protein is preferably composed of less than about 400 amino acids, usually less than about 200 and often less than about 100 amino acids, and at least about 7 amino acids, for example, about 8 amino acids or more, for example, about 9 amino acids or more.

A method for Detecting or Diagnosing Cancer:
As demonstrated herein, the expression of LRRC42 gene was found to be significantly and specifically elevated in lung cancer (Figs. 1A and 1B), but not expressed in normal tissues (Fig. 1C). Thus, the LRRC42 genes identified herein as well as their transcription and translation products find utility as a diagnostic markers for cancers such as lung cancer. Accordingly, by measuring the expression level of LRRC42 gene in a subject-derived sample and comparing the expression level of LRRC42 gene between a subject-derived sample with a normal sample, cancer can be diagnosed or detected. More particularly, the present invention provides a method for detecting or diagnosing cancer and/or determining the presence of or a predisposition for developing cancer, more particularly an LRRC42-associated cancer such as lung cancer, by determining the expression level of LRRC42 gene in a subject-derived biological sample.

The present invention also provides a method for detecting or diagnosing cancer in a subject, such method including the step of determining an expression level of an LRRC42 gene in a subject-derived biological sample, preferably a subject-derived lung tissue sample, wherein an increase of the LRRC42 expression level as compared to a normal control level of the LRRC42 gene indicates the presence or suspicion of cancer cells in the sample, which, in turn, suggests that the subject suffers from or is at risk of developing cancer.

The expression level of the LRRC42 gene may be determined by any known method, examples of which include:
(a) detecting the mRNA of an LRRC42 gene;
(b) detecting the protein encoded by an LRRC42 gene; and
(c) detecting the biological activity of the protein encoded by an LRRC42 gene.
In the preferred embodiment, cancers to be diagnosed by the present method are lung cancers, including NSCLCs and SCLCs. NSCLCs include lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SCC).

In the context of the present invention, the term "diagnosing" is intended to encompass predictions and likelihood analysis (i.e., rendering a prognosis). Thus, the present method may be clinically used to make decisions concerning treatment modalities, including therapeutic intervention, diagnostic criteria such as disease stages, and disease monitoring and surveillance for cancer. According to the present invention, an intermediate result for examining the condition of a subject may be provided. Such intermediate result may be combined with additional information to assist a doctor, nurse, or other practitioner to diagnose that a subject suffers from the disease. Thus, the present invention contemplates the use of LRRC42 as a diagnostic marker for cancer, finding utility in the detection of cancers related thereto as well as in assessing and/or monitoring the efficacy or applicability of a cancer therapy.

The present invention may be also used to detect or identify cancerous cells in a subject-derived tissue, such cells being characterized by an increase in the expression level of the LRRC42 gene as compared to a normal control level of the LRRC42 gene indicates the presence or suspicion of cancer cells in the tissue. LRRC42 expression results may be combined with additional information to assist a doctor, nurse, or other healthcare practitioner in diagnosing a subject as afflicted with the disease. In other words, the present invention may provide a doctor with useful information to diagnose a subject as afflicted with the disease. For example, according to the present invention, when there is doubt regarding the presence of cancer cells in the tissue obtained from a subject, clinical decisions can be reached by considering the expression level of the LRRC42 gene, plus a different aspect of the disease including tissue pathology, levels of known tumor marker(s) in blood, and clinical course of the subject, etc. For example, some well-known diagnostic lung tumor markers in blood are IAP, ACT, BFP, CA19-9, CA50, CA72-4, CA130, CEA, KMO-1, NSE, SCC, SP1, Span-1, TPA, CSLEX, SLX, STN and CYFRA. Namely, in this particular embodiment of the present invention, the outcome of the gene expression analysis serves as an intermediate result for further diagnosis of a subject's disease state.

Particularly preferred embodiments of the present invention are set forth below as items [1] to [12]:
[1] A method of detecting or diagnosing cancer in a subject, including determining an expression level of LRRC42 in a subject-derived biological sample, wherein an increase of the detected level compared to a normal control level of said gene indicates that the subject suffers from or is at risk of developing cancer;
[2] The method of [1], wherein the detected expression level is at least 10% greater than the normal control level;
[3] The method of [1] or [2], wherein the expression level is detected by a method selected from among:
(a) detecting an mRNA of the LRRC42 gene,
(b) detecting a protein encoded by the LRRC42 gene, and
(c) detecting a biological activity of a protein encoded by the LRRC42 gene ;
[4] The method of [1], wherein the cancer is lung cancer;
[5] The method of [3] or [4], wherein the expression level is determined by detecting hybridization of a probe to the mRNA of the LRRC42 gene;
[6] The method of [5], wherein the expression level is determined by detecting the hybridization of a probe having a complementary sequence to a part of the mRNA of the LRRC42 gene to the mRNA of the LRRC42 gene;
[7] The method of [3] or [4] , wherein the expression level is determined by detecting the binding of an antibody against the protein encoded by the LRRC42 gene;
[8] The method of [7], wherein the expression level is determined by detecting the binding of an antibody against the protein encoded by the LRRC42 gene and the protein encoded by the LRRC42 gene;
[9] The method of any one of [1] to [8], wherein the subject-derived biological sample includes a biopsy specimen, sputum or blood;
[10] The method of any one of [1] to [9], wherein the subject-derived biological sample includes an epithelial cell;
[11] The method of [9], wherein the subject-derived biological sample includes a cancer cell;
[12] The method of [10], wherein the subject-derived biological sample includes a cancerous epithelial cell.

The method of diagnosing cancer of the present invention is described in more detail below.
A subject to be diagnosed by the present method is preferably a mammal. Exemplary mammals include, but are not limited to, e.g., human, non-human primate, mouse, rat, dog, cat, horse, and cow.
It is preferred to collect a biological sample from the subject to be diagnosed to perform the diagnosis. Any biological material can be used as the biological sample for the determination so long as it includes the objective transcription or translation product of LRRC42 gene. Examples of suitable biological samples include, but are not limited to, bodily tissues which are desired for diagnosing or are suspicion of suffering from cancer, and fluids, such as biopsy, blood, sputum and urine. Preferably, the biological sample contains a cell population including an epithelial cell, more preferably a cancerous epithelial cell or an epithelial cell derived from tissue suspected to be cancerous. Further, if necessary, the cell may be purified from the obtained bodily tissues and fluids, and then used as the biological sample.

According to the present invention, the expression level of LRRC42 in a subject-derived biological sample is determined and then correlated to a particular healthy or disease state by comparison to a control sample. The expression level can be determined at the transcription (nucleic acid) product level, using methods known in the art. For example, the mRNA of LRRC42 may be quantified using probes by hybridization methods (e.g., Northern hybridization). The detection may be carried out on a chip or an array. The use of an array is preferable for detecting the expression level of a plurality of genes (e.g., various cancer specific genes) including LRRC42. Those skilled in the art can prepare such probes utilizing the known sequence information for the LRRC42 (SEQ ID NO: 1). For example, the cDNA of LRRC42 may be used as the probes. If necessary, the probe may be labeled with a suitable label, such as dyes, fluorescent and isotopes, and the expression level of the gene may be detected as the intensity of the hybridized labels.

Alternatively, the transcription product of the LRRC42 gene may be quantified using primers by amplification-based detection methods (e.g., RT-PCR). Such primers can also be prepared based on the available sequence information of the gene. For example, the primers used in the Example (SEQ ID NO: 3 and 4) may be employed for the detection by RT-PCR or Northern blot, but the present invention is not restricted thereto.

A probe or primer suitable for use in the context of the present method will hybridize under stringent, moderately stringent, or low stringent conditions to the mRNA of the LRRC42 gene. As used herein, the phrase "stringent (hybridization) conditions" refers to conditions under which a probe or primer will hybridize to its target sequence, but to no other sequences. Stringent conditions are sequence-dependent and will be different under different circumstances. Specific hybridization of longer sequences is observed at higher temperatures than shorter sequences. Generally, the temperature of a stringent condition is selected to be about 5 degrees C lower than the thermal melting point (Tm) for a specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize to the target sequence at equilibrium. Since the target sequences are generally present at excess, at Tm, 50% of the probes are occupied at equilibrium. Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30 degrees C for short probes or primers (e.g., 10 to 50 nucleotides) and at least about 60 degrees C for longer probes or primers. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.

Alternatively, diagnosis may involve detection of a translation product. For example, the quantity of LRRC42 protein may be determined and correlated to a disease or normal state. The quantity of the translation products/proteins may be determined using, for example, immunoassay methods that use an antibody specifically recognizing the protein. The antibody may be monoclonal or polyclonal. Furthermore, any fragment or modification (e.g., chimeric antibody, scFv, Fab, F(ab')2, Fv, etc.) of the antibody may be used for the detection, so long as the fragment retains the binding ability to LRRC42 protein. Methods to prepare these kinds of antibodies for the detection of proteins are well known in the art, and any method may be employed in the present invention to prepare such antibodies and equivalents thereof.
Alternatively, the intensity of staining may be observed via immunohistochemical analysis using an antibody against LRRC42 protein. Namely, the observation of strong staining indicates increased presence of the protein and at the same time high expression level of LRRC42 gene.

Alternatively, cell proliferation enhancing activity may be correlated to the LRRC42 gene expression level. As discovered herein, inhibiting the expression of LRRC42 gene leads to suppression of cell growth in lung cancer cells; as such, the LRRC42 protein is presumed to promote cell proliferation. Thus, to determine the cell proliferation enhancing activity of LRRC42 protein, a cell is first cultured in the presence of a biological sample. Then, by detecting the speed of proliferation, or by measuring the cell cycle or the colony forming ability, the cell proliferation enhancing activity of the biological sample can be determined and the relative LRRC42 expression correlated thereto.
In the context of the present invention, methods for detecting or identifying cancer in a subject or cancer cells in a subject-derived biological sample begin with a determination of LRRC42 gene expression level. Once determined, using any of the aforementioned techniques, this value is as compared to a control level.

In the context of the present invention, the phrase "control level" refers to the expression level of a test gene detected in a control sample and encompasses both a normal control level and a cancer control level. The phrase "normal control level" refers to a level of gene expression detected in a normal healthy individual or in a population of individuals known not to be suffering from cancer. A normal individual is one with no clinical symptom of lung cancer. A normal control level can be determined using a normal cell obtained from a non-cancerous tissue. A "normal control level" may also be the expression level of a test gene detected in a normal healthy tissue or cell of an individual or population known not to be suffering from lung cancer cancer. On the other hand, the phrase "cancer control level" refers to an expression level of a test gene detected in the cancerous tissue or cell of an individual or population suffering from lung cancer. An increase in the expression level of LRRC42 detected in a subject-derived sample as compared to a normal control level indicates that the subject (from which the sample has been obtained) suffers from or is at risk of developing lung cancer. In the context of the present invention, the subject-derived biological sample may be any tissues obtained from test subjects, e.g., patients suspected of having cancer. For example, tissues may include epithelial cells. More particularly, tissues may be epithelial cells collected from suspected cancerous area. Alternatively, the expression level of LRRC42 in a sample can be compared to a cancer control level of the LRRC42 gene. A similarity between the expression level of a sample and the cancer control level indicates that the subject (from which the sample has been obtained) suffers from or is at risk of developing cancer. When the expression levels of other cancer-related genes are also measured and compared, a similarity in the gene expression pattern between the sample and the reference that is cancerous indicates that the subject is suffering from or at a risk of developing cancer.

The control level may be determined at the same time with the test biological sample by using a sample(s) previously collected and stored from a subject/subjects whose disease state (cancerous or non-cancerous) is/are known. Alternatively, the control level may be determined by a statistical method based on the results obtained by analyzing previously determined expression level(s) of LRRC42 gene in samples from subjects whose disease state are known. Furthermore, the control level can be a database of expression patterns from previously tested cells. Moreover, according to an aspect of the present invention, the expression level of LRRC42 gene in a biological sample may be compared to multiple control levels, which control levels are determined from multiple reference samples. It is preferred to use a control level determined from a reference sample derived from a tissue type similar to that of the subject-derived biological sample. Moreover, it is preferred, to use the standard value of the expression levels of LRRC42 gene in a population with a known disease state. The standard value may be obtained by any method known in the art. For example, a range of mean +/- 2 S.D. or mean +/- 3 S.D. may be used as standard value.

To improve the accuracy of the diagnosis, the expression level of other cancer-associated genes, for example, genes known to be differentially expressed in lung cancer may also be determined, in addition to the expression level of the LRRC42 gene. Furthermore, in the case where the expression levels of multiple cancer-related genes are compared, a similarity in the gene expression pattern between the sample and the reference that is cancerous indicates that the subject is suffering from or at a risk of developing lung cancer.

In the context of the present invention, gene expression levels are deemed to be "altered" or "increased" when the gene expression changes or increases by, for example, 10%, 25%, or 50% from, or at least 0.1 fold, at least 0.2 fold, at least 0.5 fold, at least 2 fold, at least 5 fold, or at least 10 fold or more compared to a control level. Accordingly, the expression level of cancer marker genes including LRRC42 in a biological sample can be considered to be increased if it increases from the normal control level of the corresponding cancer marker gene by, for example, 10% or more, 25% or more, or 50% or more; or increases to more than 1.1 fold, more than 1.5 fold, more than 2.0 fold, more than 5.0 fold, more than 10.0 fold, or more. The expression level of the target gene can be determined by detecting, e.g., determined by the hybridization intensity of nucleic acid probes to gene transcripts in a sample.

Difference between the expression levels of a test biological sample and the control level can be normalized to the expression level of control nucleic acids, e.g., housekeeping genes, whose expression levels are known not to differ depending on the cancerous or non-cancerous state of the cell. Exemplary control genes include, but are not limited to, beta-actin, glyceraldehyde 3 phosphate dehydrogenase, and ribosomal protein P1.

The findings of the present invention reveal that LRRC42 is not only a useful diagnostic marker, but is also suitable target for cancer therapy. Therefore, cancer treatment targeting LRRC42 can be achieved by the present invention. In the present invention, the cancer treatment targeting LRRC42 refers to suppression or inhibition of LRRC42 activity and/or expression in the cancer cells. Any anti-LRRC42 agents may be used for the cancer treatment targeting LRRC42. In the present invention, the anti-LRRC42 agents include following substance or active ingredient:
(a) a double-stranded molecule of the present invention,
(b) DNA encoding thereof, and
(c) a vector encoding thereof.

Accordingly, in a preferred embodiment, the present invention provides a method of (i) diagnosing whether a subject has the cancer to be treated with anti- LRRC42 agent, and/or (ii) selecting a subject for cancer treatment targeting LRRC42, which method includes the steps of:
a) determining the expression level of LRRC42 in cancer cells or tissue(s) obtained from a subject who is suspected to have the cancer to be treated;
b) comparing the expression level of LRRC42 with a normal control level;
c) diagnosing the subject as having the cancer to be treated, if the expression level of LRRC42 is increased as compared to the normal control level; and
d) selecting the subject for cancer treatment, if the subject is diagnosed as having the cancer to be treated, in step c).

Alternatively, such a method may include the steps of:
a) determining the expression level of LRRC42 in cancer cells or tissue(s) obtained from a subject who is suspected to have the cancer to be treated;
b) comparing the expression level of LRRC42 with a cancerous control level;
c) diagnosing the subject as having the cancer to be treated, if the expression level of LRRC42 is similar or equivalent to the cancerous control level; and
d) selecting the subject for cancer treatment, if the subject is diagnosed as having the cancer to be treated, in step c).

A kit for Diagnosing Cancer:
The present invention also provides a kit for diagnosing cancer, which may also be useful in monitoring the efficacy of a cancer therapy. The present invention also provides a kit for determining a subject suffering from cancer that can be treated with the double-stranded molecule of the present invention or vector encoding thereof, which may also be useful in assessing and/or monitoring the efficacy of a cancer treatment. Preferably, the cancer to be diagnosed by the present kit is lung cancer, including NSCLC and SCLC. More preferably, the kit includes at least one reagent for detecting the expression level of the LRRC42 gene in a subject-derived biological sample, which reagent may be selected from among:
(a) a reagent for detecting mRNA of the LRRC42 gene;
(b) a reagent for detecting the LRRC42 protein; and
(c) a reagent for detecting the biological activity of the LRRC42 protein.

Suitable reagents for detecting mRNA of the LRRC42 gene include nucleic acids that specifically bind to or identify the LRRC42 mRNA, such as oligonucleotides that have a complementary sequence to a part of the LRRC42 mRNA. These kinds of oligonucleotides are exemplified by primers and probes that are specific to the LRRC42 mRNA. These kinds of oligonucleotides may be prepared based on methods well known in the art. If needed, the reagent for detecting the LRRC42 mRNA may be immobilized on a solid matrix. Moreover, more than one reagent for detecting the LRRC42 mRNA may be included in the kit.

A probe or primer of the present invention is typically a substantially purified oligonucleotide. The oligonucleotide typically includes a region of nucleotide sequence that hybridizes under stringent conditions to at least about 2000, 1000, 500, 400, 350, 300, 250, 200, 150, 100, 50, or 25 bases of consecutive sense strand nucleotide sequence of a nucleic acid having an LRRC42 sequence, or an anti sense strand nucleotide sequence of a nucleic acid having an LRRC42 sequence, or of a naturally occurring mutant of these sequences. In particular, for example, in a preferred embodiment, an oligonucleotide having 5-50 bases in length can be used as a primer for amplifying the genes, to be detected. More preferably, mRNA or cDNA of an LRRC42 gene can be detected with oligonucleotide probe or primer having 15- 30 bases in length. In preferred embodiments, length of the oligonucleotide probe or primer can be selected from 15-25 bases. Assay procedures, devices, or reagents for the detection of gene by using such oligonucleotide probe or primer are well known (e.g. oligonucleotide microarray or PCR). In these assays, probes or primers can also contain tag or linker sequences. Further, probes or primers can be modified with detectable label or affinity ligand to be captured. Alternatively, in hybridization based detection procedures, a polynucleotide having a few hundreds (e.g., about 100-200) bases to a few kilo (e.g., about 1000-2000) bases in length can also be used for a probe (e.g., northern blotting assay or cDNA microarray analysis).

On the other hand, suitable reagents for detecting the LRRC42 protein include antibodies against the LRRC42 protein. The antibody may be monoclonal or polyclonal. Furthermore, any fragment or modification (e.g., chimeric antibody, scFv, Fab, F(ab')2, Fv, etc.) of the antibody may be used as the reagent, so long as the fragment retains the binding ability to the LRRC42 protein. Methods to prepare these kinds of antibodies for the detection of proteins are well known in the art, and any method may be employed in the present invention to prepare such antibodies and equivalents thereof. Furthermore, the antibody may be labeled with signal generating molecules via direct linkage or an indirect labeling technique. Labels and methods for labeling antibodies and detecting the binding of antibodies to their targets are well known in the art and any labels and methods may be employed for the present invention. Moreover, more than one reagent for detecting the LRRC42 protein may be included in the kit.

Furthermore, the biological activity of the LRRC42 protein can be determined by, for example, measuring the cell proliferating activity due to the expressed LRRC42 protein in the biological sample. For example, the cell may be cultured in the presence of a subject-derived biological sample, and then by detecting the speed of proliferation, or by measuring the cell cycle or the colony forming ability the cell proliferating activity of the biological sample can be determined. If needed, the reagent for detecting the LRRC42 mRNA may be immobilized on a solid matrix. Moreover, more than one reagent for detecting the biological activity of the LRRC42 protein may be included in the kit.

The kit may contain more than one of the aforementioned reagents. Furthermore, the kit may include a solid matrix and reagent for binding a probe against the LRRC42 gene or antibody against the LRRC42 protein, a medium and container for culturing cells, positive and negative control reagents, and a secondary antibody for detecting an antibody against the LRRC42 protein. For example, tissue samples obtained from subject suffering from cancer or not may serve as useful control reagents. A kit of the present invention may further include other materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts (e.g., written, tape, CD-ROM, URL etc.) with instructions for use. These reagents and such may be provided in a container with a label. Suitable containers include bottles, vials, and test tubes. The containers may be formed from a variety of materials, such as glass or plastic.

As an embodiment of the present invention, when the reagent is a probe against the LRRC42 mRNA, the reagent may be immobilized on a solid matrix, such as a porous strip, to form at least one detection site. The measurement or detection region of the porous strip may include a plurality of sites, each containing a nucleic acid (probe). A test strip may also contain sites for negative and/or positive controls. Alternatively, control sites may be located on a strip separated from the test strip. Optionally, the different detection sites may contain different amounts of immobilized nucleic acids, i.e., a higher amount in the first detection site and lesser amounts in subsequent sites. Upon the addition of test sample, the number of sites displaying a detectable signal provides a quantitative indication of the amount of LRRC42 mRNA present in the sample. The detection sites may be configured in any suitably detectable shape and are typically in the shape of a bar or dot spanning the width of a test strip.

The kit of the present invention may further include positive and/or negative controls sample, and/or an LRRC42 standard sample. The positive control sample of the present invention may be prepared by collecting LRRC42 positive samples. Such LRRC42 positive samples may be obtained, for example, from established lung cancer cell lines, including lung adenocarcinoma cell (ADC) lines such as A427, NCI-H1781, A549, LC319 and the like; lung squamous cell carcinoma (SCC) cell lines such as NCI-H26, EBC-1, NCI-H520, NCI-H2170 and the like; and SCLC cell lines such as DMS114, DMS273, SBC-3, SBC-5, H196, H446 and the like. Alternatively, the LRRC42 positive samples may be obtained from clinical lung cancer tissues, including lung adenocarcinoma tissues, lung squamous cell carcinoma tissues and SCLC tissues. Alternatively, positive control samples may be prepared by determined a cut-off value and preparing a sample containing an amount of an LRRC42 mRNA or protein more than the cut-off value. Herein, the phrase "cut-off value" refers to the value dividing between a normal range and a cancerous range. For example, one skilled in the art may be determine a cut-off value using a receiver operating characteristic (ROC) curve. The present kit may include an LRRC42 standard sample containing a cut-off value amount of an LRRC42 mRNA or polypeptide. On the contrary, negative control samples may be prepared from non-cancerous cell lines or non-cancerous tissues such as normal lung tissues, or may be prepared by preparing a sample containing an LRRC42 mRNA or protein less than cut-off value.

Alternatively, the present invention provides use of a reagent for preparing a diagnostic reagent for diagnosing cancer. In some embodiments, the reagent can be selected from the group consisting of:
(a) a reagent for detecting mRNA of the LRRC42 gene;
(b) a reagent for detecting the LRRC42 protein; and
(c) a reagent for detecting the biological activity of the LRRC42 protein.
Specifically, such reagent is an oligonucleotide that hybridizes to the mRNA of the LRRC42 gene, or an antibody that binds to the LRRC42 protein.

Screening for an Anti-cancer Substance:
Through the present invention, it has been demonstrated that LRRC42 is involved in cancer cell growth. Accordingly, substances that suppress an expression level of LRRC42 gene and/or a biological activity of LRRC42 polypeptide are expected to be useful for either or both of treating and preventing cancer. Such substances can be screened using an LRRC42 gene, polypeptides encoded by the LRRC42 gene, or transcriptional regulatory region of the LRRC42 gene. Thus, the present invention also provides a method of screening for a candidate substance for either or both of treating and preventing cancer using LRRC42 gene, LRRC42 polypeptide, or transcriptional regulatory region of the LRRC42 gene.

In the context of the present invention, substances to be identified through the present screening methods may be any compound or composition including several compounds. Furthermore, the test substance exposed to a cell or protein according to the screening methods of the present invention may be a single substance or a combination of substances. When a combination of substances is used in the methods, the substances may be contacted sequentially or simultaneously.

The substances screened by the present screening method may be suitable candidate substances for either or both of treating and preventing cancer, and/or inhibiting cancer cell growth. In the present invention, the cancer is preferably characterized by an association with LRRC42 overexpression. Accordingly, the screened substances may be preferably applied to the cancers correlated or associated with LRRC42 overexpression. In the preferred embodiments, the cancers correlated or associated with LRRC42 overexpression are lung cancer, preferably NSCLCs or SCLCs. NSCLCs include lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SCC).

Any test substance, for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts from marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds (including nucleic acid constructs, such as antisense RNA, siRNA, Ribozymes, and aptamer etc.) and natural compounds can be used in the screening methods of the present invention. The test substance of the present invention can be also obtained using any of the numerous approaches in combinatorial library methods known in the art, including (1) biological libraries, (2) spatially addressable parallel solid phase or solution phase libraries, (3) synthetic library methods requiring deconvolution, (4) the "one-bead one-compound" library method and (5) synthetic library methods using affinity chromatography selection. The biological library methods using affinity chromatography selection is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, Anticancer Drug Des 1997, 12: 145-67). Examples of methods for the synthesis of molecular libraries can be found in the art (DeWitt et al., Proc Natl Acad Sci USA 1993, 90: 6909-13; Erb et al., Proc Natl Acad Sci USA 1994, 91: 11422-6; Zuckermann et al., J Med Chem 37: 2678-85, 1994; Cho et al., Science 1993, 261: 1303-5; Carell et al., Angew Chem Int Ed Engl 1994, 33: 2059; Carell et al., Angew Chem Int Ed Engl 1994, 33: 2061; Gallop et al., J Med Chem 1994, 37: 1233-51). Libraries of compounds may be presented in solution (see Houghten, Bio/Techniques 1992, 13: 412-21) or on beads (Lam, Nature 1991, 354: 82-4), chips (Fodor, Nature 1993, 364: 555-6), bacteria (US Pat. No. 5,223,409), spores (US Pat. No. 5,571,698; 5,403,484, and 5,223,409), plasmids (Cull et al., Proc Natl Acad Sci USA 1992, 89: 1865-9) or phage (Scott and Smith, Science 1990, 249: 386-90; Devlin, Science 1990, 249: 404-6; Cwirla et al., Proc Natl Acad Sci USA 1990, 87: 6378-82; Felici, J Mol Biol 1991, 222: 301-10; US Pat. Application 2002103360).
A compound in which a part of the structure of the substance screened by any one of the present screening methods is converted by addition, deletion and/or replacement, is included in the substances obtained by the screening methods of the present invention.

Furthermore, when a candidate substance obtained by the present screening method is a proteins, for obtaining a DNA encoding the protein, either the whole amino acid sequence of the protein may be determined to deduce the nucleic acid sequence coding for the protein, or partial amino acid sequence of the obtained protein may be analyzed to prepare an oligo DNA as a probe based on the sequence, and screen cDNA libraries with the probe to obtain a DNA encoding the protein. The obtained DNA may be confirmed it's usefulness in preparing the candidate substance for treating or preventing cancer.
Test substances used in the screenings described herein may also be antibodies that specifically bind to an LRRC42 protein or partial peptides thereof that lack the biological activity of the original proteins in vivo.
Although the construction of test substance libraries is well known in the art, herein below, additional guidance in identifying test substances and construction libraries of such substances for the present screening methods are provided.

(i) Molecular modeling:
Construction of test substance libraries is facilitated by knowledge of the molecular structure of substances known to have the properties sought, and/or the molecular structure of LRRC42 protein. One approach to preliminary screening of test substances suitable for further evaluation utilizes computer modeling of the interaction between the test substance and its target.
Computer modeling technology allows for the visualization of the three-dimensional atomic structure of a selected molecule and the rational design of new substances that will interact with the molecule. The three-dimensional construct typically depends on data from x-ray crystallographic analysis or NMR imaging of the selected molecule. The molecular dynamics require force field data. The computer graphics systems enable prediction of how a new substance will link to the target molecule and allow experimental manipulation of the structures of the substance and target molecule to perfect binding specificity. Prediction of what the molecule-substance interaction will be when small changes are made in one or both requires molecular mechanics software and computationally intensive computers, usually coupled with user-friendly, menu-driven interfaces between the molecular design program and the user.

An example of the molecular modeling system described generally above includes the CHARMM and QUANTA programs, Polygen Corporation, Waltham, Mass. CHARMM performs the energy minimization and molecular dynamics functions. QUANTA performs the construction, graphic modeling and analysis of molecular structure. QUANTA allows interactive construction, modification, visualization, and analysis of the behavior of molecules with each other.

A number of articles have been published on the subject of computer modeling of drugs interactive with specific proteins, examples of which include Rotivinen et al. Acta Pharmaceutica Fennica 1988, 97: 159-66; Ripka, New Scientist 1988, 54-8; McKinlay & Rossmann, Annu Rev Pharmacol Toxiciol 1989, 29: 111-22; Perry & Davies, Prog Clin Biol Res 1989, 291: 189-93; Lewis & Dean, Proc R Soc Lond 1989, 236: 125-40, 141-62; and, with respect to a model receptor for nucleic acid components, Askew et al., J Am Chem Soc 1989, 111: 1082-90.
Other computer programs that screen and graphically depict chemicals are available from companies such as BioDesign, Inc., Pasadena, Calif., Allelix, Inc, Mississauga, Ontario, Canada, and Hypercube, Inc., Cambridge, Ontario. See, e.g., DesJarlais et al., J Med Chem 1988, 31: 722-9; Meng et al., J Computer Chem 1992, 13: 505-24; Meng et al., Proteins 1993, 17: 266-78; Shoichet et al., Science 1993, 259: 1445-50.

Once a putative inhibitor has been identified, combinatorial chemistry techniques can be employed to construct any number of variants based on the chemical structure of the identified putative inhibitor, as detailed below. The resulting library of putative inhibitors, or "test substances" may be screened using the methods of the present invention to identify test substances suited to the treatment and/or prophylaxis of cancer and/or the prevention of post-operative recurrence of cancer, particularly wherein the cancer is lung cancer.

(ii) Combinatorial chemical synthesis:
Combinatorial libraries of test substances may be produced as part of a rational drug design program involving knowledge of core structures existing in known inhibitors. This approach allows the library to be maintained at a reasonable size, facilitating high throughput screening. Alternatively, simple, particularly short, polymeric molecular libraries may be constructed by simply synthesizing all permutations of the molecular family making up the library. An example of this latter approach would be a library of all peptides six amino acids in length. Such a peptide library could include every 6 amino acid sequence permutation. This type of library is termed a linear combinatorial chemical library.

Preparation of combinatorial chemical libraries is well known to those of skill in the art, and may be generated by either chemical or biological synthesis. Combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., US Patent 5,010,175; Furka, Int J Pept Prot Res 1991, 37: 487-93; Houghten et al., Nature 1991, 354: 84-6). Other chemistries for generating chemical diversity libraries can also be used. Such chemistries include, but are not limited to: peptides (e.g., PCT Publication No. WO 91/19735), encoded peptides (e.g., WO 93/20242), random bio-oligomers (e.g., WO 92/00091), benzodiazepines (e.g., US Patent 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (DeWitt et al., Proc Natl Acad Sci USA 1993, 90:6909-13), vinylogous polypeptides (Hagihara et al., J Amer Chem Soc 1992, 114: 6568), nonpeptidal peptidomimetics with glucose scaffolding (Hirschmann et al., J Amer Chem Soc 1992, 114: 9217-8), analogous organic syntheses of small compound libraries (Chen et al., J. Amer Chem Soc 1994, 116: 2661), oligocarbamates (Cho et al., Science 1993, 261: 1303), and/or peptidylphosphonates (Campbell et al., J Org Chem 1994, 59: 658), nucleic acid libraries (see Ausubel, Current Protocols in Molecular Biology 1995 supplement; Sambrook et al., Molecular Cloning: A Laboratory Manual, 1989, Cold Spring Harbor Laboratory, New York, USA), peptide nucleic acid libraries (see, e.g., US Patent 5,539,083), antibody libraries (see, e.g., Vaughan et al., Nature Biotechnology 1996, 14(3):309-14 and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al., Science 1996, 274: 1520-22; US Patent 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Gordon EM. Curr Opin Biotechnol. 1995 Dec 1;6(6):624-31.; isoprenoids, US Patent 5,569,588; thiazolidinones and metathiazanones, US Patent 5,549,974; pyrrolidines, US Patents 5,525,735 and 5,519,134; morpholino compounds, US Patent 5,506,337; benzodiazepines, 5,288,514, and the like).
Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 MPS, 390 MPS, Advanced Chem Tech, Louisville KY, Symphony, Rainin, Woburn, MA, 433A Applied Biosystems, Foster City, CA, 9050 Plus, Millipore, Bedford, MA). In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, N.J., Tripos, Inc., St. Louis, MO, 3D Pharmaceuticals, Exton, PA, Martek Biosciences, Columbia, MD, etc.).

(iii) Other candidates:
Another approach uses recombinant bacteriophage to produce libraries. Using the "phage method" (Scott & Smith, Science 1990, 249: 386-90; Cwirla et al., Proc Natl Acad Sci USA 1990, 87: 6378-82; Devlin et al., Science 1990, 249: 404-6), very large libraries can be constructed (e.g., 10⁶ -10⁸ chemical entities). A second approach uses primarily chemical methods, of which the Geysen method (Geysen et al., Molecular Immunology 1986, 23: 709-15; Geysen et al., J Immunologic Method 1987, 102: 259-74); and the method of Fodor et al. (Science 1991, 251: 767-73) are examples. Furka et al. (14th International Congress of Biochemistry 1988, Volume #5, Abstract FR:013; Furka, Int J Peptide Protein Res 1991, 37: 487-93), Houghten (US Patent 4,631,211) and Rutter et al. (US Patent 5,010,175) describe methods to produce a mixture of peptides that can be tested as agonists or antagonists.
Aptamers are macromolecules composed of nucleic acid that bind tightly to a specific molecular target. Tuerk and Gold (Science. 249:505-510 (1990)) discloses SELEX (Systematic Evolution of Ligands by Exponential Enrichment) method for selection of aptamers. In the SELEX method, a large library of nucleic acid molecules {e.g., 10¹⁵ different molecules) can be used for screening.

I. Protein based screening methods
The present invention provides methods of screening for a candidate substance applicable to either or both of the treatment and prevention of cancer using an LRRC42 polypeptide.
In the context of the present screening method, the LRRC42 polypeptide to be used may be, for example, a purified polypeptide, a soluble protein, a form bound to a carrier or a fusion protein fused with other polypeptides. Further, the LRRC42 polypeptide may be a recombinant polypeptide, a protein derived from the nature or a partial peptide thereof.
In addition to naturally-occurring LRRC42 polypeptides, functional equivalents of the polypeptides may be included in LRRC42 polypeptides used for the present screening so long as the modified peptide retains at least one biological activity of the original polypeptide. Preferred examples of such functional equivalents are described above in the section entitled "The LRRC42 gene and LRRC42 protein".

The polypeptides may be further linked to other substances, so long as the linking process and linked substance do not interfere with the biological activity of the original polypeptide and/or fragment. Usable substances include, for example: peptides, lipids, sugar and sugar chains, acetyl groups, natural and synthetic polymers, etc. These kinds of modifications may be performed to confer additional functions or to stabilize the polypeptide and fragments. The polypeptides used for the present method may be obtained from nature as naturally occurring proteins via conventional purification methods or through chemical synthesis based on a selected amino acid sequence. For example, conventional peptide synthesis methods that can be adopted for the synthesis include:
1) Peptide Synthesis, Interscience, New York, 1966;
2) The Proteins, Vol. 2, Academic Press, New York, 1976;
3) Peptide Synthesis (in Japanese), Maruzen Co., 1975;
4) Basics and Experiment of Peptide Synthesis (in Japanese), Maruzen Co., 1985;
5) Development of Pharmaceuticals (second volume) (in Japanese), Vol. 14 (peptide synthesis), Hirokawa, 1991;
6) WO99/67288; and
7) Barany G. & Merrifield R.B., Peptides Vol. 2, "Solid Phase Peptide Synthesis", Academic Press, New York, 1980, 100-118.

Alternatively, the polypeptides may be obtained by adapting any known genetic engineering methods to the production of the instant polypeptides (e.g., Morrison J., J Bacteriology 1977, 132: 349-51; Clark-Curtiss & Curtiss, Methods in Enzymology (eds. Wu et al.) 1983, 101: 347-62). For example, first, a suitable vector including a polynucleotide encoding the objective protein in an expressible form (e.g., downstream of a regulatory sequence including a promoter) is prepared, transformed into a suitable host cell, and then the host cell is cultured to produce the protein. More specifically, a gene encoding an LRRC42 polypeptide are expressed in host (e.g., animal) cells and such by inserting the gene into a vector for expressing foreign genes, such as pSV2neo, pcDNA I, pcDNA3.1, pCAGGS, or pCD8. A promoter may be used for the expression. Any commonly used promoters may be employed, including, for example, the SV40 early promoter (Rigby in Williamson (ed.), Genetic Engineering, vol. 3. Academic Press, London, 1982, 83-141), the EF-alpha promoter (Kim et al., Gene 1990, 91:217-23), the CAG promoter (Niwa et al., Gene 1991, 108:193), the RSV LTR promoter (Cullen, Methods in Enzymology 1987, 152:684-704), the SR-alpha promoter (Takebe et al., Mol Cell Biol 1988, 8:466), the CMV immediate early promoter (Seed et al., Proc Natl Acad Sci USA 1987, 84:3365-9), the SV40 late promoter (Gheysen et al., J Mol Appl Genet 1982, 1:385-94), the Adenovirus late promoter (Kaufman et al., Mol Cell Biol 1989, 9:946), the HSV TK promoter, and such. The introduction of the vector into host cells to express an LRRC42 polypeptide may be performed according to any conventional methods, for example, the electroporation method (Chu et al., Nucleic Acids Res 1987, 15:1311-26), the calcium phosphate method (Chen et al., Mol Cell Biol 1987, 7:2745-52), the DEAE dextran method (Lopata et al., Nucleic Acids Res 1984, 12:5707-17; Sussman et al., Mol Cell Biol 1985, 4:1641-3), the Lipofectin method (Derijard B, Cell 1994, 7:1025-37; Lamb et al., Nature Genetics 1993, 5:22-30; Rabindran et al., Science 1993, 259:230-4), and such.
LRRC42 polypeptides may also be produced in vitro using a conventional in vitro translation system.

(i) Screening for an LRRC42 Binding Substance:
In the context of the present invention, an over-expression of LRRC42 gene was detected in lung cancer, in spite of no expression in normal organs (Fig. 1). Accordingly, using the LRRC42 gene and proteins encoded thereby, the present invention provides a method of screening for a substance that binds to LRRC42 polypeptide. Due to the expression of LRRC42 gene in cancer, a substance binds to LRRC42 polypeptide is expected to suppress the proliferation of cancer cells, and thus be useful for either or both of treating and preventing cancer. Therefore, the present invention also provides a method of screening for a candidate substance that suppresses the proliferation of cancer cells, and a method for screening a candidate substance for either or both of treating and preventing cancer using the LRRC42 polypeptide. On particular, an embodiment of this screening method includes the steps of:
(a) contacting a test substance with an LRRC42 polypeptide;
(b) detecting the binding activity between the polypeptide and the test substance; and
(c) selecting the test substance that binds to the polypeptide.

Alternatively, according to the present invention, the potential therapeutic effect of a test substance for either or both of treating and preventing cancer can also be evaluated or estimated. In some embodiments, the present invention provides a method for evaluating or estimating a therapeutic effect of a test substance for treating and/or preventing cancer and/or inhibiting cancer associated with over-expression of LRRC42, the method including steps of:
(a) contacting a test substance with a polypeptide encoded by a polynucleotide of LRRC42;
(b) detecting the binding activity between the polypeptide and the test substance; and
(c) correlating the potential therapeutic effect and the test substance, wherein the potential therapeutic effect is shown, when a substance binds to the polypeptide.

In the context of the present invention, the therapeutic effect may be correlated with the binding level of the test substance and LRRC42 protein(s). For example, when the test substance binds to an LRRC42 protein, the test substance may identified or selected as a candidate substance having the requisite therapeutic effect. Alternatively, when the test substance does not bind to an LRRC42 protein, the test substance may characterized as having no significant therapeutic effect.
The method of the present invention is described in more detail below.

The LRRC42 polypeptide to be used for screening may be a recombinant polypeptide or a protein derived from the nature or a partial peptide thereof. The polypeptide to be contacted with a test substance may be, for example, a purified polypeptide, a soluble protein, a form bound to a carrier or a fusion protein fused with other polypeptides. In preferred embodiments, the LRRC42 polypeptide is isolated from cells expressing LRRC42, or chemically synthesized to be contacted with a test substance in vitro.
In preferred embodiment, test substances used by the present invention may be proteins such as antibodies or synthetic chemical compounds. As a method of screening substances that bind to an LRRC42 polypeptide, many methods well known by a person skilled in the art may be used. Such a screening may be conducted by, for example, immunoprecipitation method.

When immunoprecipitation method is used, it is preferred that an LRRC42 polypeptide contains an antibody recognition site. LRRC42 polypeptides to be used for the present screening method may be prepared as described above.
Alternatively, the polypeptide encoded by LRRC42 gene can be expressed as a fusion protein including a recognition site (epitope) of a monoclonal antibody by introducing the epitope of the monoclonal antibody, whose specificity has been revealed, to the N- or C- terminus of the polypeptide. A commercially available epitope-antibody system can be used (Experimental Medicine 13: 85-90 (1995)). Vectors that can express a fusion protein with, for example, beta-galactosidase, maltose binding protein, glutathione S-transferase, green fluorescence protein (GFP) and so on by the use of its multiple cloning sites are commercially available. A fusion protein prepared by introducing only small epitopes composed of several to a dozen amino acids so as not to change the property of the LRRC42 polypeptide by the fusion is also provided herein. Epitopes, such as polyhistidine (His-tag), influenza aggregate HA, human c-myc, FLAG, Vesicular stomatitis virus glycoprotein (VSV-GP), T7 gene 10 protein (T7-tag), human simple herpes virus glycoprotein (HSV-tag), E-tag (an epitope on monoclonal phage) and such, and monoclonal antibodies recognizing them can be used as the epitope-antibody system for screening proteins binding to the LRRC42 polypeptide (Experimental Medicine 13: 85-90 (1995)).

In the context of immunoprecipitation, an immune complex is formed by adding these antibodies to cell lysate prepared using an appropriate detergent. The immune complex is composed of the LRRC42 polypeptide, a polypeptide having the binding ability with the LRRC42 polypeptide, and an antibody. Immunoprecipitation can be also conducted using antibodies against the LRRC42 polypeptide, besides using antibodies against the above epitopes, which antibodies can be prepared as described above. An immune complex can be precipitated, for example by Protein A sepharose or Protein G sepharose when the antibody is a mouse IgG antibody. If the polypeptide encoded by LRRC42 gene is prepared as a fusion protein with an epitope, such as GST, an immune complex can be formed in the same manner as in the use of the antibody against the LRRC42 polypeptide, using a substance specifically binding to these epitopes, such as glutathione-Sepharose 4B.
Immunoprecipitation can be performed by following or according to, for example, the methods in the literature (Harlow and Lane, Antibodies, 511-52, Cold Spring Harbor Laboratory publications, New York (1988)).

SDS-PAGE is commonly used for analysis of immunoprecipitated proteins and the bound protein can be analyzed by the molecular weight of the protein using gels with an appropriate concentration. Since the protein bound to the LRRC42 polypeptide is difficult to detect by a common staining method, such as Coomassie staining or silver staining, the detection sensitivity for the protein can be improved by culturing cells in culture medium containing radioactive isotope, ³⁵S-methionine or ³⁵S-cystein, labeling proteins in the cells, and detecting the proteins. The target protein can be purified directly from the SDS-polyacrylamide gel and its sequence can be determined, when the molecular weight of a protein has been revealed.

West-Western blotting analysis (Skolnik et al., Cell 65: 83-90 (1991)) can be used as a method of screening for proteins binding to the LRRC42 polypeptide. In particular, a protein binding to the LRRC42 polypeptide can be obtained by preparing a cDNA library from cultured cells expected to express a protein binding to the LRRC42 polypeptide using a phage vector (e.g., ZAP), expressing the protein on LB-agarose, fixing the protein expressed on a filter, reacting the purified and labeled LRRC42 polypeptide with the above filter, and detecting the plaques expressing proteins bound to the LRRC42 polypeptide according to the label. The polypeptide of the invention may be labeled by utilizing the binding between biotin and avidin, or by utilizing an antibody that specifically binds to the LRRC42, or a peptide or polypeptide (for example, GST) that is fused to the LRRC42 polypeptide. Methods using radioisotope or fluorescence and such may be also used.
Alternatively, in another embodiment of the screening method of the present invention, a two-hybrid system utilizing cells may be used ("MATCHMAKER Two-Hybrid system", "Mammalian MATCHMAKER Two-Hybrid Assay Kit", "MATCHMAKER one-Hybrid system" (Clontech); "HybriZAP Two-Hybrid Vector System" (Stratagene); the references "Dalton and Treisman, Cell 68: 597-612 (1992)", "Fields and Sternglanz, Trends Genet 10: 286-92 (1994)").

In the two-hybrid system, a polypeptide of the invention is fused to the SRF-binding region or GAL4-binding region and expressed in yeast cells. A cDNA library is prepared from cells expected to express a protein binding to the polypeptide of the invention, such that the library, when expressed, is fused to the VP16 or GAL4 transcriptional activation region. The cDNA library is then introduced into the above yeast cells and the cDNA derived from the library is isolated from the positive clones detected (when a protein binding to the polypeptide of the invention is expressed in yeast cells, the binding of the two activates a reporter gene, making positive clones detectable). A protein encoded by the cDNA can be prepared by introducing the cDNA isolated above to E. coli and expressing the protein. Examples of suitable reporter genes include, but are not limited to, the Ade2 gene, lacZ gene, CAT gene, luciferase gene and such can be used in addition to the HIS3 gene.

A substance binding to an LRRC42 polypeptide may also be screened using affinity chromatography. For example, an LRRC42 polypeptide may be immobilized on a carrier of an affinity column, and a composition containing test substances is applied to the column. A composition herein may be, for example, cell extracts, cell lysates, antibody libraries etc. After loading test substances, the column is washed, and substances bound to the LRRC42 polypeptide can be collected. When the test substance is a protein, the amino acid sequence of the obtained protein is analyzed, an oligo DNA is synthesized based on the sequence, and cDNA libraries are screened using the oligo DNA as a probe to obtain a DNA encoding the protein.

A biosensor using the surface plasmon resonance phenomenon may be used as a mean for detecting or quantifying the bound substance in the present invention. When such a biosensor is used, the interaction between an LRRC42 polypeptide and a test substance can be observed real-time as a surface plasmon resonance signal, using only a minute amount of polypeptide and without labeling (for example, BIAcore, Pharmacia). Therefore, it is possible to evaluate the binding between an LRRC42 polypeptide and a test substance using a biosensor such as BIAcore.

The methods of screening for molecules that bind when the immobilized LRRC42 polypeptide is exposed to synthetic chemical substances, or natural substance banks or a random phage peptide display library, and the methods of screening using high-throughput based on combinatorial chemistry techniques (Wrighton et al., Science 273: 458-64 (1996); Verdine, Nature 384: 11-13 (1996); Hogan, Nature 384: 17-9 (1996)) to isolate not only proteins but chemical substances that bind to the LRRC42 protein (including agonist and antagonist) are well known to one skilled in the art.

In addition to the full length of LRRC42 polypeptide, partial peptides and fragments of the polypeptides may be used for the present screening, so long as the fragment utilized retains at least one biological activity of the natural occurring LRRC42. Examples of biological activities contemplated by the present invention include cell proliferation enhancing activity, a binding activity to GATAD2B polypeptide and so on. A partial LRRC42 peptide used for screenings in accordance with the present invention typically contains, at a minimum, at least one binding domain of LRRC42, more preferably GATAD2B-binding region. In a similar fashion, a partial GATAD2B peptide suitable for use in connection with screenings of the present invention typically contains, at a minimum, at least one binding domain of GATAD2B, more preferably the LRRC42-binding region.

Full length and fragment peptide may both be further linked to other substances, so long as the peptides and fragments retain the requisite biological activity. Useful substances include: peptides, lipids, sugar and sugar chains, acetyl groups, natural and synthetic polymers, etc. These kinds of modifications may be performed to confer additional functions or to stabilize the polypeptide and fragments.

In sum, the LRRC42 polypeptide to be contacted with a test substance may take the form a purified polypeptide, a soluble protein, a full length peptide or a partial peptide or fragment or a fusion protein fused with other polypeptides. Test substances screened by the present method as substances that bind to LRRC42 polypeptide can be candidate substances that has the potential to treat or prevent cancers. Potential of these candidate substances to treat or prevent cancers may be evaluated by second and/or further screening to identify therapeutic substance for cancers. For example, these candidate substances may further examined their ability of suppressing cancer cell proliferation by being contacted with a cancer cell overexpressing LRRC42 gene.

(ii) Screening for a Substance that Suppresses the Biological Activity of LRRC42:
In the context of present invention, the LRRC42 protein is characterized as having the activity of promoting cell proliferation of cancer cells (Fig. 3). Using this biological activity as an index, the present invention provides a method for screening a substance that suppresses the proliferation of cancer cells expressing LRRC42, and a method of screening for a substance for either or both of treating and preventing the cancer, particular LRRC42-associated cancers such as lung cancer. Thus, the present invention provides a method of screening for a substance for either or both of treating and preventing cancer using the polypeptide encoded by LRRC42 gene including the steps as follows:
(a) contacting a test substance with a polypeptide encoded by a polynucleotide of LRRC42;
(b) detecting the biological activity of the polypeptide of step (a); and
(c) selecting the test substance that suppresses the biological activity of the polypeptide encoded by the polynucleotide of LRRC42 as compared to the biological activity of the polypeptide detected in the absence of the test substance.

According to the present invention, the therapeutic effect of the test substance in suppressing the biological activity (e.g., the cell-proliferating activity) of LRRC42, or a candidate substance for either or both of treating and preventing cancer may be evaluated. Therefore, the present invention also provides a method of screening for a candidate substance that suppresses the biological activity of LRRC42, or a candidate substance for either or both of treating and preventing cancer, using the LRRC42 polypeptide or fragments thereof, including the following steps:
a) contacting a test substance with the LRRC42 polypeptide or a functional fragment thereof; and
b) detecting the biological activity of the polypeptide or fragment of step (a), and
c) correlating the biological activity of b) with the therapeutic effect of the test substance.

Alternatively, in some embodiments, the present invention provides a method for evaluating or estimating a therapeutic effect of a test substance in the context of the treatment, prevention or inhibition of a cancer associated with over-expression of LRRC42, the method including steps of:
(a) contacting a test substance with the LRRC42 polypeptide or a functional fragment thereof;
(b) detecting the biological activity of the polypeptide or fragment of step (a); and
(c) correlating the potential therapeutic effect and the test substance, wherein the potential therapeutic effect is shown, when a substance suppresses the biological activity of the polypeptide encoded by the polynucleotide of LRRC42 gene as compared to the biological activity of the polypeptide detected in the absence of the test substance.
Such cancer includes lung cancer.

In the context of the present invention, the therapeutic effect may be correlated with the biological activity of the LRRC42 polypeptide or a functional fragment thereof. For example, when the test substance suppresses or inhibits the biological activity of the LRRC42 polypeptide or a functional fragment thereof as compared to a level detected in the absence of the test substance, the test substance may identified or selected as the candidate substance having the therapeutic effect. Alternatively, when the test substance does not suppress or inhibit the biological activity of the LRRC42 polypeptide or a functional fragment thereof as compared to a level detected in the absence of the test substance, the test substance may identified as the substance having no significant therapeutic effect.
The method of the present invention is described in more detail below.

Any polypeptides can be used for screening so long as they suppress a biological activity of the LRRC42 protein. Such biological activity includes cell-proliferating activity of the LRRC42 protein. For example, LRRC42 protein can be used and polypeptides functionally equivalent to these proteins can also be used. Such polypeptides may be expressed endogenously or exogenously by cells.

In another aspect, the present invention also provides a screening method following the method described in the above "Screening" section, such method including the steps of:
a) contacting a test substance with the LRRC42 polypeptide or a fragment thereof;
b) detecting the binding between the polypeptide or fragment and the test substance;
c) selecting the test substance that binds to the polypeptide;
d) contacting the test substance selected in step c) with the LRRC42 polypeptide or a fragment thereof;
e) comparing the biological activity of the polypeptide or fragment with the biological activity detected in the absence of the substance; and
f) selecting the substance that suppresses the biological activity of the polypeptide as a candidate substance for treating or preventing lung cancer.

The substance isolated by this screening is a candidate for antagonists of the polypeptide encoded by LRRC42 gene. The term "antagonist" refers to molecules that inhibit the function of the polypeptide by binding thereto. This term also refers to molecules that reduce or inhibit expression of the gene encoding LRRC42. Moreover, a substance isolated by this screening is a candidate for substances which inhibit the in vivo interaction of the LRRC42 polypeptide with molecules (including DNAs and proteins).

When the biological activity to be detected in the present method is cell proliferation, it can be detected, for example, by preparing cells which express the LRRC42 polypeptide, culturing the cells in the presence of a test substance, and determining the speed of cell proliferation, measuring the cell cycle and such, as well as by measuring survival cells or the colony forming activity, for example, shown in Fig. 3. The substances that reduce the speed of proliferation of the cells expressed LRRC42 are selected as candidate substance for treating or preventing cancer. In some embodiments, cells expressing LRRC42 gene may be isolated cells or cultured cells, which exogenously or endogenously express LRRC42 gene in vitro.

More specifically, the method includes the step of:
(a) contacting a test substance with cells overexpressing LRRC42;
(b) measuring cell-proliferating activity; and
(c) selecting the test substance that reduces the cell-proliferating activity in the comparison with the cell-proliferating activity in the absence of the test substance.
In preferable embodiments, the method of the present invention may further include the steps of:
(d) selecting the test substance that has no effect to the cells no or little expressing LRRC42.

The phrase "suppress the biological activity" as defined herein are preferably at least 10% suppression of the biological activity of LRRC42 in comparison with that in the absence of the test substance, more preferably at least 25%, 50% or 75% suppression and most preferably at 90% suppression.
In the preferred embodiments, control cells that do not express LRRC42 polypeptide are used. Accordingly, the present invention also provides a method of screening for a candidate substance that inhibits cell growth or a candidate substance for either or both of treating and preventing an LRRC42- associated disease, using the LRRC42 polypeptide or fragments thereof including the steps as follows:
a) culturing cells which express an LRRC42 polypeptide or a functional fragment thereof, and control cells that do not express an LRRC42 polypeptide or a functional fragment thereof in the presence of the test substance;
b) detecting the biological activity of the cells which express the protein and control cells; and
c) selecting the test substance that inhibits the biological activity in the cells which express the protein as compared to the proliferation detected in the control cells and in the absence of the test substance. As revealed herein, suppressing the biological activity of LRRC42 polypeptide reduces cell growth. Thus, by screening for a candidate substance that inhibits the biological activity of LRRC42 polypeptide, candidate substance that have the potential to treat and/or prevent cancers can be identified. The potential of these candidate substances to treat or prevent cancers may be evaluated by second and/or further screening to identify therapeutic substances for cancers. For example, when a substance that inhibits the biological activity of an LRRC42 polypeptide also inhibits the activity of a cancer, it may be concluded that such a substance has an LRRC42 specific therapeutic effect.

(iii) Screening for a Substance that Inhibits the Binding between LRRC42 and GATAD2B:
As demonstrated herein, LRRC42 polypeptide directly interacts with GATAD2B polypeptide (Fig. 4A). Accordingly, a substance that inhibits the binding between LRRC42 polypeptide and GATAD2B polypeptide can be identified using the binding of LRRC42 polypeptide and GATAD2B polypeptide as an index. In view thereof, it is an object of the present invention to provide a method of screening for a substance that inhibits the binding between LRRC42 polypeptide and GATAD2B polypeptide.

Furthermore, as demonstrated in Examples, siRNAs against LRRC42 (si-LRRC42) lead to suppression of the LRRC42 expression and decrease of the GATAD2B protein level (Fig.4C). These results suggest that LRRC42 polypeptide is involved in stabilization of GATAD2B polypeptide. GATAD2B polypeptide is a constituent of MeCP1 complex that is capable of repressing transcription of methylated DNA. DNA methylation of tumor suppressor genes, such as Rb, p15, p15, p16 and so on, is common feature of various cancer including lung cancer (Lewandowska J, et al. Mutagenesis 2011; Vaissiere T, et al. Cancer Res 2009;69:243-52). Accordingly, LRRC42 polypeptide plays a role in transcription repression of tumor suppressor genes through stabilization of GATAD2B polypeptide and consequently, contributes tumorigenesis. Therefore, LRRC42-GATAD2B interaction is a good target for cancer therapy.

Accordingly, substances that inhibit the binding between LRRC42 polypeptide and GATAD2B polypeptide are useful for cancer therapeutic agents. Thus, the present invention also provides a method of screening for a candidate substance that inhibits or reduces the growth of cancer cells, and a candidate substance for either or both of treating and preventing cancers, e.g. lung cancer.

Accordingly, the present invention provides the following methods of [1] to [5]:
[1] A method of screening for a substance that inhibits or reduces the binding between an LRRC42 polypeptide and a GATAD2B polypeptide, such method including the steps of:
(a) contacting an LRRC42 polypeptide or functional equivalent thereof with a GATAD2B polypeptide or functional equivalent thereof in the presence of a test substance;
(b) detecting a binding level between the polypeptides in the step (a);
(c) comparing the binding level detected in the step (b) with those detected in the absence of the test substance; and
(d) selecting the test substance that reduces or inhibits the binding level between the polypeptides;
[2] A method of screening for a candidate substance suitable for either or both of the treatment and prevention of cancer or that inhibits cancer cell growth, such method including the steps of:
(a) contacting an LRRC42 polypeptide or functional equivalent thereof with a GATAD2B polypeptide or functional equivalent thereof, in the presence of a test substance;
(b) detecting the binding level between the polypeptides in the step (a);
(c) comparing the binding level detected in the step (b) with those detected in the absence of the test substance; and
(d) selecting the test substance that inhibits or reduces the binding level between the polypeptides;
[3] The method of [1] or [2], wherein the functional equivalent of the LRRC42 polypeptide includes an amino acid sequence of a GATAD2B-binding domain of the LRRC42 polypeptide;
[4] The method of [1] or [2], wherein the functional equivalent of the GATAD2B polypeptide includes an amino acid sequence of an LRRC42 binding domain of the GATAD2B polypeptide;
[5] The method of any one of [2] to [4], wherein the cancer is lung cancer.

According to the present invention, the therapeutic effect of a candidate substance on the inhibition of the cancer cell growth or a candidate substance in connection with either or both of the treatment and prevention of cancer may be evaluated. Therefore, the present invention also provides a method of screening for a candidate substance that suppresses the proliferation of cancer cells, and a method of screening for a candidate substance suited to either or both of the treatment and prevention cancer.

An illustrative example of such a method includes the steps of:
(a) contacting an LRRC42 polypeptide or functional equivalent thereof with a GATAD2B polypeptide or functional equivalent thereof in the presence of a test substance;
(b) detecting the level of binding between the polypeptides in the step (a);
(c) comparing the binding level detected in the step (b) with those detected in the absence of the test substance; and
(d) correlating the binding level of (c) with the therapeutic effect of the test substance.

Alternatively, in other embodiments, the present invention may provide a method for evaluating or estimating the therapeutic effect of a test substance in connection with either or both of the treatment and prevention of cancer or the inhibition of cancer, the method including steps of:
(a) contacting an LRRC42 polypeptide or functional equivalent thereof with a GATAD2B polypeptide or functional equivalent thereof in the presence of a test substance;
(b) detecting a binding level between the polypeptides in the step (a);
(c) comparing the binding level detected in the step (b) with those detected in the absence of the test substance; and
(d) correlating the potential therapeutic effect and the test substance, wherein the potential therapeutic effect is shown, when a test substance reduces the binding level.

In the context of the present invention, therapeutic effect may be correlated with the binding level of an LRRC42 polypeptide and a GATAD2B polypeptide. For example, when a test substance reduces the binding level of LRRC42 and GATAD2B proteins as compared to a binding level detected in the absence of the test substance, the test substance may identified or selected as a candidate substance having the desired therapeutic effect. Alternatively, when the test substance does not reduce the binding level of LRRC42 polypeptide and GATAD2B polypeptide as compared to a binding level detected in the absence of the test substance, the test substance may identified as the substance having no significant therapeutic effect.

In the context of the present invention, a functional equivalent of an LRRC42 polypeptide or GATAD2B polypeptide will have a biological activity equivalent to an LRRC42 polypeptide or GATAD2B polypeptide (see, "Genes and Proteins"). In typical embodiments, functional equivalents of an LRRC42 polypeptide includes a GATAD2B-binding domain of the LRRC42 polypeptide. Similarly, in typical embodiments, functional equivalents of a GATAD2B polypeptide includes an LRRC42-binding domain of the GATAD2B polypeptide.

In the context of screening for substances that inhibit or reduce the binding between LRRC42 polypeptide and GATAD2B polypeptide, many methods well known by one skilled in the art can be used. Such a screening can be conducted via, for example, an immunoprecipitation, West-Western blotting analysis (Skolnik et al., Cell 65: 83-90 (1991)), a two-hybrid system utilizing cells ("MATCHMAKER Two-Hybrid system", "Mammalian MATCHMAKER Two-Hybrid Assay Kit", "MATCHMAKER one-Hybrid system" (Clontech); "HybriZAP Two-Hybrid Vector System" (Stratagene); the references "Dalton and Treisman, Cell 68: 597-612 (1992)", "Fields and Sternglanz, Trends Genet 10: 286-92 (1994)"), affinity chromatography and a biosensor using the surface plasmon resonance phenomenon. Those methods can be conducted in a manner similar to the methods described above under the item "(i) Screening for an LRRC42 Binding Substance ".

A polypeptide to be used for screening can be a recombinant polypeptide or a protein derived from natural sources, or a partial peptide thereof. In preferred embodiments, the polypeptide is isolated from cells expressing LRRC42 or GATAD2B, or chemically synthesized. In addition, a polynucleotide to be used for screening can be a synthesized polynucleotide or a DNA derived from natural sources, or a partial oligonucleotide thereof. Any test substances aforementioned can be used for screening.

In some embodiments, the screening method of the present invention may be carried out in a cell-based assay using cells expressing both of an LRRC42 polypeptide and a GATAD2B polypeptide. Cells expressing LRRC42 polypeptide and GATAD2B polypeptide include, for example, cell lines established from cancer, e.g. lung cancer. Alternatively, the cells may be prepared through transformation with polynucleotides encoding an LRRC42 polypeptide and a GATAD2B polypeptide. Such transformation may be carried out using an expression vector encoding both LRRC42 polypeptide and GATAD2B polypeptide, or expression vectors encoding either LRRC42 polypeptide or GATAD2B polypeptide. The screening method of the present invention can be conducted by incubating such cells in the presence of a test substance. The binding between LRRC42 polypeptide and GATAD2B polypeptide can be detected by immunoprecipitation assay using an anti- LRRC42 antibody or anti-GATAD2B antibody.
When immunoprecipitation method is used, it is preferred that an LRRC42 polypeptide and a GATAD2B polypeptide contains antibody recognition sites. For example, an LRRC42 polypeptide and/or GATAD2B polypeptide may be prepared as fusion proteins that include the polypeptide and a commercially available epitope. Methods for preparing such fusion proteins are described above.

In immunoprecipitation, an immune complex may be formed by adding antibodies against epitopes fused to LRRC42 polypeptide and/or GATAD2B polypeptide to cell lysate prepared using an appropriate detergent. The immune complex consists of the LRRC42 polypeptide, the GATAD2B polypeptide, and the antibody. Immunoprecipitation can be also conducted using antibodies against the LRRC42 polypeptide or GATAD2B polypeptide. Those antibodies can also be prepared as described above. An immune complex can be precipitated, for example, by Protein A sepharose or Protein G sepharose when the antibody is a mouse IgG antibody.

In the present invention, it is revealed that suppression of the binding between LRRC42 polypeptide and GATAD2B polypeptide lead to suppression of the growth of cancer cells. Therefore, when a substance inhibits the binding between LRRC42 polypeptide and GATAD2B polypeptide, the inhibition is indicative of a potential therapeutic effect in a subject. In the present invention, a potential therapeutic effect refers to a clinical benefit with a reasonable expectation. In the present invention, such clinical benefit may include;
(a) a reduction of the binding between LRRC42 polypeptide and GATAD2B polypeptide,
(b) a decrease in size, prevalence, or metastatic potential of the cancer in the subject,
(c) the prevention of further cancer formation, or
(d) the prevention or alleviation of a clinical symptom of cancer.

II. Screening for a Substance that Alters the Expression of LRRC42:
In the context of the present invention, a decrease in the expression of LRRC42 by siRNA results in the inhibition of cancer cell proliferation (Figs.2A, 2B and 2C). Accordingly, the present invention provides a method of screening for a substance that inhibits the expression of LRRC42. A substance that inhibits the expression of LRRC42 is expected to suppress the proliferation of cancer cells, and thus is useful for either or both of treating and preventing cancer, particularly LRRC42-associated cancers such as lung cancer. Therefore, the present invention also provides a method for screening a substance that suppresses the proliferation of cancer cells, and a method for screening a candidate substance for either or both of treating and preventing cancer. In the context of the present invention, such screening may include, for example, the following steps:
(a) contacting a test substance with a cell expressing LRRC42; and
(b) selecting the test substance that reduces the expression level of LRRC42 as compared to a control level.

In the context of the present invention, such screening may include, for example, the following steps:
a) contacting a test substance with a cell expressing the LRRC42 gene;
b) detecting the expression level of the LRRC42 gene; and
c) correlating the expression level of b) with the therapeutic effect of the test substance.

In the context of present invention, the therapeutic effect may be correlated with the expression level of the LRRC42 gene. For example, when the test substance reduces the expression level of the LRRC42 gene as compared to a level detected in the absence of the test substance, the test substance may identified or selected as the candidate substance having the therapeutic effect. Alternatively, when the test substance does not reduce the expression level of the LRRC42 gene as compared to a level detected in the absence of the test substance, the test substance may identified as the substance having no significant therapeutic effect.
The method of the present invention is described in more detail below.

Cells expressing the LRRC42 include, for example, cell lines established from lung cancer or cell lines transfected with LRRC42 expression vectors; any of such cells can be used for the above screening of the present invention. The expression level can be estimated by methods well known to one skilled in the art, for example, RT-PCR, Northern blot assay, Western blot assay, immunostaining and flow cytometry analysis. The phrase "reduce the expression level" as defined herein are preferably at least 10% reduction of expression level of LRRC42 in comparison to the expression level in absence of the substance, more preferably at least 25%, 50% or 75% reduced level and most preferably at least 95% reduced level. The substance herein includes chemical compounds, double-strand nucleotides, and so on. The preparation of the double-strand nucleotides will be described bellow. In the method of screening, a substance that reduces the expression level of LRRC42 can be selected as candidate substances to be used for the treatment or prevention of cancer. In some embodiments, cells expressing LRRC42 gene may be isolated cells or cultured cells, which exogenously or endogenously express LRRC42 gene in vitro.

Accordingly, the screening method of the present invention may include the following steps:
(a) contacting a test substance with a cell into which a vector, including the transcriptional regulatory region of LRRC42 gene and a reporter gene that is expressed under the control of the transcriptional regulatory region, has been introduced;
(b) measuring the expression or activity of said reporter gene; and
(c) selecting the test substance that reduces the expression or activity of said reporter gene.

Suitable reporter genes and host cells are well known in the art. Illustrative reporter genes include, but are not limited to, luciferase, green fluorescence protein (GFP), Discosoma sp. Red Fluorescent Protein (DsRed), Chrolamphenicol Acetyltransferase (CAT), lacZ and beta-glucuronidase (GUS), and host cell is COS7, HEK293, HeLa and so on. The reporter construct required for the screening can be prepared by connecting reporter gene sequence to the transcriptional regulatory region of LRRC42 gene. The transcriptional regulatory region of LRRC42 gene herein is the region from transcription stat site to at least 500bp upstream, preferably 1000bp, more preferably 5000 or 10000bp upstream. A nucleotide segment containing the transcriptional regulatory region can be isolated from a genome library or can be propagated by PCR. The reporter construct required for the screening can be prepared by connecting reporter gene sequence to the transcriptional regulatory region of the gene. Methods for identifying a transcriptional regulatory region, and also assay protocol are well known (Molecular Cloning third edition chapter 17, 2001, Cold Springs Harbor Laboratory Press).

The vector containing the reporter construct is introduced into host cells and the expression or activity of the reporter gene is detected by methods well known in the art (e.g., using luminometer, absorption spectrometer, flow cytometer and so on). "Reduces the expression or activity" as defined herein are preferably at least 10% reduction of the expression or activity of the reporter gene in comparison with in absence of the test substance, more preferably at least 25%, 50% or 75% reduction and most preferably at least 95% reduction.

Alternatively, in some embodiments, the present invention also provides a method for evaluating or estimating a therapeutic effect of a test substance on treating or preventing cancer or inhibiting cancer associated with over-expression of LRRC42, the method including steps of:
(a) contacting a test substance with a cell into which a vector, including the transcriptional regulatory region of LRRC42 gene and a reporter gene that is expressed under the control of the transcriptional regulatory region, has been introduced;
(b) measuring the expression level or activity of said reporter gene; and
(c) correlating the potential therapeutic effect and the test substance, wherein the potential therapeutic effect is shown, when a test substance reduces the expression level or activity of said reporter gene.

According to the present invention, the therapeutic effect of the test substance on inhibiting the cancer cell growth or a candidate substance for treating or preventing LRRC42- associating disease may be evaluated. Therefore, the present invention also provides a method for screening for a candidate substance that suppresses the proliferation of cancer cells, and a method for screening for a candidate substance for treating or preventing LRRC42 associating disease.

According to another aspect, the present invention provides a method which includes the following steps of:
(a) contacting a test substance with a cell into which a vector, composed of the transcriptional regulatory region of the LRRC42 gene and a reporter gene that is expressed under the control of the transcriptional regulatory region, has been introduced;
(b) detecting the expression level or activity of the reporter gene; and
(c) correlating the expression level of (b) with the therapeutic effect of the test substance.

In the context of the present invention, the therapeutic effect may be correlated with the expression or activity of said reporter gene. For example, when the test substance reduces the expression or activity of said reporter gene as compared to a level detected in the absence of the test substance, the test substance may identified or selected as the candidate substance having the therapeutic effect. Alternatively, when the test substance does not reduce the expression or activity of said reporter gene as compared to a level detected in the absence of the test substance, the test substance may identified as the substance having no significant therapeutic effect.

By screening for candidate substances that (i) bind to the LRRC42 polypeptide; (ii) suppress/reduce the biological activity (e.g., the cell-proliferating activity) of the LRRC42 polypeptide; (iii) reduce the expression level of LRRC42 gene; (iv) inhibit the binding between LRRC42 polypeptide and GATAD2B polypeptide, candidate substances that have the potential to treat or prevent cancers (e.g., lung cancer) can be identified. The therapeutic potential of these candidate substances may be evaluated by second and/or further screening to identify therapeutic substance for cancers. For example, when a substance that binds to the LRRC42 polypeptide inhibits the above-described activities of cancer, it may be concluded that such a substance has the LRRC42-specific therapeutic effect.

Double Stranded Molecules:
As used herein, the term "isolated double-stranded molecule" refers to a nucleic acid molecule that inhibits expression of a target gene and includes, for example, short interfering RNA (siRNA; e.g., double-stranded ribonucleic acid (dsRNA) or small hairpin RNA (shRNA)) and short interfering DNA/RNA (siD/R-NA; e.g. double-stranded chimera of DNA and RNA (dsD/R-NA) or small hairpin chimera of DNA and RNA (shD/R-NA)).

As used herein, a target sequence is a nucleotide sequence within mRNA or cDNA sequence of a gene, which will result in suppress of translation of the whole mRNA if a double-stranded nucleic acid molecule of the invention was introduced within a cell expressing the gene. A nucleotide sequence within mRNA or cDNA sequence of a gene can be determined to be a target sequence when a double-stranded polynucleotide including a sequence corresponding to the target sequence inhibits expression of the gene in a cell expressing the gene. The double stranded polynucleotide by which suppresses the gene expression may have the target sequence and 3'overhang having 2 to 5 nucleotides in length (e.g., uu). When a target sequence is shown by cDNA sequence, a sense strand sequence of a double-stranded cDNA, i.e., a sequence that mRNA sequence is converted into DNA sequence, is used for defining a target sequence.

A double-stranded molecule is composed of a sense strand that has a sequence corresponding to a target sequence and an antisense strand that has a complementary sequence to the target sequence, and the antisense strand hybridizes with the sense strand at the complementary sequence to form a double-stranded molecule. Herein, the phrase "corresponding to" means converting a target sequence according to the kind of nucleic acid that constitutes a sense strand of a double-stranded molecule. For example, when a target sequence is shown in DNA sequence and a sense strand of a double-stranded molecule has an RNA region, base "t"s within the RNA region is replaced with base "u"s. On the other hand, when a target sequence is shown in RNA sequence and a sense strand of a double-stranded molecule has a DNA region, base "u"s within the DNA region is replaced with "t"s. In the context of the present invention, the target sequences are mainly shown in DNA. In other words, the present invention also provides a double-stranded molecule whose target sequence includes or is limited to SEQ ID NO: 7 or SEQ ID NO: 8 which is shown in DNA but can be replaced with RNA.

Also, a complementary sequence to a target sequence for an antisense strand of a double-stranded molecule can be defined according to the kind of nucleic acid that constitutes the antisense strand.
A double-stranded molecule may have one or two 3'overhangs having 2 to 5 nucleotides in length (e.g., uu) and/or a loop sequence that links a sense strand and an antisense strand to form hairpin structure, in addition to a sequence corresponding to a target sequence and complementary sequence thereto.

As use herein, the term "siRNA" refers to a double-stranded RNA molecule that prevents translation of a target mRNA. Standard techniques of introducing siRNA into the cell are used, including those in which DNA is a template from which RNA is transcribed. The siRNA includes an LRRC42 sense nucleic acid sequence (also referred to as "sense strand"), an LRRC42 antisense nucleic acid sequence (also referred to as "antisense strand") or both. The siRNA may be constructed such that a single transcript has both the sense and complementary antisense nucleic acid sequences of the target gene, e.g., a hairpin. The siRNA may be either a dsRNA or shRNA.

As used herein, the term "dsRNA" refers to a construct of two RNA molecules composed of complementary sequences to one another and that have annealed together via the complementary sequences to form a double-stranded RNA molecule. The nucleotide sequence of two strands may include not only the "sense" or "antisense" RNAs selected from a protein coding sequence of target gene sequence, but also RNA molecule having a nucleotide sequence selected from non-coding region of the target gene.

The term "shRNA", as used herein, refers to an siRNA having a stem-loop structure, composed of first and second regions complementary to one another, i.e., sense and antisense strands. The degree of complementarity and orientation of the regions are sufficient such that base pairing occurs between the regions, the first and second regions are joined by a loop region, the loop results from a lack of base pairing between nucleotides (or nucleotide analogs) within the loop region. The loop region of an shRNA is a single-stranded region intervening between the sense and antisense strands and may also be referred to as "intervening single-strand".

As use herein, the term "siD/R-NA" refers to a double-stranded polynucleotide molecule which is composed of both RNA and DNA, and includes hybrids and chimeras of RNA and DNA and prevents translation of a target mRNA. Herein, a hybrid indicates a molecule wherein a polynucleotide composed of DNA and a polynucleotide composed of RNA hybridize to each other to form the double-stranded molecule; whereas a chimera indicates that one or both of the strands composing the double stranded molecule may contain RNA and DNA. Standard techniques of introducing siD/R-NA into the cell are used. The siD/R-NA includes an LRRC42 sense nucleic acid sequence (also referred to as "sense strand"), an LRRC42 antisense nucleic acid sequence (also referred to as "antisense strand") or both. The siD/R-NA may be constructed such that a single transcript has both the sense and complementary antisense nucleic acid sequences from the target gene, e.g., a hairpin. The siD/R-NA may be either a dsD/R-NA or shD/R-NA.

As used herein, the term "dsD/R-NA" refers to a construct of two molecules composed of complementary sequences to one another and that have annealed together via the complementary sequences to form a double-stranded polynucleotide molecule. The nucleotide sequence of two strands may include not only the "sense" or "antisense" polynucleotides sequence selected from a protein coding sequence of target gene sequence, but also polynucleotide having a nucleotide sequence selected from non-coding region of the target gene. One or both of the two molecules constructing the dsD/R-NA are composed of both RNA and DNA (chimeric molecule), or alternatively, one of the molecules is composed of RNA and the other is composed of DNA (hybrid double-strand).

The term "shD/R-NA", as used herein, refers to an siD/R-NA having a stem-loop structure, composed of a first and second regions complementary to one another, i.e., sense and antisense strands. The degree of complementarity and orientation of the regions are sufficient such that base pairing occurs between the regions, the first and second regions are joined by a loop region, the loop results from a lack of base pairing between nucleotides (or nucleotide analogs) within the loop region. The loop region of an shD/R-NA is a single-stranded region intervening between the sense and antisense strands and may also be referred to as "intervening single-strand".

As used herein, an "isolated nucleic acid" is a nucleic acid removed from its original environment (e.g., the natural environment if naturally occurring) and thus, synthetically altered from its natural state. In the context of the present invention, examples of isolated nucleic acid includes DNA, RNA, and derivatives thereof.
Double-stranded molecules (e.g., siRNA and the like) against target gene(s) can be used to reduce the expression level of said gene(s). Herein, the term "double-stranded molecule" refers to a nucleic acid molecule that inhibits expression of a target gene including, for example, short interfering RNA (siRNA; e.g., double-stranded ribonucleic acid (dsRNA) or small hairpin RNA (shRNA)) and short interfering DNA/RNA (siD/R-NA; e.g., double-stranded chimera of DNA and RNA (dsD/R-NA) or small hairpin chimera of DNA and RNA (shD/R-NA)) as described in "Definitions". In the context of the present invention, a double-stranded molecule against LRRC42 is a molecule that hybridizes to its target sequence within the LRRC42 mRNA, decreases or inhibits production of LRRC42 protein encoded by LRRC42 gene by associating with the normally single-stranded mRNA transcript of the gene, thereby interferes with translation and thus, inhibits expression of the protein. As demonstrated herein, the expression of LRRC42 in several cancer cell lines was inhibited by dsRNA (Fig. 2). Accordingly, the present invention provides isolated double-stranded molecules that are capable of inhibiting the expression of an LRRC42 gene when introduced into a cell expressing the gene. The target sequence of double-stranded molecule may be designed by an siRNA design algorithm such as that mentioned below.
Examples of LRRC42 target sequences include nucleotide sequence of SEQ ID NO: 7 or 8.

Double stranded molecules of particular interest in the context of the present invention are set forth in items [1] to [18] below:
[1] An isolated double-stranded molecule that, when introduced into a cell, inhibits expression of the LRRC42 gene and cell proliferation, such molecules composed of a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded molecule;
[2] The double-stranded molecule of [1], wherein said double-stranded molecule acts on mRNA, matching a target sequence of SEQ ID NO: 7 or 8;
[3] The double-stranded molecule of [1] or [2], wherein the sense strand contains a nucleotide sequence corresponding to a target sequence of SEQ ID NO: 7 or 8;
[4] The double-stranded molecule of any one of [1] to [3], wherein the sense strand hybridize with antisense strand at the target sequence to form the double-stranded molecule having a less than about 100 nucleotide pairs in length;
[5] The double-stranded molecule of [4], wherein the sense strand hybridize with antisense strand at the target sequence to form the double-stranded molecule having less than about 75 nucleotide pairs in length;
[6] The double-stranded molecule of [5], wherein the sense strand hybridize with antisense strand at the target sequence to form the double-stranded molecule having less than about 50 nucleotide pairs in length;
[7] The double-stranded molecule of [6], wherein the sense strand hybridize with antisense strand at the target sequence to form the double-stranded molecule having less than about 25 nucleotide pairs in length;
[8] The double-stranded molecule of [7], wherein the sense strand hybridize with antisense strand at the target sequence to form the double-stranded molecule having a between about 19 and about 25 nucleotide pairs in length;
[9] The double-stranded molecule of any one of [1] to [8], composed of a single polynucleotide having both the sense and antisense strands linked by an intervening single-strand;
[10] The double-stranded molecule of [9], having the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand containing a nucleotide sequence corresponding to a target sequence of SEQ ID NO: 7 or 8 is the intervening single-strand composed of 3 to 23 nucleotides, and [A'] is the antisense strand containing a sequence complementary to [A];
[11] The double-stranded molecule of any one of [1] to [10], composed of RNA;
[12] The double-stranded molecule of any one of [1] to [10], composed of both DNA and RNA;
[13] The double-stranded molecule of [12], wherein the molecule is a hybrid of a DNA polynucleotide and an RNA polynucleotide;
[14] The double-stranded molecule of [13] wherein the sense and the antisense strands are composed of DNA and RNA, respectively;
[15] The double-stranded molecule of [12], wherein the molecule is a chimera of DNA and RNA;
[16] The double-stranded molecule of [15], wherein a region flanking to the 3'-end of the antisense strand, or both of a region flanking to the 5'-end of sense strand and a region flanking to the 3'-end of antisense strand are RNA;
[17] The double-stranded molecule of [16], wherein the flanking region is composed of 9 to 13 nucleotides; and
[18] The double-stranded molecule of any one of [1] to [17], wherein the molecule contains one or two 3' overhang(s).
The double-stranded molecule of the present invention is described in more detail below.

Methods for designing double-stranded molecules having the ability to inhibit target gene expression in cells are known. (See, for example, US Patent No. 6,506,559, herein incorporated by reference in its entirety). For example, a computer program for designing siRNAs is available from the Ambion website (http://www.ambion.com/techlib/misc/siRNA_finder.html).
Such a computer program selects target nucleotide sequences for double-stranded molecules based on the following protocol.

Selection of Target Sites:
1. Beginning with the AUG start codon of the transcript, scan downstream for AA di-nucleotide sequences. Record the occurrence of each AA and the 3' adjacent 19 nucleotides as potential siRNA target sites. Tuschl et al. don't recommend designing siRNA to the 5' and 3' untranslated regions (UTRs) and regions near the start codon (within 75 bases) as these may be richer in regulatory protein binding sites, and UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNA endonuclease complex.
2. Compare the potential target sites to the appropriate genome database (human, mouse, rat, etc.) and eliminate from consideration any target sequences with significant homology to other coding sequences. Basically, BLAST, which can be found on the NCBI server at: www.ncbi.nlm.nih.gov/BLAST/, is used (Altschul SF et al., Nucleic Acids Res 1997 Sep 1, 25(17): 3389-402).
3. Select qualifying target sequences for synthesis. Selecting several target sequences along the length of the gene to evaluate is typical.

Using the above protocol, the target sequences of the double-stranded molecules against the LRRC42 gene were designed as nucleotide sequences of SEQ ID NO: 7 and 8.
Double-stranded molecules targeting the above-mentioned target sequences were respectively examined for their ability to suppress the growth of cells expressing the LRRC42 gene.
Accordingly, the present invention provides double-stranded molecule targeting the sequences of SEQ ID NO: 7 and 8 for LRRC42 gene,
The double-stranded molecule of the present invention may be directed to a single target LRRC42 gene sequence or may be directed to a plurality of target LRRC42 gene sequences.

A double-stranded molecule of the present invention targeting the above-mentioned targeting sequence of LRRC42 gene include isolated polynucleotide that contain the nucleic acid sequences of target sequences and/or complementary sequences to the target sequence. Example of polynucleotide targeting LRRC42 gene includes that containing the sequence of SEQ ID NO: 7 or 8 and/or complementary sequences to these nucleotide sequences; However, the present invention is not limited to this example, and minor modifications in the aforementioned nucleic acid sequences are acceptable so long as the modified molecule retains the ability to suppress the expression of LRRC42 gene. Herein, the phrase "minor modification" as used in connection with a nucleic acid sequence indicates one, two or several substitution, deletion, addition or insertion of nucleic acids to the sequence.

In an embodiment, a double-stranded molecule is composed of two polynucleotides, one polynucleotide has a sequence corresponding to a target sequence, i.e., sense strand, and another polypeptide has a complementary sequence to the target sequence, i.e., antisense strand. The sense strand polynucleotide and the antisense strand polynucleotide hybridize to each other to form double-stranded molecule. Examples of such double-stranded molecules include dsRNA and dsD/R-NA.

In an another embodiment, a double-stranded molecule is composed of a polynucleotide that has both a sequence corresponding to a target sequence, i.e., sense strand, and a complementary sequence to the target sequence, i.e., antisense strand. Generally, the sense strand and the antisense strand are linked by a intervening strand, and hybridize to each other to form a hairpin loop structure. Examples of such double-stranded molecule include shRNA and shD/R-NA.

In other words, a double-stranded molecule of the present invention is composed a sense strand polynucleotide having a nucleotide sequence of the target sequence and anti-sense strand polynucleotide having a nucleotide sequence complementary to the target sequence, and both of polynucleotides hybridize to each other to form the double-stranded molecule. In the double-stranded molecule including the polynucleotides, a part of the polynucleotide of either or both of the strands may be RNA, and when the target sequence is defined with a DNA sequence, the nucleotide "t" within the target sequence and complementary sequence thereto is replaced with "u".

In one embodiment of the present invention, such a double-stranded molecule of the present invention includes a stem-loop structure, composed of the sense and antisense strands. The sense and antisense strands may be joined by a loop. Accordingly, the present invention also provides the double-stranded molecule composed of a single polynucleotide containing both the sense strand and the antisense strand linked or flanked by an intervening single-strand.

In the present invention, double-stranded molecules targeting the LRRC42 gene may have a sequence selected from among SEQ ID NOs: 7 and 8 as a target sequence. Accordingly, preferable examples of the double-stranded molecule of the present invention include a polynucleotide and a complementary sequence thereto, and a polynucleotide that has a sequence corresponding to SEQ ID NOs: 7 and 8 and a complementary sequence thereto.
In the context of the present invention, the term "several" as applies to nucleic acid substitutions, deletions, additions and/or insertions may mean 3-7, preferably 3-5, more preferably 3-4, even more preferably 3 nucleic acid residues.

According to the present invention, a double-stranded molecule of the present invention can be tested for its suppression ability using the methods utilized in the Examples. In the Examples herein below, double-stranded molecules composed of sense strands of various portions of LRRC42 mRNA or antisense strands complementary thereto were tested in vitro for their ability to decrease production of LRRC42 gene product in cancer cell lines according to standard methods. For example, reduction in LRRC42 gene product in cells contacted with the candidate double-stranded molecule compared to cells cultured in the absence of the candidate molecule can be detected by, e.g. RT-PCR using primers for the LRRC42 mRNA mentioned under Example 1, in the section entitled "Semiquantitative reverse transcription RT-PCR". Sequences that decrease the production of an LRRC42 gene product in in vitro cell-based assays can then be tested for their inhibitory effects on cell growth. Sequences that inhibit cell growth in in vitro cell-based assay can then be tested for their in vivo suppression ability using animals with cancer, e.g. nude mouse xenograft models, to confirm decreased production of an LRRC42 gene product and decreased cancer cell growth.

When the isolated polynucleotide is RNA or derivatives thereof, base "t" should be replaced with "u" in the nucleotide sequences. As used herein, the term "complementary" refers to Watson-Crick or Hoogsteen base pairing between nucleotides units of a polynucleotide, and the term "binding" means the physical or chemical interaction between two polynucleotides. When the polynucleotide includes modified nucleotides and/or non-phosphodiester linkages, these polynucleotides may also bind each other as same manner. Generally, complementary polynucleotide sequences hybridize under appropriate conditions to form stable duplexes containing few or no mismatches. However, the present invention extends to complementary sequences that include mismatches of one or more nucleotides. In addition, the sense strand and antisense strand of the isolated polynucleotide of the present invention can form double-stranded molecule or hairpin loop structure by the hybridization. In a preferred embodiment, such duplexes contain no more than 1 mismatch for every 10 matches. In an especially preferred embodiment, where the strands of the duplex are fully complementary, such duplexes contain no mismatches.

The complementary or antisense polynucleotide is preferably less than 1714 nucleotides in length for LRRC42. Preferably, the polynucleotide is less than 500, 200, 100, 75, 50, or 25 nucleotides in length for LRRC42. The isolated polynucleotides of the present invention are useful for forming double-stranded molecules against LRRC42 gene or preparing template DNAs encoding the double-stranded molecules. When the polynucleotides are used for forming double-stranded molecules, the polynucleotide may be longer than 19 nucleotides, preferably longer than 21 nucleotides, and more preferably has a length of between about 19 and 25 nucleotides.
Accordingly, the present invention provides a double-stranded molecule composed of a sense strand and an antisense strand, wherein the sense strand is a nucleotide sequence corresponding to a target sequence. In preferable embodiments, the sense strand hybridizes with antisense strand at the target sequence to form the double-stranded molecule having between 19 and 25 nucleotide pairs in length.

The double-stranded molecule serves as a guide for identifying homologous sequences in mRNA for the RISC complex, when the double-stranded molecule is introduced into cells. The identified target RNA is cleaved and degraded by the nuclease activity of Dicer, through which the double-stranded molecule eventually decreases or inhibits production (expression) of the polypeptide encoded by the RNA. Thus, a double-stranded molecule of the invention can be defined by its ability to generate a single-strand that specifically hybridizes to the mRNA of the LRRC42 gene under stringent conditions. Herein, the portion of the mRNA that hybridizes with the single-strand generated from the double-stranded molecule is referred to as "target sequence" or "target nucleic acid" or "target nucleotide". In the context of the present invention, the nucleotide sequence of the "target sequence" can be shown using not only the RNA sequence of the mRNA, but also the DNA sequence of cDNA synthesized from the mRNA.

The double-stranded molecules of the invention may contain one or more modified nucleotides and/or non-phosphodiester linkages. It is well known in the art to introduce chemical modifications well known in the art that are capable of increasing stability, availability, and/or cell uptake of the double-stranded molecule. A person skilled in the art will recognize the wide array of chemical modification that may be incorporated into the present molecules (WO03/070744; WO2005/045037). For example, in one embodiment, modifications can be used to provide improved resistance to degradation or improved uptake. Examples of such modifications include, but are not limited to, phosphorothioate linkages, 2'-O-methyl ribonucleotides (especially on the sense strand of a double-stranded molecule), 2'-deoxy-fluoro ribonucleotides, 2'-deoxy ribonucleotides, "universal base" nucleotides, 5'-C- methyl nucleotides, and inverted deoxybasic residue incorporation (US20060122137).

In another embodiment, modifications can be used to enhance the stability or to increase targeting efficiency of the double-stranded molecule. Examples of such modifications include, but are not limited to, chemical cross linking between the two complementary strands of a double-stranded molecule, chemical modification of a 3' or 5' terminus of a strand of a double-stranded molecule, sugar modifications, nucleobase modifications and/or backbone modifications, 2 -fluoro modified ribonucleotides and 2'-deoxy ribonucleotides (WO2004/029212). In another embodiment, modifications can be used to increased or decreased affinity for the complementary nucleotides in the target mRNA and/or in the complementary double-stranded molecule strand (WO2005/044976). For example, an unmodified pyrimidine nucleotide can be substituted for a 2-thio, 5-alkynyl, 5-methyl, or 5-propynyl pyrimidine. Additionally, an unmodified purine can be substituted with a 7-deaza, 7-alkyl, or 7-alkenyl purine. In another embodiment, when the double-stranded molecule is a double-stranded molecule with a 3' overhang, the 3'- terminal nucleotide overhanging nucleotides may be replaced by deoxyribonucleotides (Elbashir SM et al., Genes Dev 2001 Jan 15, 15(2): 188-200). For further details, published documents such as US20060234970 are available. However, the present invention should not construed as limited to these examples; any of a number of conventional chemical modifications may be employed for the double-stranded molecules of the present invention so long as the resulting molecule retains the ability to inhibit the expression of the target gene.

The double-stranded molecules of the present invention may include both DNA and RNA, e.g., dsD/R-NA or shD/R-NA. For example, a hybrid polynucleotide of a DNA strand and an RNA strand or a DNA-RNA chimera polynucleotide shows increased stability and are thus contemplated herein. Mixing of DNA and RNA, i.e., a hybrid type double-stranded molecule composed of a DNA strand (polynucleotide) and an RNA strand (polynucleotide), a chimera type double-stranded molecule containing both DNA and RNA on any or both of the single strands (polynucleotides), or the like may be formed for enhancing stability of the double-stranded molecule.

The hybrid of a DNA strand and an RNA strand may either have a DNA sense strand coupled to an RNA antisense strand, or vice versa, so long as the resulting double stranded molecule can inhibit expression of the target gene when introduced into a cell expressing the gene. In a preferred embodiment, the sense strand polynucleotide is DNA and the antisense strand polynucleotide is RNA. Also, the chimera type double-stranded molecule may have either or both of sense and antisense strands composed of DNA and RNA, so long as the resulting double-stranded molecule has an activity to inhibit expression of the target gene when introduced into a cell expressing the gene. In order to enhance stability of the double-stranded molecule, the molecule preferably contains as much DNA as possible, whereas to induce inhibition of the target gene expression, the molecule is required to be RNA within a range to induce sufficient inhibition of the expression.

A preferred chimera type double-stranded molecule contains: an upstream partial region (i.e., a region flanking to the target sequence or complementary sequence thereof within the sense or antisense strands) of RNA. Preferably, the upstream partial region indicates the 5' side (5'-end) of the sense strand and the 3' side (3'-end) of the antisense strand. Alternatively, regions flanking to 5'-end of sense strand and/or 3'-end of antisense strand may be referred to as the upstream partial region. That is, in preferred embodiments, a region flanking to the 3'-end of the antisense strand, or both of a region flanking to the 5'-end of sense strand and a region flanking to the 3'-end of antisense strand are composed of RNA. For instance, a chimera or hybrid type double-stranded molecule of the present invention may include following combinations.
sense strand:
5'-[-----DNA-----]-3'
3'-(RNA)-[DNA]-5'
:antisense strand,
sense strand:
5'-(RNA)-[DNA]-3'
3'-(RNA)-[DNA]-5'
:antisense strand, and
sense strand:
5'-(RNA)-[DNA]-3'
3'-(-----RNA-----)-5'
:antisense strand.

The upstream partial region preferably is a domain composed of 9 to 13 nucleotides counted from the terminus of the target sequence or complementary sequence thereto within the sense or antisense strands of the double-stranded molecules. Moreover, preferred examples of such chimera type double-stranded molecules include those having a strand length of 19 to 21 nucleotides in which at least the upstream half region (5' side region for the sense strand and 3' side region for the antisense strand) of the polynucleotide is RNA and the other half is DNA. In such a chimera type double-stranded molecule, the effect to inhibit expression of the target gene is much higher when the entire antisense strand is RNA (US20050004064).

In the context of the present invention, the double-stranded molecule may form a hairpin, such as a short hairpin RNA (shRNA) and short hairpin composed of DNA and RNA (shD/R-NA). The shRNA or shD/R-NA is a sequence of RNA or mixture of RNA and DNA making a tight hairpin turn that can be used to silence gene expression via RNA interference. The shRNA or shD/R-NA includes the sense target sequence and the antisense target sequence on a single strand wherein the sequences are separated by a loop sequence. Generally, the hairpin structure is cleaved by the cellular machinery into dsRNA or dsD/R-NA molecules, which are then bound to the RNA-induced silencing complex (RISC). This complex binds to and cleaves mRNAs that match the target sequence of the dsRNA or dsD/R-NA.

A loop sequence composed of an arbitrary nucleotide sequence can be located between the sense and antisense sequence in order to form the hairpin loop structure. Thus, the present invention also provides a double-stranded molecule having the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand containing a nucleotide sequence corresponding to a target sequence, [B] is an intervening single-strand and [A'] is the antisense strand containing a complementary sequence to [A]. The target sequence may be selected from among, for example, nucleotide sequences of SEQ ID NOs: 7 and 8 for LRRC42.
The present invention is not limited to these examples, and the target sequence in [A] may be modified sequences from these examples so long as the double-stranded molecule retains the ability to suppress the expression of the targeted LRRC42 gene. The region [A] hybridizes to [A'] to form a loop composed of the region [B]. The intervening single-stranded portion [B], i.e., loop sequence may be preferably 3 to 23 nucleotides in length. The loop sequence, for example, can be selected from among the following sequences (http://www.ambion.com/techlib/tb/tb_506.html). Furthermore, loop sequence composed of 23 nucleotides also provides active siRNA (Jacque JM et al., Nature 2002 Jul 25, 418(6896): 435-8, Epub 2002 Jun 26):
CCC, CCACC, or CCACACC: Jacque JM et al., Nature 2002 Jul 25, 418(6896): 435-8, Epub 2002 Jun 26;
UUCG: Lee NS et al., Nat Biotechnol 2002 May, 20(5): 500-5; Fruscoloni P et al., Proc Natl Acad Sci USA 2003 Feb 18, 100(4): 1639-44, Epub 2003 Feb 10; and
UUCAAGAGA: Dykxhoorn DM et al., Nat Rev Mol Cell Biol 2003 Jun, 4(6): 457-67.

Examples of preferred double-stranded molecules of the present invention having hairpin loop structure are shown below. In the following structure, the loop sequence can be selected from among AUG, CCC, UUCG, CCACC, CTCGAG, AAGCUU, CCACACC, and UUCAAGAGA; however, the present invention is not limited thereto:
CUUACUACCUCAGCUCAGA -[B]- UCUGAGCUGAGGUAGUAAG
(for target sequence SEQ ID NO: 7).
GACUUGUUAAAUUCCUAUU -[B]- AAUAGGAAUUUAACAAGUC
(for target sequence SEQ ID NO: 8).

Additionally, several nucleotides can be added to 3'end of the sense strand and/or antisense strand of the target sequence, as 3' overhangs so as to enhance the inhibition activity of the double-stranded molecule. The preferred examples of nucleotides constituting a 3' overhang include "t" and "u", but are not limited to. The number of nucleotides to be added is at least 2, generally 2 to 10, preferably 2 to 5. The added nucleotides form single strand at the 3'end of the antisense strand of the double-stranded molecule. In cases where double-stranded molecules consists of a single polynucleotide to form a hairpin loop structure, a 3' overhang sequence may be added to the 3' end of the single polynucleotide.

The method for preparing the double-stranded molecule is not particularly limited though it is preferable to use one of the standard chemical synthetic methods known in the art. According to the chemical synthesis method, sense and antisense single-stranded polynucleotides are separately synthesized and then annealed together via an appropriate method to obtain a double-stranded molecule. In one specific annealing embodiment, the synthesized single-stranded polynucleotides are mixed in a molar ratio of preferably at least about 3:7, more preferably about 4:6, and most preferably substantially equimolar amount (i.e., a molar ratio of about 5:5). Next, the mixture is heated to a temperature at which double-stranded molecules dissociate and then is gradually cooled down. The annealed double-stranded polynucleotide can be purified by usually employed methods known in the art. Example of purification methods include methods utilizing agarose gel electrophoresis or wherein remaining single-stranded polynucleotides are optionally removed by, e.g., degradation with appropriate enzyme.
The regulatory sequences flanking LRRC42 sequences may be identical or different, such that their expression can be modulated independently, or in a temporal or spatial manner. The double-stranded molecules can be transcribed intracellularly by cloning LRRC42 gene templates into a vector containing, e.g., an RNA pol III transcription unit from the small nuclear RNA (snRNA) U6 or the human H1 RNA promoter.

Alternatively, the double-stranded molecules may be transcribed intracellularly by cloning its coding sequence into a vector containing a regulatory sequence that directs the expression of the double-stranded molecule in an adequate cell (e.g., a RNA poly III transcription unit from the small nuclear RNA (snRNA) U6 or the human H1 RNA promoter) adjacent to the coding sequence. The regulatory sequences flanking the coding sequences of double-stranded molecule may be identical or different, such that their expression can be modulated independently, or in a temporal or spatial manner. Details of vectors which are capable of producing the double-stranded molecules are described below.

Vector containing a double-stranded molecule of the present invention:
As noted above, the present invention contemplates vectors containing one or more of the double-stranded molecules described herein, and a cell containing such a vector.
Of particular interest to the present invention are the following vectors of [1] to [10].
[1] A vector, encoding a double-stranded molecule that, when introduced into a cell, inhibits expression of LRRC42 and cell proliferation, such molecules composed of a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded molecule;
[2] The vector of [1], encoding the double-stranded molecule acts on mRNA, matching a target sequence of SEQ ID NO: 7 or 8;
[3] The vector of [1] or [2], wherein the sense strand contains a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8;
[4] The vector of any one of [1] to [3], encoding the double-stranded molecule, wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 100 nucleotide pairs in length;
[5] The vector of [4], encoding the double-stranded molecule, wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 75 nucleotide pairs in length;
[6] The vector of [5], encoding the double-stranded molecule, wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 50 nucleotide pairs in length;
[7] The vector of [6] encoding the double-stranded molecule, wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 25 nucleotide pairs in length;
[8] The vector of [7], encoding the double-stranded molecule, wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having between about 19 and about 25 nucleotide pairs in length;
[9] The vector of any one of [1] to [8], wherein the double-stranded molecule is composed of a single polynucleotide having both the sense and antisense strands linked by an intervening single-strand; and
[10] The vector of [9], encoding the double-stranded molecule having the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand containing a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8, [B] is the intervening single-strand composed of 3 to 23 nucleotides, and [A'] is the antisense strand containing a sequence complementary to [A].

The vector of the present invention is described in more detail below.
A vector of the present invention preferably encodes a double-stranded molecule of the present invention in an expressible form. Herein, the phrase "in an expressible form" indicates that the vector, when introduced into a cell, will express the molecule carried, contained or encoded therein. In a preferred embodiment, the vector includes one or more regulatory elements necessary for expression of the double-stranded molecule. Accordingly, in one embodiment, the expression vector encodes the nucleic acid sequences of the double-stranded molecule of the present invention and is adapted for expression of the double-stranded molecule. Such vectors of the present invention may be used for producing the present double-stranded molecules, or directly as an active ingredient for treating cancer.

Vectors of the present invention can be produced, for example, by cloning LRRC42 sequence into an expression vector so that regulatory sequences are operatively-linked to the LRRC42 sequence in a manner to allow expression (by transcription of the DNA molecule) of both strands (Lee NS et al., Nat Biotechnol 2002 May, 20(5): 500-5). For example, RNA molecule that is the antisense to mRNA is transcribed by a first promoter (e.g., a promoter sequence flanking to the 3' end of the cloned DNA) and RNA molecule that is the sense strand to the mRNA is transcribed by a second promoter (e.g., a promoter sequence flanking to the 5' end of the cloned DNA). The sense and antisense strands hybridize in vivo to generate a double-stranded molecule constructs for silencing of the gene. Alternatively, two vectors constructs respectively encoding the sense and antisense strands of the double-stranded molecule are utilized to respectively express the sense and anti-sense strands and then forming a double-stranded molecule construct. Furthermore, the cloned sequence may encode a construct having a secondary structure (e.g., hairpin); accordingly, a single transcript of a vector may contain both the sense and complementary antisense sequences of the target gene.

The present invention contemplates a vector that includes each or both of a combination of polynucleotides, including a sense strand nucleic acid and an antisense strand nucleic acid, wherein the antisense strand includes a nucleotide sequence which is complementary to the sense strand, wherein the transcripts of the sense strand and the antisense strand hybridize to each other to form the double-stranded molecule, and wherein the vector, when introduced into a cell expressing the LRRC42 gene, inhibits expression of the gene.

The vectors of the present invention may also be equipped so to achieve stable insertion into the genome of the target cell (see, e.g., Thomas KR & Capecchi MR, Cell 1987, 51: 503-12 for a description of homologous recombination cassette vectors). See, e.g., Wolff et al., Science 1990, 247: 1465-8; US Patent Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; and WO 98/04720. Examples of DNA-based delivery technologies include "naked DNA", facilitated (bupivacaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated ("gene gun") or pressure-mediated delivery (see, e.g., US Patent No. 5,922,687).

The vectors of the present invention include, for example, viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox (see, e.g., US Patent No. 4,722,848). This approach involves the use of vaccinia virus, e.g., as a vector to express nucleotide sequences that encode the double-stranded molecule. Upon introduction into a cell expressing the target gene, the recombinant vaccinia virus expresses the molecule and thereby suppresses the proliferation of the cell. Another example of useable vector includes Bacille Calmette Guerin (BCG). BCG vectors are described in Stover et al., Nature 1991, 351: 456-60. A wide variety of other vectors is useful for therapeutic administration and production of the double-stranded molecules; examples include adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like. See, e.g., Shata et al., Mol Med Today 2000, 6: 66-71; Shedlock et al., J Leukoc Biol 2000, 68: 793-806; and Hipp et al., In Vivo 2000, 14: 571-85.

Method of Inhibiting or Reducing Growth of a Cancer Cell or Treating Cancer using a Double-Stranded Molecule of the Present Invention:
In present invention, dsRNAs for LRRC42 were tested for their ability to inhibit cell growth. The dsRNA for LRRC42 effectively knocked down the expression of the gene in several cancer cell lines, which coincided with suppression of cell proliferation (Fig. 2).
Accordingly, the present invention provides methods for inhibiting cancer cell growth by inducing dysfunction of the LRRC42 gene via inhibiting the expression of LRRC42. LRRC42 gene expression can be inhibited by any of the aforementioned double-stranded molecules of the present invention that specifically target the LRRC42 gene.

Such ability of the present double-stranded molecules and vectors to inhibit cell growth of cancerous cell indicates that they can be used for methods for treating cancer such as lung cancer, as well as treating or preventing a post-operative, secondary, or metastatic recurrence thereof. Thus, the present invention provides methods to treat patients with cancer by administering a double-stranded molecule against LRRC42 gene or a vector expressing the molecule. The therapeutic method of the present invention may be carried out without adverse effect because LRRC42 gene was minimally detected in normal organs (Fig. 1C).

Of particular interest to the present invention are the following methods [1] to [32]:
[1] A method for inhibiting a growth of cancer cell or treating a cancer, wherein the cancer cell or the cancer expresses at least one LRRC42 gene, such method including the step of administering at least one isolated double-stranded molecule inhibiting the expression of LRRC42 in a cell over-expressing the gene and the cell proliferation or vector encoding the double-stranded molecule, wherein the double-stranded molecule is composed of a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded molecule;
[2] The method of [1], wherein the double-stranded molecule acts at mRNA which matches a target sequence of SEQ ID NO: 7 or 8;
[3] The method of [1] or [2], wherein the sense strand contains the sequence corresponding to a target sequence of SEQ ID NO: 7 or 8;
[4] The method of any one of [1] to [3], wherein the cancer is lung cancer;
[5] The method of any one of [1] to [4], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 100 nucleotide pairs in length;
[6] The method of [5], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 75 nucleotide pairs in length;
[7] The method of [6], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 50 nucleotide pairs in length;
[8] The method of [7], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having a length of less than about 25 nucleotide pairs in length;
[9] The method of [8], wherein the sense strand of the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having a length of between about 19 and about 25 nucleotide pairs in length;
[10] The method of any one of [1] to [9], wherein the double-stranded molecule is composed of a single polynucleotide containing both the sense strand and the antisense strand linked by an intervening single-strand;
[11] The method of [10], wherein the double-stranded molecule has the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand containing a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8, [B] is the intervening single strand composed of 3 to 23 nucleotides, and [A'] is the antisense strand containing a sequence complementary to [A];
[12] The method of any one of [1] to [11], wherein the double-stranded molecule is an RNA;
[13] The method of any one of [1] to [11], wherein the double-stranded molecule contains both DNA and RNA;
[14] The method of [13], wherein the double-stranded molecule is a hybrid of a DNA polynucleotide and an RNA polynucleotide;
[15] The method of [14] wherein the sense and antisense strand polynucleotides are composed of DNA and RNA, respectively;
[16] The method of [13], wherein the double-stranded molecule is a chimera of DNA and RNA;
[17] The method of [16], wherein a region flanking to the 3'-end of the antisense strand, or both of a region flanking to the 5'-end of sense strand and a region flanking to the 3'-end of antisense strand are composed of RNA;
[18] The method of [17], wherein the flanking region is composed of 9 to 13 nucleotides;
[19] The method of any one of [1] to [18], wherein the double-stranded molecule contains one or two 3' overhang(s);
[20] The method of any one of [1] to[19] , wherein the double-stranded molecule is contained in a composition which includes, in addition to the molecule, a transfection-enhancing agent and pharmaceutically acceptable carrier;
[21] The method of [1], wherein the double-stranded molecule is encoded by a vector;
[22] The method of [21], wherein the double-stranded molecule encoded by the vector acts at mRNA which matches a target sequence of SEQ ID NO: 7 or 8;
[23] The method of [21] or [22], wherein the sense strand of the double-stranded molecule encoded by the vector contains the sequence corresponding to a target sequence selected from among SEQ ID NO: 7 and 8;
[24] The method of any one of [21] to [23], wherein the cancer to be treated is lung cancer;
[25] The method of any one of [21] to [24], wherein the double-stranded molecule encoded by the vector has less than about 100 nucleotide pairs in length;
[26] The method of [25], wherein the double-stranded molecule encoded by the vector has a length of less than about 75 nucleotide pairs in length;
[27] The method of [26], wherein the double-stranded molecule encoded by the vector has less than about 50 nucleotide pairs in length;
[28] The method of [27], wherein the double-stranded molecule encoded by the vector has less than about 25 nucleotide pairs in length;
[29] The method of [28], wherein the double-stranded molecule encoded by the vector has between about 19 and about 25 nucleotide pairs in length;
[30] The method of any one of [21] to [29], wherein the double-stranded molecule encoded by the vector is composed of a single polynucleotide containing both the sense strand and the antisense strand linked by an intervening single-strand;
[31] The method of [30], wherein the double-stranded molecule encoded by the vector has the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand containing a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8, [B] is a intervening single-strand is composed of 3 to 23 nucleotides, and [A'] is the antisense strand containing a sequence complementary to [A]; and
[32] The method of any one of [21] to [31], wherein the double-stranded molecule encoded by the vector is contained in a composition which includes, in addition to the molecule, a transfection-enhancing agent and pharmaceutically acceptable carrier.

Therapeutic methods of the present invention are described in more detail below.
The growth of cells expressing an LRRC42 gene may be inhibited by contacting the cells with a double-stranded molecule against an LRRC42 gene, a vector expressing the molecule or a composition containing the same. The cell may be further contacted with a transfection agent. Suitable transfection agents are known in the art. The phrase "inhibition of cell growth" indicates that the cell proliferates at a lower rate or has decreased viability as compared to a cell not exposed to the molecule. Cell growth may be measured by any of a number of methods known in the art, e.g., using the MTT cell proliferation assay.

The growth of any kind of cell may be suppressed according to the present method so long as the cell expresses or over-expresses the target gene of the double-stranded molecule of the present invention. Exemplary cells include lung cancer.
Thus, patients suffering from or at risk of developing a disease related to the over-expression of an LRRC42 gene may be treated with the administration of a double-stranded molecule of the present invention, at least one vector expressing the molecule or a composition containing the molecule. For example, patients suffering from cancer may be treated according to the present methods. The type of cancer may be identified by standard methods according to the particular type of tumor to be diagnosed. More preferably, patients treated by the methods of the present invention are selected by detecting the expression of LRRC42 in a biopsy from the patient by RT-PCR or immunoassay. Preferably, before the treatment of the present invention, the biopsy specimen from the subject is confirmed for LRRC42 gene over-expression by methods known in the art, for example, immunohistochemical analysis or RT-PCR.

According to the present method to inhibit cell growth and thereby treat cancer, through the administration of plural kinds of the double-stranded molecules (or vectors expressing or compositions containing the same), each of the molecules may have different structures but act on mRNA that matches the same target sequence of LRRC42. Alternatively, plural kinds of the double-stranded molecules may act on mRNA that matches a different target sequence of same gene. Alternatively, for example, the method may utilize double-stranded molecules directed to one, two or more target sequence of LRRC42.

For inhibiting cell growth, a double-stranded molecule of present invention may be directly introduced into the cells in a form to achieve binding of the molecule with corresponding mRNA transcripts. Alternatively, as described above, a DNA encoding the double-stranded molecule may be introduced into cells as a vector. For introducing the double-stranded molecules and vectors into the cells, transfection-enhancing agent, such as FuGENE (Roche diagnostics), Lipofectamine 2000 (Invitrogen), Oligofectamine (Invitrogen), and Nucleofector (Wako pure Chemical), may be employed.

As noted in the "Definitions" section above, a treatment is deemed "efficacious" if it leads to clinical benefit such as, reduction in expression of LRRC42 gene, or a decrease in size, prevalence, or metastatic potential of the cancer in the subject. When the treatment is applied prophylactically, "efficacious" means that it retards or prevents cancers from forming or prevents or alleviates a clinical symptom of cancer. Efficaciousness is determined in association with any known method for diagnosing or treating the particular tumor type.

To the extent that the methods and compositions of the present invention find utility in the context of "prevention" and "prophylaxis", such terms are interchangeably used herein to refer to any activity that reduces the burden of mortality or morbidity from disease. Prevention and prophylaxis can occur "at primary, secondary and tertiary prevention levels." While primary prevention and prophylaxis avoid the development of a disease, secondary and tertiary levels of prevention and prophylaxis encompass activities aimed at the prevention and prophylaxis of the progression of a disease and the emergence of symptoms as well as reducing the negative impact of an already established disease by restoring function and reducing disease-related complications. Alternatively, prevention and prophylaxis can include a wide range of prophylactic therapies aimed at alleviating the severity of the particular disorder, e.g. reducing the proliferation and metastasis of tumors.

The treatment and/or prophylaxis of cancer and/or the prevention of postoperative recurrence thereof include any of the following steps, such as the surgical removal of cancer cells, the inhibition of the growth of cancerous cells, the involution or regression of a tumor, the induction of remission and suppression of occurrence of cancer, the tumor regression, and the reduction or inhibition of metastasis. Effectively treating and/or the prophylaxis of cancer decreases mortality and improves the prognosis of individuals having cancer, decreases the levels of tumor markers in the blood, and alleviates detectable symptoms accompanying cancer. For example, reduction or improvement of symptoms constitutes effectively treating and/or the prophylaxis includes 10%, 20%, 30% or more reduction, or stable disease.

Those of skill in the art understand that a double-stranded molecule of the present invention degrades LRRC42 mRNA in substoichiometric amounts. Without wishing to be bound by any theory, it is believed that the double-stranded molecule of the invention causes degradation of the target mRNA in a catalytic manner. Thus, as compared to standard cancer therapies, the present invention requires the delivery of significantly less double-stranded molecule at or near the site of cancer in order to exert therapeutic effect.

One skilled in the art can readily determine the optimal effective amount of the double-stranded molecule of the present invention to be administered to a given subject, by taking into account factors such as body weight, age, sex, type of disease, symptoms and other conditions of the subject; the route of administration; and whether the administration is regional or systemic. Generally, an effective amount of the double-stranded molecule of the invention is an intercellular concentration at or near the cancer site of from about 1 nanomolar (nM) to about 100 nM, preferably from about 2 nM to about 50 nM, more preferably from about 2.5 nM to about 10 nM. It is contemplated that greater or smaller amounts of the double-stranded molecule can be administered. The precise dosage required for a particular circumstance may be readily and routinely determined by one of skill in the art.
The present methods can be used to inhibit the growth or metastasis of cancer expressing LRRC42 gene; for example lung cancer. In particular, a double-stranded molecule containing a target sequence against the LRRC42 gene (e.g., SEQ ID NO: 7 and 8) is particularly preferred for the treatment of cancer.

For treating cancer, the double-stranded molecule of the present invention can also be administered to a subject in combination with a pharmaceutical composition different from the double-stranded molecule. Alternatively, the double-stranded molecule of the present invention can be administered to a subject in combination with another therapeutic method designed to treat cancer. For example, the double-stranded molecule of the present invention can be administered in combination with therapeutic methods currently employed for treating cancer or preventing cancer metastasis (e.g., radiation therapy, surgery and treatment using chemotherapeutic agents, such as cisplatin, carboplatin, cyclophosphamide, 5-fluorouracil, adriamycin, daunorubicin or tamoxifen).

In the context of the present methods, the double-stranded molecule can be administered to the subject either as a naked double-stranded molecule, in conjunction with a delivery reagent, or as a recombinant plasmid or viral vector that expresses the double-stranded molecule.
Suitable delivery reagents for administration in conjunction with the present a double-stranded molecule include the Mirus Transit TKO lipophilic reagent; lipofectin; lipofectamine; cellfectin; or polycations (e.g., polylysine), or liposomes. A preferred delivery reagent is a liposome.

Liposomes can aid in the delivery of the double-stranded molecule to a particular tissue, such as lung tumor tissue, and can also increase the blood half-life of the double-stranded molecule. Liposomes suitable for use in the context of the present invention may be formed from standard vesicle-forming lipids, which generally include neutral or negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of factors such as the desired liposome size and half-life of the liposomes in the blood stream. Varieties of methods are known for preparing liposomes, for example as described in Szoka et al., Ann Rev Biophys Bioeng 1980, 9: 467; and US Pat. Nos. 4,235,871; 4,501,728; 4,837,028; and 5,019,369, the entire disclosures of which are herein incorporated by reference.
Preferably, the liposomes encapsulating the double-stranded molecule of the present invention include a ligand molecule that can deliver the liposome to the cancer site. Ligands that bind to receptors prevalent in tumor or vascular endothelial cells, such as monoclonal antibodies that bind to tumor antigens or endothelial cell surface antigens, are preferred.
Particularly preferably, the liposomes encapsulating the present double-stranded molecule are modified so as to avoid clearance by the mononuclear macrophage and reticuloendothelial systems, for example, by having opsonization-inhibition moieties bound to the surface of the structure. In one embodiment, a liposome of the invention can include both opsonization-inhibition moieties and a ligand.

Opsonization-inhibiting moieties for use in preparing the liposomes of the invention are typically large hydrophilic polymers that are bound to the liposome membrane. As used herein, an opsonization-inhibiting moiety is "bound" to a liposome membrane when it is chemically or physically attached to the membrane, e.g., by the intercalation of a lipid-soluble anchor into the membrane itself, or by binding directly to active groups of membrane lipids. These opsonization-inhibiting hydrophilic polymers form a protective surface layer which significantly decreases the uptake of the liposomes by the macrophage-monocyte system ("MMS") and reticuloendothelial system ("RES"); e.g., as described in US Pat. No. 4,920,016, the entire disclosure of which is herein incorporated by reference. Liposomes modified with opsonization-inhibition moieties thus remain in the circulation much longer than unmodified liposomes. For this reason, such liposomes are sometimes called "stealth" liposomes.

Stealth liposomes are known to accumulate in tissues fed by porous or "leaky" microvasculature. Thus, target tissue characterized by such microvasculature defects, for example, solid tumors, will efficiently accumulate these liposomes; see Gabizon et al., Proc Natl Acad Sci USA 1988, 18: 6949-53. In addition, the reduced uptake by the RES lowers the toxicity of stealth liposomes by preventing significant accumulation in liver and spleen. Thus, liposomes of the invention that are modified with opsonization-inhibition moieties can deliver the present double-stranded molecule to tumor cells.

Opsonization-inhibiting moieties suitable for modifying liposomes are preferably water-soluble polymers with a molecular weight from about 500 to about 40,000 daltons, and more preferably from about 2,000 to about 20,000 daltons. Such polymers include polyethylene glycol (PEG) or polypropylene glycol (PPG) derivatives; e.g., methoxy PEG or PPG, and PEG or PPG stearate; synthetic polymers such as polyacrylamide or poly N-vinyl pyrrolidone; linear, branched, or dendrimeric polyamidoamines; polyacrylic acids; polyalcohols, e.g., polyvinylalcohol and polyxylitol to which carboxylic or amino groups are chemically linked, as well as gangliosides, such as ganglioside GM.sub.1. Copolymers of PEG, methoxy PEG, or methoxy PPG, or derivatives thereof, are also suitable. In addition, the opsonization-inhibiting polymer can be a block copolymer of PEG and either a polyamino acid, polysaccharide, polyamidoamine, polyethyleneamine, or polynucleotide. The opsonization-inhibiting polymers can also be natural polysaccharides containing amino acids or carboxylic acids, e.g., galacturonic acid, glucuronic acid, mannuronic acid, hyaluronic acid, pectic acid, neuraminic acid, alginic acid, carrageenan; aminated polysaccharides or oligosaccharides (linear or branched); or carboxylated polysaccharides or oligosaccharides, e.g., reacted with derivatives of carbonic acids with resultant linking of carboxylic groups.
Preferably, the opsonization-inhibiting moiety is a PEG, PPG, or derivatives thereof. Liposomes modified with PEG or PEG-derivatives are sometimes called "PEGylated liposomes".

The opsonization-inhibiting moiety can be bound to the liposome membrane by any one of numerous well-known techniques. For example, an N-hydroxysuccinimide ester of PEG can be bound to a phosphatidyl-ethanolamine lipid-soluble anchor, and then bound to a membrane. Similarly, a dextran polymer can be derivatized with a stearylamine lipid-soluble anchor via reductive amination using Na(CN)BH. sub.3 and a solvent mixture such as tetrahydrofuran and water in a 30:12 ratio at 60 degrees C.
Vectors expressing a double-stranded molecule of the present invention are discussed above. Such vectors expressing at least one double-stranded molecule of the present invention can also be administered directly or in conjunction with a suitable delivery reagent, including the Mirus Transit LT1 lipophilic reagent; lipofectin; lipofectamine; cellfectin; polycations (e.g., polylysine) or liposomes. Methods for delivering recombinant viral vectors, which express a double-stranded molecule of the present invention, to an area of cancer in a patient are within the skill of the art.

The double-stranded molecule of the present invention can be administered to the subject by any means suitable for delivering the double-stranded molecule into cancer sites. For example, the double-stranded molecule can be administered by gene gun, electroporation, or by other suitable parenteral or enteral administration routes.
Suitable enteral administration routes include oral, rectal, or intranasal delivery.

Suitable parenteral administration routes include intravesical and intravascular administration (e.g., intravenous bolus injection, intravenous infusion, intra-arterial bolus injection, intra-arterial infusion and catheter instillation into the vasculature); peri- and intra-tissue injection (e.g., peri-tumoral and intra-tumoral injection); subcutaneous injection or deposition including subcutaneous infusion (such as by osmotic pumps); direct application to the area at or near the site of cancer, for example by a catheter or other placement device (e.g., a suppository or an implant including a porous, non-porous, or gelatinous material); and inhalation. It is preferred that injections or infusions of the double-stranded molecule or vector be given at or near the site of the cancer.

The double-stranded molecule of the present invention can be administered in a single dose or in multiple doses. Where the administration of the double-stranded molecule of the present invention is by infusion, the infusion can be a single sustained dose or can be delivered by multiple infusions. Injection of the double-stranded molecule directly into the tissue is at or near the site of cancer preferred. Multiple injections of the double-stranded molecule into the tissue at or near the site of cancer are particularly preferred.

One skilled in the art can also readily determine an appropriate dosage regimen for administering the double-stranded molecule of the present invention to a given subject. For example, the double-stranded molecule can be administered to the subject once, for example, as a single injection or deposition at or near the cancer site. Alternatively, the double-stranded molecule can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more preferably from about seven to about ten days. In a preferred dosage regimen, the double-stranded molecule is injected at or near the site of cancer once a day for seven days. Where a dosage regimen requires multiple administrations, it is understood that the effective amount of a double-stranded molecule administered to the subject can include the total amount of a double-stranded molecule administered over the entire dosage regimen.

In the present invention, a cancer overexpressing LRRC42 can be treated with at least one active ingredient selected from the group consisting of:
(a) a double-stranded molecule of the present invention,
(b) DNA encoding thereof, and
(c) a vector encoding thereof.

The cancer includes, but is not limited to, lung cancer. Accordingly, prior to the administration of the double-stranded molecule of the present invention as active ingredient, it is preferable to confirm whether the expression level of LRRC42 in the cancer cells or tissues to be treated is enhanced as compared with normal cells of the same organ. Thus, in one embodiment, the present invention provides a method for treating a cancer (over)expressing LRRC42, such method including the steps of:
i) determining the expression level of LRRC42 in cancer cells or tissue(s) obtained from a subject with the cancer to be treated;
ii) comparing the expression level of LRRC42 with normal control; and
iii) administrating at least one component selected from the group consisting of
(a) a double-stranded molecule of the present invention,
(b) DNA encoding thereof, and
(c) a vector encoding thereof,
to a subject with a cancer overexpressing LRRC42 compared with normal control. Alternatively, the present invention also provides a pharmaceutical composition containing at least one component selected from the group consisting of:
(a) a double-stranded molecule of the present invention,
(b) DNA encoding thereof, and
(c) a vector encoding thereof,
for use in administrating to a subject having a cancer overexpressing LRRC42. In other words, the present invention further provides a method for identifying a subject to be treated with:
(a) a double-stranded molecule of the present invention,
(b) DNA encoding thereof, or
(c) a vector encoding thereof,
which method may include the step of determining an expression level of LRRC42 in subject-derived cancer cells or tissue(s), wherein an increase of the level compared to a normal control level of the gene indicates that the subject has cancer which may be treated with.

The method of treating a cancer of the present invention will be described in more detail below.
A subject to be treated by the present method is preferably a mammal. Exemplary mammals include, but are not limited to, e.g., human, non-human primate, mouse, rat, dog, cat, horse, and cow.
According to the present invention, the expression level of LRRC42 in cancer cells or tissues obtained from a subject is determined. The expression level can be determined at the transcription (nucleic acid) product level, using methods known in the art. For example, the mRNA of LRRC42 may be quantified using probes by hybridization methods (e.g., Northern hybridization). The detection may be carried out on a chip or an array. The use of an array is preferable for detecting the expression level of LRRC42. Those skilled in the art can prepare such probes utilizing the sequence information of LRRC42. For example, the cDNA of LRRC42 may be used as the probes. If necessary, the probes may be labeled with a suitable label, such as dyes, fluorescent substances and isotopes, and the expression level of the gene may be detected as the intensity of the hybridized labels.
Furthermore, the transcription product of LRRC42 (e.g., SEQ ID NO: 1) may be quantified using primers by amplification-based detection methods (e.g., RT-PCR). Such primers may be prepared based on the available sequence information of the gene.

Specifically, a probe or primer used for the present method hybridizes under stringent, moderately stringent, or low stringent conditions to the mRNA of LRRC42. As used herein, the phrase "stringent (hybridization) conditions" refers to conditions under which a probe or primer will hybridize to its target sequence, but not to other sequences. Stringent conditions are sequence-dependent and will be different under different circumstances. Specific hybridization of longer sequences is observed at higher temperatures than shorter sequences. Generally, the temperature of a stringent condition is selected to be about 5 degrees C lower than the thermal melting point (Tm) for a specific sequence at a defined ionic strength and pH. The Tm is the temperature (under a defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to their target sequence hybridize to the target sequence at equilibrium. Since the target sequences are generally present at excess, at Tm, 50% of the probes are occupied at equilibrium. Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30 degrees C for short probes or primers (e.g., 10 to 50 nucleotides) and at least about 60 degrees C for longer probes or primers. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.

Alternatively, the translation product may be detected for the diagnosis of the present invention. For example, the quantity of observed protein (SEQ ID NO: 2) may be determined. Methods for determining the quantity of the protein as the translation product include immunoassay methods that use an antibody specifically recognizing the protein. The antibody may be monoclonal or polyclonal. Furthermore, any fragment or modification (e.g., chimeric antibody, scFv, Fab, F(ab')2, Fv, etc.) of the antibody may be used for the detection, so long as the fragment or modified antibody retains the binding ability to the LRRC42 protein. Methods to prepare these kinds of antibodies for the detection of proteins are well known in the art, and any method may be employed in the present invention to prepare such antibodies and equivalents thereof.

As another method to detect the expression level of LRRC42 gene based on its translation product, the intensity of staining may be measured via immunohistochemical analysis using an antibody against the LRRC42 protein. Namely, in this measurement, strong staining indicates increased presence/level of the protein and, at the same time, high expression level of LRRC42 gene.
The expression level of a target gene, e.g., the LRRC42 gene, in cancer cells can be determined to be increased if the level increases from the control level (e.g., the level in normal cells) of the target gene by, for example, 10%, 25%, or 50%; or increases to more than 1.1 fold, more than 1.5 fold, more than 2.0 fold, more than 5.0 fold, more than 10.0 fold, or more.

The control level may be determined at the same time with the cancer cells by using a sample(s) previously collected and stored from a subject/subjects whose disease state(s) (cancerous or non-cancerous) is/are known. In addition, normal cells obtained from non-cancerous regions of an organ that has the cancer to be treated may be used as normal control. Alternatively, the control level may be determined by a statistical method based on the results obtained by analyzing previously determined expression level(s) of LRRC42 gene in samples from subjects whose disease states are known. Furthermore, the control level can be derived from a database of expression patterns from previously tested cells. Moreover, according to an aspect of the present invention, the expression level of LRRC42 gene in a biological sample may be compared to multiple control levels, which are determined from multiple reference samples. It is preferred to use a control level determined from a reference sample derived from a tissue type similar to that of the subject-derived biological sample. Moreover, it is preferred to use the standard value of the expression levels of LRRC42 gene in a population with a known disease state. The standard value may be obtained by any method known in the art. For example, a range of mean +/- 2 S.D. or mean +/- 3 S.D. may be used as the standard value.

In the context of the present invention, a control level determined from a biological sample that is known to be non-cancerous is referred to as a "normal control level". On the other hand, if the control level is determined from a cancerous biological sample, it is referred to as a "cancerous control level".
When the expression level of LRRC42 gene is increased as compared to the normal control level, or is similar/equivalent to the cancerous control level, the subject may be diagnosed with cancer to be treated.

Compositions containing a double-stranded molecule of the present invention:
In addition to the above, the present invention also provides pharmaceutical composition that include the present double-stranded molecule or the vector coding for the molecules. Of particular interest to the present invention are the following compositions [1] to [32]:
[1] A composition for inhibiting growth of a cancer cell or treating a cancer, wherein the cancer and the cancer cell express at least one LRRC42 gene, including isolated double-stranded molecule that inhibits the expression of LRRC42 and the cell proliferation, or vector encoding the double-stranded molecule, wherein the molecule is composed of a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded molecule;
[2] The composition of [1], wherein the double-stranded molecule acts at mRNA which matches a target sequence of SEQ ID NO: 7 or 8;
[3] The composition of [1] or [2], wherein the double-stranded molecule, wherein the sense strand contains a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8;
[4] The composition of any one of [1] to [3], wherein the cancer to be treated is lung cancer;
[5] The composition of any one of [1] to [4], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 100 nucleotide pairs in length;
[6] The composition of [5], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 75 nucleotide pairs in length;
[7] The composition of [6], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 50 nucleotide pairs in length;
[8] The composition of [7], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having less than about 25 nucleotide pairs in length;
[9] The composition of [8], wherein the sense strand of the double-stranded molecule hybridizes with antisense strand at the target sequence to form the double-stranded molecule having between about 19 and about 25 nucleotide pairs in length;
[10] The composition of any one of [1] to [9], wherein the double-stranded molecule is composed of a single polynucleotide containing the sense strand and the antisense strand linked by an intervening single-strand;
[11] The composition of [10], wherein the double-stranded molecule has the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand sequence contains a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8, [B] is the intervening single-strand consisting of 3 to 23 nucleotides, and [A'] is the antisense strand contains a sequence complementary to [A];
[12] The composition of any one of [1] to [11], wherein the double-stranded molecule is an RNA;
[13] The composition of any one of [1] to [11], wherein the double-stranded molecule is DNA and/or RNA;
[14] The composition of [13], wherein the double-stranded molecule is a hybrid of a DNA polynucleotide and an RNA polynucleotide;
[15] The composition of [14], wherein the sense and antisense strand polynucleotides are composed of DNA and RNA, respectively;
[16] The composition of [13], wherein the double-stranded molecule is a chimera of DNA and RNA;
[17] The composition of [16], wherein a region flanking to the 3'-end of the antisense strand, or both of a region flanking to the 5'-end of sense strand and a region flanking to the 3'-end of antisense strand are composed of RNA;
[18] The composition of [17], wherein the flanking region is composed of 9 to 13 nucleotides;
[19] The composition of any one of [1] to [18], wherein the double-stranded molecule contains one or two 3' overhang(s);
[20] The composition of any one of [1] to [19], wherein the composition includes a transfection-enhancing agent and pharmaceutically acceptable carrier;
[21] The composition of [1], wherein the double-stranded molecule is encoded by a vector and contained in the composition;
[22] The composition of [21], wherein the double-stranded molecule encoded by the vector acts at mRNA which matches a target sequence of SEQ ID NO: 7 or 8;
[23] The composition of [21] or [22], wherein the sense strand of the double-stranded molecule encoded by the vector contains the sequence corresponding to a target sequence of SEQ ID NO: 7 or 8;
[24] The composition of any one of [21] to [23], wherein the cancer to be treated is lung cancer;
[25] The composition of any one of [22] to [24], wherein the double-stranded molecule encoded by the vector has a length of less than about 100 nucleotides;
[26] The composition of [25], wherein the double-stranded molecule encoded by the vector has less than about 75 nucleotide pairs in length;
[27] The composition of [26], wherein the double-stranded molecule encoded by the vector has less than about 50 nucleotide pairs in length;
[28] The composition of [27], wherein the double-stranded molecule encoded by the vector has less than about 25 nucleotide pairs in length;
[29] The composition of [28], wherein the double-stranded molecule encoded by the vector has between about 19 and about 25 nucleotide pairs in length;
[30] The composition of any one of [21] to [29], wherein the double-stranded molecule encoded by the vector is composed of a single polynucleotide containing both the sense strand and the antisense strand linked by an intervening single-strand;
[31] The composition of [30], wherein the double-stranded molecule has the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is the sense strand containing a sequence corresponding to a target sequence of SEQ ID NO: 7 or 8, [B] is a intervening single-strand composed of 3 to 23 nucleotides, and [A'] is the antisense strand containing a sequence complementary to [A]; and
[32] The composition of any one of [21] to [31], wherein the composition includes a transfection-enhancing agent and pharmaceutically acceptable carrier.

Suitable compositions of the present invention are described in additional detail below.
The double-stranded molecule of the present invention is preferably formulated as pharmaceutical compositions prior to administering to a subject, according to techniques known in the art. Pharmaceutical composition of the present invention is characterized as being at least sterile and pyrogen-free. As used herein, "pharmaceutical composition" includes formulation for human and veterinary use. As used herein, "pharmaceutical formulations" include formulations for human and veterinary use. Thus, the compositions may be used as pharmaceuticals for humans and other mammals, such as mice, rats, guinea-pigs, rabbits, cats, dogs, sheep, pigs, cattle, monkeys, baboons, and chimpanzees.

In the context of the present invention, suitable pharmaceutical formulations of the present invention include those suitable for oral, rectal, nasal, topical (including buccal, sub-lingual, and transdermal), vaginal or parenteral (including intramuscular, subcutaneous and intravenous) administration, or for administration by inhalation or insufflation. Other formulations include implantable devices and adhesive patches that release a therapeutic agent. When desired, the above-described formulations may be adapted to give sustained release of the active ingredient. Methods for preparing pharmaceutical compositions of the present invention are within the skill in the art, for example as described in Remington's Pharmaceutical Science, 17th ed., Mack Publishing Company, Easton, Pa. (1985), the entire disclosure of which is herein incorporated by reference.

The present pharmaceutical composition contains the double-stranded molecule or vector encoding that of the present invention (e.g., 0.1 to 90% by weight), or a pharmaceutically acceptable salt of the molecule, mixed with a pharmaceutically acceptable carrier medium. Preferred physiologically acceptable carrier media are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid and the like.
According to the present invention, the composition may contain plural kinds of the double-stranded molecules, each of the molecules may be directed to the same target sequence, or different target sequences of LRRC42. For example, the composition may contain double-stranded molecules directed to the LRRC42 gene or its gene products. Alternatively, for example, the composition may contain double-stranded molecules directed to one, two or more target sequences LRRC42.

Furthermore, the present composition may contain a vector coding for one or plural double-stranded molecules. For example, the vector may encode one, two or several kinds of the present double-stranded molecules. Alternatively, the present composition may contain plural kinds of vectors, each of the vectors coding for a different double-stranded molecule.
Moreover, the present double-stranded molecule may be contained as liposomes in the present composition. See the section entitled "Methods of Treating Cancer using the Double-Stranded Molecule" for details of liposomes.

Pharmaceutical compositions of the present invention can also include conventional pharmaceutical excipients and/or additives. Examples of suitable pharmaceutical excipients include stabilizers, antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents. Suitable additives include physiologically biocompatible buffers (e.g., tromethamine hydrochloride), additions of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (for example calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate). Pharmaceutical compositions of the present invention can be packaged for use in liquid form, or can be lyophilized.
For solid compositions, conventional nontoxic solid carriers can be used; for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.

For example, a solid pharmaceutical composition for oral administration can include any of the carriers and excipients listed above and 10-95%, preferably 25-75%, of one or more double-stranded molecule of the invention. A pharmaceutical composition for aerosol (inhalational) administration can include 0.01-20% by weight, preferably 1-10% by weight, of one or more double-stranded molecule of the present invention encapsulated in a liposome as described above, and propellant. A carrier can also be included as desired; e.g., lecithin for intranasal delivery.
In addition to the above, the present composition may contain other pharmaceutically active ingredients so long as they do not inhibit the in vivo function of the double-stranded molecules of the present invention. For example, the composition may contain chemotherapeutic agents conventionally used for treating cancers. The pharmaceutical compositions may also contain other active ingredients such as antimicrobial agents, immunosuppressants or preservatives. Furthermore, it should be understood that, in addition to the ingredients particularly mentioned above, the formulations of this invention may include other agents conventional in the art having regard to the type of formulation in question; for example, those suitable for oral administration may include flavoring agents.

In another embodiment, the present invention provides for the use of the double-stranded nucleic acid molecule of the present invention in manufacturing a pharmaceutical composition for treating a cancer characterized by the expression of LRRC42 gene. For example, the present invention relates to a use of double-stranded nucleic acid molecule inhibiting the expression of an LRRC42 gene in a cell, which molecule includes a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded nucleic acid molecule and target to a sequence of SEQ ID NO: 7 or 8, for manufacturing a pharmaceutical composition for treating cancer expressing LRRC42 gene.
The present invention further provides the double-stranded nucleic acid molecules of the present invention for use in treating a cancer expressing the LRRC42 gene.

Alternatively, the present invention further provides a method or process for manufacturing a pharmaceutical composition for treating a cancer characterized by the expression of LRRC42 gene, wherein the method or process includes a step for formulating a pharmaceutically or physiologically acceptable carrier with a double-stranded nucleic acid molecule inhibiting the expression of LRRC42 gene in a cell, which over-expresses the gene, which molecule includes a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded nucleic acid molecule and target to a sequence of SEQ ID NO: 7 or 8 as active ingredients.

In another embodiment, the present invention provides a method or process for manufacturing a pharmaceutical composition for treating a cancer characterized by the expression of LRRC42 gene, wherein the method or process includes a step for admixing an active ingredient with a pharmaceutically or physiologically acceptable carrier, wherein the active ingredient is a double-stranded nucleic acid molecule inhibiting the expression of LRRC42 gene in a cell, which over-expresses the gene, which molecule includes a sense strand and an antisense strand complementary thereto, hybridized to each other to form the double-stranded nucleic acid molecule and targets to a sequence of SEQ ID NO: 7 or 8.

Hereinafter, the present invention is described in more detail with reference to the Examples. However, the following materials, methods and examples only illustrate aspects of the invention and in no way are intended to limit the scope of the present invention. As such, methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.
Example 1: General Methods
Lung cancer cell lines and tissue samples.
The human lung cancer cell lines used in this study were as follows: lung adenocarcinomas (ADC) A549, LC319, PC14, NCI-H1373 and NCI-H1781; lung squamous cell carcinomas (SCC) SKMES-1, LU61, NCI-H520, NCI-H1703 and NCI-H2170; one large cell carcinoma (LCC) LX1 and small cell lung carcinomas (SCLC) DMS114, DMS273, SBC-3, and SBC-5. All cells were grown in monolayers in appropriate medium supplemented with 10% FCS and were maintained at 37 degrees C in atmospheres of humidified air with 5% CO₂. Human small airway epithelial cells (SAEC) were grown in optimized medium purchased from Cambrex Bio Science, Inc. Primary lung cancer tissue samples had been obtained with informed consent as described previously (Kikuchi T, et al. Oncogene 2003;22:2192-205., Taniwaki M, et al. Int J Oncol 2006;29:567-75.). This study and the use of all clinical materials were approved by individual institutional ethical committees.

Semiquantitative reverse transcription-PCR.
Total RNA was extracted from cultured cells using the TRIzol reagent (Life Technologies, Inc.) according to the manufacturer's protocol. Extracted RNAs were treated with DNase I (Nippon Gene) and reversely transcribed using oligo(dT) primer and SuperScript II. Semiquantitative reverse transcription-PCR (RT-PCR) experiments were carried out with the following synthesized LRRC42-specific primers or with beta-actin (ACTB)-specific primers as an internal control: LRRC42, 5'-GCCAGGAGTCAAAGAAGAGC-3' (SEQ ID NO:3) and 5'- CCTCCCACACCACAAAAGTA-3' (SEQ ID NO:4); ACTB, 5'-GAGGTGATAGCATTGCTTTCG-3' (SEQ ID NO:5) and 5'-CAAGTCAGTGTACAGGTAAGC-3' (SEQ ID NO:6); GARAD2B,
5'-TCCCCCATCTTGGTGATAAA-3' (SEQ ID NO:13) and
5'-CCCAACCCCAATCTATCCTT-3' (SEQ ID NO:14).
PCR reactions were optimized for the number of cycles to ensure product intensity within the logarithmic phase of amplification.

Northern blot analysis.
Human multiple-tissue blots (BD Biosciences Clontech) were hybridized with a ³²P-labeled PCR product of LRCC42. The cDNA probe of LRRC42 was prepared by RT-PCR using following the primers: 5'-GACCAGATCGTTCTGCAGTG-3' (SEQ ID NO: 11) and 5'-CCTCCCACACCACAAAAGTA-3' (SEQ ID NO: 12). Prehybridization, hybridization, and washing were done according to the supplier's recommendations. The blots were autoradiographed at -80 degrees C for 14 days with intensifying BAS screens (Bio-Rad).

Immunofluorescence analysis.
Cells were plated onto glass coverslips (Becton Dickinson Labware), fixed with 4% paraformaldehyde, and permeablilized with 0.1% Triton X-100 in PBS for 5 minutes at room temperature. Non-specific binding was blocked by CASBLOCK (ZYMED) or 5% Skim milk for 10 minutes at room temperature. Cells were then incubated for 60 minutes at room temperature, or for overnight at 4 degrees C with primary antibodies for mouse monoclonal anti-Flag antibody and anti-GATAD2B antibody diluted in PBS containing 1% BSA. After being washed with PBS, the cells were stained by Alexa Fluor 488-conjugated secondary antibody (Molecular Probes) for 60 min at room temperature. After another wash with PBS, each specimen was mounted with Vectashield (Vector Laboratories, Inc.) containing 4', 6'-diamidine-2'- phenylindolendihydrochrolide (DAPI) and visualized with Spectral Confocal Scanning Systems (TSC SP2 AOBS: Leica Microsystems).

RNA interference assay.
To evaluate the biological functions of LRRC42 in lung cancer cells, the present inventors used small interfering RNA (siRNA) duplexes against the target genes (Sigma). The target sequences of the synthetic oligonucleotides for RNA interference were as follows: control-1: (EGFP, enhanced green fluorescence protein [GFP] gene, a mutant of Aequorea gictoria GFP), 5'-GAAGCAGCACGACUUCUUC-3' (corresponding to SEQ ID NO:9); control-2 (LUC, luciferase gene from Photinus pyralis), 5'-CGUACGCGGAAUACUUCGA-3' (corresponding to SEQ ID NO:10); si-LRRC42-#1, 5'-CUUACUACCUCAGCUCAGA-3' (corresponding to SEQ ID NO:7); si-LRRC42-#2, 5'-GACUUGUUAAAUUCCUAUU-3' (corresponding to SEQ ID NO:8). Lung cancer cell lines, LC319 and SBC-3 were plated onto 10-cm dishes (5.0X10⁵ per dish), and transfected with either of the siRNA oligonucleotides (100 nmol/L) using 30 micro-L of Lipofectamine 2000 (Invitrogen) according to the manufacturers' instructions. After seven days of incubation, these cells were stained by Giemsa solution to assess colony formation, and cell numbers were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay.

Western blotting.
Cells were lysed with radioimmunoprecipitation assay buffer [50 mmol/L Tris-HCl (pH 8.0), 150 mmol/L NaCl, 1% NP40, 0.5% deoxychorate-Na, 0.1% SDS] containing Protease Inhibitor Cocktail Set III (Calbiochem). Protein samples were separated by SDS-polyacrylamide gels and electroblotted onto Hybond-ECL nitrocellulose membranes (GE Healthcare Bio-Sciences). Blots were incubated with a mouse monoclonal anti-Flag antibody and anti-GATAD2B antibody. Antigen-antibody complexes were detected using secondary antibodies conjugated to horseradish peroxidase (GE Healthcare Bio-Sciences). Protein bands were visualized by enhanced chemiluminescence Western blotting detection reagents (GE Healthcare Bio-Sciences).

Cell-growth assay.
The entire coding sequence of LRRC42 was cloned into the appropriate site of COOH-terminal Flag-tagged pCAGGS plasmid vector. COS-7 and DMS114 cells transfected either with plasmids expressing Flag-tagged LRRC42 or with mock plasmids were grown for seven days in DMEM containing 10% FCS in the presence of appropriate concentrations of geneticin (G418). Viability of cells was evaluated by MTT assay; briefly, cell-counting kit-8 solution (DOJINDO) was added to each dish at a concentration of 1/10 volume, and the plates were incubated at 37 degrees C for additional 30 minutes. Absorbance was then measured at 490 nm, and at 630 nm as a reference, with a Microplate Reader 550 (BIO-RAD).

Coimmunnoprecipitation and matrix-assisted laser desorption/ionizing-time of flight mass spectrometry mapping of LRRC42-associated proteins.
Cells extracts from lung cancer cell line SBC-3 which was transfected with LRRC42 expression or mock vector were precleared by incubation at 4 degrees C for 1 hour with 80 micro-L of protein G-agarose beads in a final volume of 200 micro-L of immunoprecipitation buffer (0.5% NP40, 50 mmol/L Tris-HCl, 150 mmol/L NaCl) in the presence of proteinase inhibitor. After centrifugation at 1,000 rpm for 5 min at 4 degrees C, the supernatants were incubated at 4 degrees C with anti-Flag M2 agarose for 3 h. The beads were then collected by centrifugation at 5,000 rpm for 1 min and washed six times with 1 mL of each immunoprecipitation buffer. The washed beads were resuspended in 30 micro-L of Laemmli sample buffer and boiled for 5 min, and the proteins were separated using 5% to 20% SDS PAGE gels (Bio-Rad). After electrophoresis, the gels were stained with SilverQuest (Invitrogen). Protein bands specifically found in extracts which was transfected with LRRC42 vector were excised and served for matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) analysis (AXIMA-CFR, SHIMADZU BIOTECH).

Example 2: LRRC42 expression in lung tumors and normal tissues.
To identify novel target molecules for the development of therapeutic agents and/or diagnostic biomarkers of lung cancer, the present inventors previously performed gene expression profile analysis of 120 lung carcinomas using cDNA microarray containing 27,648 genes or expressed sequence tags (Daigo Y, and Nakamura Y. Gen Thorac Cardiovasc Surg 2008;56:43-53., Kikuchi T, et al. Oncogene 2003;22:2192-205., Kakiuchi S, et al. Mol Cancer Res 2003;1:485-99., Kakiuchi S, et al. Hum Mol Genet 2004;13:3029-43., Kikuchi T, et al. Int J Oncol 2006; 28:799-805., Taniwaki M, et al. Int J Oncol 2006;29:567-75.). The present inventors identified LRRC42 that showed 3-fold or higher level of expression in more than 50% of 120 lung cancer samples, and confirmed its transactivation by semiquantitative RT-PCR experiments in 11 of 15 additional lung-cancer tissues and in 8 of 15 lung-cancer cell lines (Figs. 1A and 1B). Northern-blot analysis with an LRRC42 as a probe identified a 1.7-kb transcript only in testis among normal human tissues examined (Fig. 1C). Performed immunofluorescence analysis was performed to examine the subcellular localization of exogenous LRRC42 in COS-7 cells. LRRC42 protein was detected in the nucleus of COS-7 cells that were transfected with LRRC42 expression vector (Fig. 1D).

Example 3: Inhibition of growth of lung cancer cells by siRNA against LRRC42.
To assess whether LRRC42 is essential for growth or survival of lung cancer cells, synthetic oligonucleotide siRNAs against LRRC42 were transfected into lung adenocarcinoma LC319 and small cell lung cancer SBC-3 cells in which LRRC42 was endogenously overexpressed. The mRNA levels of LRRC42 in the cells transfected with si-LRRC42-#1 or -#2 were significantly decreased in comparison with cells transfected with either control siRNAs (Fig. 2A). After seven days of incubation, the significant decreases were observed in the numbers of colonies and the number of viable cells measured by MTT assay (Figs. 2B and 2C).

Example 4: Growth-promoting effect of LRRC42.
To clarify a potential role of LRRC42 in carcinogenesis, the inventers constructed plasmids expressing either LRRC42 (COOH-terminal Flag-tagged pCAGGS plasmid vector) or mock vector. To assess whether LRRC42 plays an essential role in cell growth, growth assay was performed using COS-7 and DMS114 transfected with LRRC42 expression plasmids and detected the growth-promoting activity of cells overexpressing LRRC42, compared with those transfected with mock vector. This result suggests that LRRC42 contributes to tumorigenesis (Figs. 3A and 3B).

Example 5: Interaction and colocalization of LRRC42 with GATAD2B.
To elucidate the function of LRRC42, the present inventors screened a protein(s) that could interact with LRRC42. Lysates of SBC-3 cells which was transfected with LRRC42 expression vector (carboxyl-terminal Flag-tagged pCAGGS plasmid vector) or mock vector were extracted and immunoprecipitated with anti-Flag M2 agarose. The protein complex was separated by SDS-PAGE and visualized by silver staining. A 65-kDa band, which was detectable in lysates of cells transfected with LRRC42 vector, but not in those with mock vector, was extracted. The peptide sequence determined by mass spectrometry indicated the protein to be a human GATAD2B (GATA zinc finger domain containing 2B). GATAD2B was firstly identified as a component of the MeCP1 complex that represses transcription through preferential binding, remodeling and deacetylation of methylated nucleosomes (Feng Q, et al. Mol Cell Biol 2002; 22:536-46). Subsequently, interaction between exogenous LRRC42 and endogenous GATAD2B in SBC-3 cells was confirmed using anti-GATAD2B antibody (ATLAS) by coimmunoprecipitation experiment (Fig. 4A). Also, immunofluorescence analysis was conducted and found colocalization of exogenous LRRC42 with endogenous GATAD2B in nucleus of SBC-3 cells which were transfected with LRRC42 expression vectors (Fig. 4B). Then, GATAD2B expression in human lung cancer samples and cell lines was examined by semi-quantitative RT-PCR, and found coexpression of LRRC42 and GATAD2B in many human lung cancer cells (Figs.4D and 4E). To evaluate the relationship between LRRC42 and GATAD2B in cancer cells, the present inventors examined the protein level of GATAD2B after suppressing GATAD2B expression in LC319 and SBC-3. Treatment of siRNA oligonucleotides against LRRC42 (si-LRRC42) suppressed the expression of endogenous LRRC42 compared to the control siRNA (si-EGFP). Intriguingly, the protein level of GATAD2B was decreased in cells treated with si-LRRC42, while the transcript level of GATAD2B was not changed (Fig. 4C). Accordingly, this data suggests that LRRC42 stabilizes GATAD2B protein.

Discussion
Recent advances in understanding the biological mechanisms underlying cancer development have driven the design of new therapeutic approaches, termed 'targeted therapies', that selectively interfere with molecules or pathways involved in tumor growth and progression. Inactivation of growth factors and their receptors on tumor cells as well as the inhibition of oncogenic tyrosine kinase pathways and the inhibition of molecules that control specific functions in cancer cells constitute the main rational bases of new cancer treatments tailored for individual patients. Small-molecule inhibitors and monoclonal antibodies are major components of these targeted approaches for a number of human malignancies (Ciavarella S, et al. BioDrugs 2010; 24:77-88.). Molecular targeted cancer therapies hold the promise of being more selective for cancer cells than normal cells, thus harming fewer normal cells, reducing side effects, and improving quality of life. Toward identification of molecular targets for drug development, the detailed gene expression profiles of 120 clinical lung cancer samples were previously analyzed using cDNA microarray data and investigated loss-of-function phenotypes by RNA interference systems (Kato T, et al. Cancer Res 2005;65:5638-46., Furukawa C, et al. Cancer Res 2005;65:7102-10., Ishikawa N, et al. Cancer Res 2005;65:9176-84., Suzuki C, et al. Cancer Res 2005;65:11314-25., Ishikawa N, et al. Cancer Sci 2006;97:737-45., Takahashi K, et al. Cancer Res 2006;66:9408-19., Hayama S et al. Cancer Res 2006;66:10339-48., Kato T, et al. Clin Cancer Res 2007;13:434-42., Suzuki C, et al. Mol Cancer Ther 2007;6:542-51., Yamabuki T, et al. Cancer Res 2007;67:2517-25., Hayama S, et al. Cancer Res 2007; 67:4113-22., Taniwaki M, et al. Clin Cancer Res 2007;13:6624-31., Ishikawa N, et al. Cancer Res 2007;67:11601-11., Mano Y et al. Cancer Sci 2007;98:1902-13., Kato T, et al. Cancer Res 2007; 67:8544-53., Kato T, et al. Clin Cancer Res 2008;14:2363-70., Dunleavy EM, et al. Cell 2009;137:485-97., Hirata D, et al. Clin Cancer Res 2009,15:256-66., Suda T, et al. Cancer Sci 2007;98:1803-8., Mizukami Y, et al. Cancer Sci 2008;99:1448-54., Harao M, et al. Int J Cancer 2008;123:2616-25.). Through this systematic analysis, LRRC42 was found to be frequently over-expressed in the majority of clinical lung cancer cases as well as lung cancer cell lines, while its expression was absent in normal tissues except testis (Figs. 1A, 1B and 1C). These results suggest that LRRC42 is a cancer-testis antigen. Furthermore, it was demonstrated that knockdown of LRRC42 expression resulted in inhibition of cancer cell growth (Figs. 2A, 2B and 2C). Accordingly, the LRRC42 gene product appears to play an indispensable role in the growth and progression of lung-cancer cells. Additional evidence supporting the significance of LRRC42 in carcinogenesis was also obtained. Namely, the expression of LRRC42 resulted in the significant promotion of cell growth (Figs. 3A and 3B). Taken together, these results strongly suggest that LRRC42 is likely to be an important growth factor for lung cancer cells and imply that LRRC42 could serve as a valuable target for the development of anticancer agents for lung cancer.

LRR proteins participate in many biologically important processes, such as hormone-receptor interactions, enzyme inhibition, cell adhesion and cellular trafficking. A number of recent studies revealed the involvement of LRR proteins in early mammalian development (Tong ZB, et al. Mamm Genome 2000;11:281-7.), neural development (Mutai H, et al. Biochem Biophys Res Comm 2000;274:427-33.), cell polarization (Bilder D, et al. Nature 2000;403:676-80.), regulation of gene expression (Linhoff MW, et al. Mol Cell Biol 2001;21:3001-11.) and apoptosis signaling (Inohara N, et al. J Biol Chem 1999;274:14560-67). It was shown that LRR domains may be critical for the morphology and dynamics of the cytoskeleton (Wu H, et al. Nat Struct Biol 2000; 7:575-9, Xu P, et al. Proc Natl Acad Sci USA 1997; 94:3685-90.). In all these processes, the LRR domains appear to mediate protein-protein interactions. Accordingly, inhibiting the interactions between LRRC42 and other proteins may contribute to the disruption of lung carcinogenesis because LRRC42 is overexpressed in lung cancer.

Taken together, the data herein reveal that LRRC42 interacts with GATAD2B and stabilizes its protein (Fig. 4). GATAD2B is a constituent of MeCP1 complex that is capable of repressing transcription of methylated DNA. DNA methylation of tumor suppressor gene, like Rb, p14, p15, p16 and so on, is a common feature of various human cancer including lung cancer (Lewandowska J,et al. Mutagenesis 2011, Vaissiere T, et al. Cancer Res 2009;69:243-52). MBD2 (Methyl-CpG-binding domain 2), also a component of MeCP1 complex, is capable of binding specifically to methylated DNA and known to be interacted with GATAD2B (Zhang Y, et al. Genes Dev 1999;13:1924-35, Brackertz M, et al. J Biol Chem 2002;277:40958-66). It was reported that MBD2 is involved in silencing of p16/p14 locus in human colon carcinomas cell line. Thus, it is possible that MeCP1 complex containing GATAD2B stabilized by LRRC42 and MBD2 is responsible for suppression of tumor suppressor genes through binding of methylated DNA that could contribute to lung tumorigenesis.
In conclusion, human LRRC42 is essential for growth and survival of lung cancers. The data herein suggest toward the design of new anticancer drugs that specifically target LRRC42 and/or the LRRC42-GATAD2B interaction for the treatment of lung cancer patients.

The data provided herein add to a comprehensive understanding of cancers, facilitate development of novel diagnostic strategies, and provide clues for identification of molecular targets for therapeutic drugs and preventative agents. Such information contributes to a more profound understanding of tumorigenesis, and provides indicators for developing novel strategies for diagnosis, treatment, and ultimately prevention of cancers.
In particular, the gene-expression analysis of cancers described herein, using the combination of laser-capture dissection and genome-wide cDNA microarray, identify LRRC42 as a gene that is markedly elevated in cancer as compared to normal organs. As such, it finds utility in the context of cancer diagnosis, prevention and therapy. For example, given its differential expression, LRRC42 can be conveniently used as a molecular diagnostic marker for identifying and detecting cancer, in particular, lung cancer. Accordingly, the LRRC42 gene and the proteins encoded thereby find utility in diagnostic kits and assays of cancer.

The present invention further demonstrates that the cell growth may be suppressed by a double-stranded nucleic acid molecule that specifically targets the LRRC42 gene. Thus, the double-stranded nucleic acid molecule is useful for the development of anti-cancer pharmaceuticals. Furthermore, LRRC42 polypeptide is a useful target for the development of anti-cancer pharmaceuticals. Furthermore, GATAD2B was identified as the gene that is interacted with LRRC42. For example, substances that block the expression of LRRC42 protein or inhibit its activity, or block the interaction between LRRC42 protein and GATAD2B protein may find therapeutic utility as anti-cancer agents, particularly anti-cancer agents for the treatment of lung cancer.

All publications, databases, sequences, patents, and patent applications cited herein are herby incorporated by reference.
While the invention has been described in detail and with reference to specific embodiments thereof, it is to be understood that the foregoing description is exemplary and explanatory in nature and is intended to illustrate the invention and its preferred embodiments. Through routine experimentation, one skilled in the art will readily recognize that various changes and modifications can be made therein without departing from the spirit and scope of the invention. Thus, the invention is intended to be defined not by the above description, but by the following claims and their equivalents.

Claims (29)

1. A method of detecting or diagnosing cancer or a predisposition for developing the cancer in a subject, comprising a step of determining an expression level of an LRRC42 gene in a subject-derived biological sample, wherein an increase of said LRRC42 gene expression level as compared to a normal control level of said gene indicates that said subject suffers from or is at risk of developing cancer, wherein the expression level is determined by a method selected from the group consisting of:
   (a) detecting an mRNA of an LRRC42 gene;
   (b) detecting a protein encoded by an LRRC42 gene; and
   (c) detecting a biological activity of a protein encoded by an LRRC42 gene.
2. The method of claim 1, wherein said LRRC42 gene expression is at least 10% greater than said normal control level.
3. The method of claim 1, wherein the subject-derived biological sample is a biopsy specimen.
4. The method of claim 1, wherein the cancer is lung cancer.
5. A kit for diagnosing cancer or a predisposition therefore, which comprises a reagent selected from the group consisting of:
   (a) a reagent for detecting an mRNA of an LRRC42 gene;
   (b) a reagent for detecting a protein encoded by an LRRC42 gene; and
   (c) a reagent for detecting a biological activity of a protein encoded by an LRRC42 gene.
6. The kit of claim 5, wherein the reagent is a probe or a primer set to the mRNA of LRRC42 gene, or an antibody against the protein encoded by the LRRC42 gene.
7. A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
   (a) contacting a test substance with an LRRC42 polypeptide or a fragment thereof;
   (b) detecting the binding activity between the polypeptide or the fragment and the test substance; and
   (c) selecting the test substance that binds to the polypeptide or the fragment as a candidate substance for either or both of treating and preventing cancer.
8. A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
   (a) contacting a test substance with a cell expressing an LRRC42 gene;
   (b) detecting an expression level of the LRRC42 gene in the cell of the step (a); and
   (c) selecting the test substance that reduces the expression level detected in the step (b) in comparison with the expression level of an LRRC42 gene detected in the absence of the test substance.
9. A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
   (a) contacting a test substance with an LRRC42 polypeptide or a fragment thereof;
   (b) detecting a biological activity of the polypeptide or the fragment of the step (a); and
   (c) selecting the test substance that suppresses the biological activity of the polypeptide or the fragment detected in the step (b) in comparison with the biological activity detected in the absence of the test substance.
10. The method of claim 9, wherein the biological activity is a cell proliferative activity.
11. A method of screening for a candidate substance for either or both of treating and preventing cancer, or inhibiting a cancer cell growth, said method comprising the steps of:
    a) contacting a test substance with a cell into which a vector comprising the transcriptional regulatory region of LRRC42 genes and a reporter gene that is expressed under the control of the transcriptional regulatory region has been introduced,
    b) measuring the expression and/or activity levels of said reporter gene in the step (a); and
    c) selecting a substance that reduces the expression and/or activity levels of said reporter gene detected in the step (b) in comparison with the expression and/or activity levels in the absence of the test substance.
12. A method of screening for a candidate substance for either or both of treating and preventing cancer, inhibiting cancer cell growth or the binding between an LRRC42 polypeptide and a GATAD2B polypeptide, wherein the method comprises the steps of:
    a) contacting an LRRC42 polypeptide or a functional equivalent thereof with a GATAD2B polypeptide or a functional equivalent thereof, in the presence of a test substance;
    b) detecting the binding between the polypeptides; and
    c) selecting the test substance that inhibits the binding between the polypeptides.
13. The method of claim 12, wherein the functional equivalent of the LRRC42 polypeptide comprises a GATAD2B-binding domain of the LRRC42 polypeptide.
14. The method of claim 12 or 13, wherein the functional equivalent of the GATAD2B polypeptide comprises an LRRC42-binding domain of the GATAD2B polypeptide.
15. The method of any one of claims 7 to 12, wherein the cancer is lung cancer.
16. An isolated double-stranded molecule comprising a sense strand and an antisense strand complementary thereto, wherein the strands hybridize to each other to form the double-stranded molecule, wherein the sense strand comprises a nucleotide sequence corresponding to a target sequence selected from the group consisting of SEQ ID NO: 7 and 8, and wherein said double-stranded molecule, when introduced into a cell expressing an LRRC42 gene, inhibits an expression of said gene as well as cell proliferation.
17. The double-stranded molecule of claim 16, wherein the sense strand hybridizes with antisense strand at the target sequence to form the double-stranded molecule having between 19 and 25 nucleotide pairs in length.
18. The double-stranded molecule of claim 16 or 17, wherein the double-stranded molecule has one or two 3' overhangs at the 3' ends of the sense strand and/or the antisense strand.
19. The double-stranded molecule of any one of claims 16 to 18, wherein said double-stranded molecule is a single polynucleotide comprising the sense strand and the antisense strand linked via a single-stranded nucleotide sequence.
20. The double-stranded molecule of claim 19, wherein said polynucleotide has the general formula 5'-[A]-[B]-[A']-3' or 5'-[A']-[B]-[A]-3', wherein [A] is a sense strand comprising a nucleotide sequence corresponding to a target sequence selected from the group consisting of SEQ ID NOs: 7 and 8; [B] is a nucleotide sequence consisting of about 3 to about 23 nucleotides; and [A'] is an antisense strand comprising a sequence complementary to [A].
21. A vector encoding the double-stranded molecule of any one of claims 16 to 20.
22. A method of either or both of treating and preventing cancer in a subject, said method comprising the step of administering to said subject a pharmaceutically effective amount of a double-stranded molecule against an LRRC42 gene or a vector encoding thereof, wherein the double-stranded molecule inhibits an expression of an LRRC42 gene as well as cell proliferation when introduced into a cell expressing LRRC42 gene.
23. The method of claim 22, wherein the double-stranded molecule is that of any one of claims 16 to 20.
24. The method of claim 22, wherein the vector is that of claim 21.
25. The method of any one of claims 22 to 24, wherein the cancer is lung cancer.
26. A composition for either or both of treating and preventing cancer, said composition comprising a pharmaceutically effective amount of a double-stranded molecule against an LRRC42 gene or a vector encoding thereof, and a pharmaceutically acceptable carrier, wherein the double-stranded molecule inhibits an expression of an LRRC42 gene as well as cell proliferation when introduced into a cell expressing LRRC42 gene.
27. The composition of claim 26, wherein the double-stranded molecule is that of any one of claims 16 to 20.
28. The composition of claim 26, wherein the vector is that of claim 21.
29. The composition of any one of claims 26 to 28, wherein the cancer is lung cancer.

Images