(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 4 March 2010 (04.03.2010) WO 2010/024852 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/68 (2006.01) C07H 21/02 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (21) International Application Number: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, PCT/US2009/004582 DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, 10 August 2009 (10.08.2009) KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (25) Filing Language: English NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (26) Publication Language: English SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/190,369 28 August 2008 (28.08.2008) US (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant (for all designated States except US): GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, NESTEC S.A. [CH/CH]; Avenue Nestle 55, CH-1800 ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, Vevey (CH). TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, (72) Inventors; and MC, MK, MT, NL, NO, PL, PT, RO, SE, SI, SK, SM, (75) Inventors/Applicants (for US only): PAN, Yuanlong TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, [US/US]; 2743 Quail Valley Drive, Chesterfield, MO ML, MR, NE, SN, TD, TG). 6301 7 (US). HANNAH, Steven [US/US]; 293 High Ridge Court, Chesterfield, MO 63017 (US). MIDDLE- Published: TON, Rondo [US/US]; 12366 Country Glen Lane, Creve — with international search report (Art. 21(3)) Coeur, MO 63 141 (US). (74) Agent: GUFFEY, Wendell, Ray; Nestle Purina Petcare Global Resources, Inc., Checkerboard Square, St. Louis, MO 63 164 (US). (54) Title: GENE EXPRESSION PROFILES ASSOCIATED WITH LEAN PHENOTYPE AND USES THEREOF (57) Abstract: Gene expression profiles associated with improved or maintained lean body mass or reduced body fat are dis- closed. The gene expression profiles were determined in adipose, liver, and muscle tissue of animals subjected to lean-promoting regimens such as consumption of a high protein diet, ingestion of conjugated linolenic acid, and/or increased exercise. Methods of using such profiles for the identification of pharmaceutical substances, nutraceutical substances, dietary substances, or treatment regimens that modulate or contribute to desired phenotypes in animals are also disclosed GENE EXPRESSION PROFILES ASSOCIATED WITH LEAN PHENOTYPE AND USES THEREOF CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application claims priority to U.S. Provisional Application Serial No. 61/190369 filed August 28, 2008, the disclosure of which is incorporated herein by reference. BACKGROUND OF THE INVENTION Field of the Invention [0002] The invention relates generally to nutritional or pharmaceutical modulation of body composition and particularly to gene expression profiles associated with improved or maintained lean body mass or reduced body fat and the use of such profiles for the identification of pharmaceutical, nutraceutical, or dietary substances that modulate or contribute to desired phenotypes in animals. Description of the Related Art [0003] Body weight is primarily a function of lean body mass and fat mass in an individual. Lean body mass is the weight of bones, muscles, organs, body water, and all other non-fat constituents of the body. Fat mass is the weight of the body's storage lipids. Disproportionate or excessive fat mass is a hallmark for an individual being overweight or obese. [0004] Excess fat mass and obesity are recognized as a worldwide health problem among humans. The World Health Organization estimates that there are over 1 billion overweight adults, with just under one third of them classified as obese. In addition, obesity is also increasingly recognized as a problem for animals, particularly for companion animals such as dogs and cats. According to the Centers for Disease Control (CDC), obesity is closely associated with at least a risk of other health problems, including hypertension, dyslipidemia, Type II diabetes, heart disease, stroke, sleep apnea, and certain cancers such as breast, endometrial, and colon cancers. Risk factors for an individual becoming obese include genetics, emotions/stress, overeating, and a sedentary lifestyle. [0005] Enhancing lean body mass can enhance the body's basal metabolic rate. Enhancing metabolic rate can facilitate the loss of excess fat mass when dietary caloric intake is insufficient to meet the body's energy needs or can reduce the accumulation of fat mass when dietary caloric intake exceeds the body's maintenance energy requirement. Various approaches to increase lean body mass have been described. One such approach is dietary supplementation with conjugated linoleic acid (CLA). CLA is a term used to describe isomers of octadecdienoic acid that are found in many foods such as dairy products (Terpstra AHM (2004) Am. J. Clin. Nutr. 79:352-61). CLA has been shown to reduce fat mass in mice and humans and has been implicated in an increase in lean body mass (Bhattacharya A et al. (2005) J. Nutr. 135: 1124- 30; Gaullier J-M et al. (2004) Am. J. Clin. Nutr. 79:1 118-25; Blankson H et al. (2000) J. Nutr. 130:2943- 8; and, Park Y et al. (1997) Lipids 32:853-8). Another approach to increase lean body mass is consumption of a high protein diet. Studies suggest that diets with higher protein content, coupled with reduced carbohydrate consumption and/or regular exercise, can enhance the loss of fat mass and reduce the loss of lean body mass (Layman DK et al. (2005) J. Nutr. 135:1903-10; Layman DK et al. (2004) J. Nutr. 134:968S-73S; Marsset-Baglieri A et al. (2004) J. Nutr. 134:2646-52; and, Due A et al. (2004) Int. J. Obes. Relat. Metab. Disord. 28:1283-90). A third approach to increase lean body mass and decrease fat mass is regular exercise (Bhattacharya A et al. (2005) J. Nutr. 135:1 124-30; Layman DK et al. (2005) J. Nutr. 135:1903-10; and, Tsai AC et al. (2003) J. Nutr. Biochem. 14:541-9). [0006] Various studies have evaluated different aspects of the genetics of lean body mass and obesity. Association studies have revealed links between bodyweight, overweight, and obesity and polymorphisms in various genes (Chagnon YC et al. (2003) Obesity Res. 11:313-67). Similarly, association studies have identified genes relating to body fat mass, percentage of body fat, and skin folds, body fat distribution (waist-to-hip ratio, waist circumference, etc.), resting energy expenditure, and adipocyte lipolysis (Chagnon YC et al. (2003) Obesity Res. 11:313-67). In addition, studies have evaluated associations between candidate genes and changes in body weight, including genes associated with spontaneous weight gain over time, genes associated with endurance training-induced changes in fat mass, and genes associated with weight loss during a three year lifestyle change (Chagnon YC et al. (2003) Obesity Res. 11:313-67). A listing of all such genes can be found in the prior art (Chagnon YC et al. (2003) Obesity Res. 11:313-67). Studies have also analyzed the genetic aspects of lean body mass. Lean body mass studies have linked polymorphisms in Type 1 Deiodinase with higher lean body mass and muscle strength (Peeters RP et al. (2005) J. Clin. Endocrinol. 90:256-63), and polymorphisms in the glucocorticoid receptor with higher muscle mass and muscle strength (van Rossum EFC et al. (2004) J. Clin. Endocrinol. 89:4004-9). [0007] Although lean body mass and fat mass are directly related, few studies have attempted to explore the genetic mechanisms that mediate a higher proportion of one type relative to the other. A detailed knowledge of these mechanisms would provide a better understanding of the conditions that favor a high level of lean body mass and/or reduced body fat and would provide a better understanding of how to promote a lean phenotype in an animal. Because a higher proportion of lean body mass, especially relative to fat mass, has positive implications for improved health and decreased risk for obesity-related ailments, it is desirable for an individual to increase the ratio of lean body mass to fat mass, either by increasing lean body mass and/or by reducing body fat. SUMMARY OF THE INVENTION [0008] It is, therefore, an object of the invention to provide one or more genes or gene segments that are differentially expressed in animals exhibiting a lean phenotype resulting from one or more lean phenotype- promoting treatments comprising (1) administration of CLA, (2) consumption of a high protein diet, and (3) increased exercise. [0009] It is another object of the invention to provide a combination comprising a plurality of polynucleotides that are differentially expressed in animals exhibiting a lean phenotype resulting from one or more lean phenotype-promoting treatments comprising (1) administration of CLA, (2) consumption of a high protein diet, and (3) increased exercise. [0010] It is another object of the invention to provide compositions of two or more polynucleotide or polypeptide probes suitable for detecting the expression of genes differentially expressed in animals exhibiting a lean phenotype resulting from one or more lean phenotype-promoting treatments comprising (1) administration of CLA, (2) consumption of a high protein diet, and (3) increased exercise, and devices such as substrate arrays containing the probes.