US010468120B2 United States Patent ( 10 ) Patent No.: US 10,468,120 B2 Hakozaki et al. (45 ) Date of Patent : * Nov . 5 , 2019 (54 ) METHOD OF GENERATING A 2008/0280844 A1 * 11/2008 Lessnick C12Q 1/6886 HYPERPIGMENTATION CONDITION GENE 514/44 A 2009/0017080 A1 1/2009 Tanner et al. EXPRESSION SIGNATURE 2010/0189669 A1 * 7/2010 Hakozaki 424/60 2010/0292085 A1 * 11/2010 Lum GOIN 33/5067 (71 ) Applicant: The Procter & Gamble Company , 506/7 Cincinnati, OH (US ) 2011/0150798 A1 6/2011 Bacus 2011/0269852 A1 * 11/2011 McDaniel 514/789 ( 72 ) Inventors: Tomohiro Hakozaki, Cincinnati, OH 2012/0149773 A1 * 6/2012 Park A61K 31/203 (US ) ; Wenzhu Zhao , Mason , OH (US ) ; 514/552 Robert Lloyd Binder , Montgomery, 2013/0165470 A1 * 6/2013 Isfort A61K 31/439 OH (US ) ; Jun Xu , Mason , OH (US ) 514/289 (73 ) Assignee : The Procter & Gamble Company , FOREIGN PATENT DOCUMENTS Cincinnati , OH (US ) WO WO 2003/100557 12/2003 WO WO 2005/040416 5/2005 ( * ) Notice : Subject to any disclaimer, the term of this WO 2012011904 A1 1/2012 patent is extended or adjusted under 35 WO 2012116081 A2 8/2012 WO WO2012116081 8/2012 U.S.C. 154 ( b ) by 162 days . WO WO 2014/028572 2/2014 This patent is subject to a terminal dis claimer. OTHER PUBLICATIONS ( 21) Appl. No .: 13 /851,873 Affymetrix HGU133A 2.0 ( release 33 , submitted Oct. 30 , 2012 ) , Affymetrix.com . * Filed : Hakozaki et al. ( 2002 )British Journal of Dermatology 147.1 (2002 ) : ( 22 ) Mar. 27 , 2013 20-31 . * Aoki et al . (British Journal of Dermatology 156.6 (2007 ) : 1214 (65 ) Prior Publication Data 1223 ) . * US 2013/0261006 A1 Oct. 3 , 2013 Kang et al. ( Journal of Investigative Dermatology ( 2011) 131, 1692-1700 ) . * Robinson et al. ( J Am Acad Dermatol Sup 60 ( 2009 ) [Poster pre sentation ] ). * Related U.S. Application Data Niacinamide Research Update , P & Gbeauty , uploaded 2011, pp . (60 ) 1-6 . * Provisional application No. 61/ 618,115 , filed on Mar. Ozsolak et al . RNA sequencing: advances, challenges and oppor 30 , 2012 . tunities. Nature Reviews Genetics , vol. 12 , Feb. 2011, pp . 87-98 . ( Year : 2011 ) . * (51 ) Int. Cl. Yamaguchi et al. The regulation of skin pigmentation . The Journal GOIN 33/48 ( 2006.01 ) of Biological Chemistry , vol. 282 , pp . 27557-27561. ( Year : 2007 ) .* GOIN 33/50 ( 2006.01 ) Millikin , Cheri et al. “ Topical N - acetyl glucosamine and niacinamide G16B 20/00 (2019.01 ) affect pigmentation relevant gene expression in in vitro geonomics C12Q 1/6881 ( 2018.01) experimentation ” Journal American Acadamy of Dermatology, Feb. C12N 15/10 (2006.01 ) 2007 . C12Q 1/6883 ( 2018.01 ) (Continued ) G16B 25/00 (2019.01 ) (52 ) U.S. CI. Primary Examiner — Russell S Negin ??? G16B 20/00 ( 2019.02 ) ; C12N 15/1072 (74 ) Attorney, Agent, or Firm John G. Powell (2013.01 ) ; C12Q 1/6881 (2013.01 ) ; C12Q 1/6883 ( 2013.01 ) ; GOIN 33/5044 ( 2013.01 ) ; ( 57 ) ABSTRACT C12Q 2600/148 ( 2013.01 ) ; C12Q 2600/158 A method of generating a hyperpigmentation condition gene ( 2013.01 ) ; G16B 25/00 (2019.02 ) expression signature for use in identifying connections (58 ) Field of Classification Search between perturbagens and genes associated with a skin None pigmentation condition . The method includes providing a See application file for complete search history. gene expression profile for a reference sample of human skin cells not affected with a pigmentation condition ; generating (56 ) References Cited a gene expression profile for a sample of human skin cells from a subject exhibiting the hyperpigmentation condition ; U.S. PATENT DOCUMENTS comparing the expression profiles to determine a gene 3,755,560 A 8/1973 Dickert et al. expression signature that includes a set of differentially 4,421,769 A 12/1983 Dixon et al. expressed genes ; assigning an identifier to each gene con 4,677,120 A 6/1987 Parish et al . stituting the gene expression signature and ordering the 4,885,311 A 12/1989 Parish et al . identifiers according to the direction of differential expres 5,049,584 A 9/1991 Purcell et al . 5,124,356 A 6/1992 Purcell et al. sion to create one or more gene expression signature lists ; RE34,075 E 9/1992 Purcell et al . and storing the one or more gene expression signature lists 2002/0169562 A1 11/2002 Stephanopoulos on at least one computer readable medium . 2007/0040306 A1 2/2007 Morel et al . 2007/0205226 A1 9/2007 Honda et al. 4 Claims, 73 Drawing Sheets US 10,468,120 B2 Page 2 ( 56 ) References Cited Subramanian,, A. et al , Gene set enrichment analysis: A knowledge based approach for interpreting genome -wide expression profiles . (2005 ) Proc .Natl . Acad Sci U.S.A , 102 , 15545-15550 . OTHER PUBLICATIONS International Search Report ; PCT/US2013 / 034055 ; dated Jun . 11 , Bissett , Donald , et al . “ Genomic Expression Changes Induced by 2013 ; 17 pages . Topical N - acetylGlucosamine in Skin Equivalent Cultures in Vitro ” International Search Report PCT/ US2013 /034052 ; dated Jun . 11 , Journal of Cosmetic Dermatology , 6 ( 4 ) : 232-238 ;Dec . 2007 . 2013 ; 18 pages. Yumiko , I., et al . “ Identification of Novel Hair -Growth Inducers by International Search Report PCT/ US2013 /034054 ; dated Jun . 13 , means of Connectivity Mapping” , FASEB Journal, vol. 24 , May 2013 ; 18 pages . 2010 . International Search Report PCT/ US2013 /034117 ; dated Jun . 11 , Hughes , T.R. et al. “ Functional discovery via a compendium of 2013 ; 17 pages . expression profiles ” Cell vol. 102 , 109-126 ( 2000 ) . Mills , K.J. “ Dandruff/ seborrhoeic dermatitis is characterized by an Jagetia G. C. et al , “ Genotoxic Effect of Hydroquinone on the inflammatory genomic signature and possible immune dysfunction ” Cultured Mouse Spleenocytes” Toxicology Letter 121( 1 ): 15-20 , 2001 . Transcriptional Analysis of the condition and treatment effects of Lamb, Justin , et al . “ Connectivity Map : Gene Expression Signatures zinc pyrithione 2012 British Association of Dermatologists 166 to Connect Small Molecules , Genes , and Disease ” , Science , vol. (Suppl 2 ) , pp . 33-40 . 313 , 2006 . Mihaly , J. “ Decreased retinoid concentration and retinoid signaling M. Hollander et al. “ Nonparametric Statistical Methods” ; Wiley, pathways in human atopic dermatitis” 2011 John Wiley & Sons, New York , ed . 2 , 1999 see , e.g. , pp . 178-185. Experimental Dermatology, 20 , pp . 326-330 . Raynaud E. et al. , “ Depigmentation for cosmetic purposes : preva Ding -Dar , L. “ Retinoid -Responsive Trascriptional Changes in Epi lence and side - effects in a female population in Senegal ” Ann dermal Keratinocytes ” J. Cellular Physiology 220 : pp . 427-329 ; Dermatol Venereol 128 (6-7 ) :720-724 , 2001 ( abstract ) . 2009 . Shimizu K. et al. , “ The skin - lightening effects of artocarpin on Guttman - Yassky E., et al ., “ Major differences in inflammatory UVB - induced pigmentation " Planta Med 68 ( 1 ) :79-81 , 2002 . dendritic cells and their products distinguish atopic dermatitis from Sivapirabu , G. et al. , “ Topical Nicotinamide Modulates Cellular psoriasis ” , J. Allergy Clin . Immunol. , vol . 119 , No. 5 , pp . 1210 Energy Metabolism and Provides Broad -Spectrum Protection Against 1217 , May, 2007 , USA . Ultraviolet Radiation - Induced Immunosuppression in Humans” , British Journal of Dermatology 2009 . * cited by examiner U.S. Patent Nov. 5 , 2019 Sheet 1 of 73 US 10,468,120 B2 FIG . 1 Table A : Pigmentation control targets and some Benchiriark Agents Pigmentation Control Target Effective Agent Examples Examples Tyrosinase inhibition Hydroquinone , resorcinols , kojic acid , arbuun , deoxy -arbutin , Tyrosinase copper chelarion Inhibition of tyrosinaSC Glucosamiste , N - acetyl glucosamine , tunicamycin Melanosome transfer Niacinamide , proteise inhibitors Inhibit binding of alpha -MSH U N -undecylenoyl - phenylalanine melanocyte Down regulation of tyrosinase Retinoid (01 : 30s -reunoic acid , retinol and its esters, Vitamin C compounds, vitamin E , sultl?ydryl compounds Anti - inflammatory agent Hydrocortisone, phytosterol, glycyrrhetimo acid , trailefnamic acid , chandiile extract Increase epidermal turnover Reunoids, salicylic acid , alplia -bydroxy acids alpha -keto acids . kadenosino monophospitwe U.S. Patent Nov. 5 , 2019 Sheet 2 of 73 US 10,468,120 B2 FIG . 2A Table B : Age Spot Signature ; top 200 up -regulated 32 203941 at INT99 integrator complex subunit 9 NM 018250 0.00012 204736 s , at CSPG4 chondroitin sulfate proteoglycan NM_001897 0.00033 218567 x DDPP3 dipeptidyl -peptidase 3 NM_005700 0.0XX05 ) 200630_Xat SET SET translocation (myeloid leukemia - associated ) AV702810 0.00059 207145 ar MSIN myostatin NM 05259 0.00000 214333_x_at IDH3G isocitrate dehydrogenase 3 (NAD + ) ganuma 169268 0.00073 207365 K 31 USP34 ubiquitin specific peptidase 34 NM 014709 0.00096 217953_at PHD finger protein 3 ALO50329 0.00097 217586_x_at N35922 2152013_X_all UG0651606 AK022362 0.00120 202396 at TCERGI transcription elongation regulator 1 NM 006706 0.00123 203518_at LYST lysosomal trafficking regulator NM COX) 81 0.00132 221692 s at MRPL34 mitochondrial ribosomal protein L34 AB049652 0.00157 202573 at CSNKIG2 casein kinase 1 , gamma 2 ALS30441 000168 210232 at CDC42 cell division cycle 42 (GTP binding protein , 25kDa ) M35543 0.000184 202704_at transducer Of ERBB2 , 1 AA675892 0.00186 217040_x at SOX15 SRY ( sex deterinining region Y )-box 15 AB025355 0.00188 217759_at TRIM44 tripartite moul- containing 44 BF431488 0.00190 216859_x_at AL080112 0.00254 212254 at DST dystonin A1798790 0.00266 211464 x at CASPO caspase 6 , apoptosis - related cysteine peptidase U20537 0.00272 206765 at KCN32