US 12,380,963 B2
Gene expression signature of hyperprogressive disease (HPD) in patients after anti-PD-1 immunotherapy
Donghai Xiong, Franklin, WI (US); Ming You, Elm Grove, WI (US); and Yian Wang, Milwaukee, WI (US)
Assigned to The Medical College of Wisconsin, Inc., Milwaukee, WI (US)
Filed by The Medical College of Wisconsin, Inc., Milwaukee, WI (US)
Filed on Oct. 14, 2020, as Appl. No. 17/070,668.
Claims priority of provisional application 62/914,652, filed on Oct. 14, 2019.
Prior Publication US 2021/0110886 A1, Apr. 15, 2021
Int. Cl. G16B 20/20 (2019.01); C07K 16/28 (2006.01); C12Q 1/6886 (2018.01); G16B 5/20 (2019.01); G16B 25/00 (2019.01); G16H 50/20 (2018.01)
CPC G16B 20/20 (2019.02) [C07K 16/2818 (2013.01); C12Q 1/6886 (2013.01); G16B 5/20 (2019.02); G16B 25/00 (2019.02); G16H 50/20 (2018.01); C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01)] 14 Claims
 
1. A method comprising:
(a) processing a tumor sample from a patient to obtain nucleic acid data, the nucleic acid data comprising RNA expression level data for a plurality of genes;
(b) measuring the RNA expression levels of a subset of selected genes from the plurality, the selected genes consisting of AAK1, ACOT1, ACOT2, ADAR, AFF1, ANKS6, ANXA5, ARID2, ARL1, ARMC9, ATF7IP, AITP11C, ATP5L, BAZ1B, BAZ2A, C17orf97, CAMSAP1, CARD8, CCNA1, CCNT1, CD63, CD96, CHD4, CLSTN3, COL4A1, COL4A2, COMMD9, CORO1C, CPT1A, CREBZF, CSNK1G1, CTLA4, CYP2D6, DGKD, DIAPH1, EID2, ELK4, EP300, ERN1, FAHD1, FAM104B, FBXL17, FPGT, FUBP3, FUCA2, GALNT10, GALNT2, GAPVD1, GATAD2B, GBF1, GOLIM4, GPR18, HADH, HHLA3, HIVEP1, HIVEP2, HMBS, HPGDS, HSPG2, KDM6B, KDR, KLHDC8B, LAMTOR3, LGALS12, LNPEP, LRP6, MAGEH1, MEF2D, MTIF3, NFE2L2, NOTCH3, NPLOC4, NSD1, NUP188, OBSCN, OTUD7B, PAK2, PCDHGB7, PHF8, PPM1L, PPP2R3C, PTPN3, PTS, RANGAP1, SATB1, SERPINF1, SETX, SLC25A34, SLC27A1, SLC38A6, SLC6A6, SMURF1, SNAPC4, SORT1, SPEN, SPIN2A, SPP1, SSBP2, OBFC1, SYTL4, TCF4, TEX261, TGOLN2, TIMM8B, TLN1, TMEM99, TNFRSF25, TNKS2, TRIO, TRIP12, TSC2, TSPAN3, UBTF, KIAA2018, VHL, WDR44, YWHAE, YWHAQ, ZFP36L1, ZNF609, and ZNF878;
(c) measuring the difference in expression level of the subset of selected genes in (b) compared to control expression levels;
(d) based on the measuring in (c), classifying a likelihood that the patient develops hyperprogesssive disease (HPD) in response to anti-PD-1 immunotherapy.