US 11,840,732 B2
Diagnostic methods
Göran Landberg, Gothenburg (SE); Anders Ståhlberg, Gothenburg (SE); and Joakim Håkansson, Borås (SE)
Assigned to ISCAFF PHARMA AB, Gothenburg (SE)
Appl. No. 16/347,763
Filed by ISCAFF PHARMA AB, Gothenburg (SE)
PCT Filed Nov. 3, 2017, PCT No. PCT/EP2017/078176
§ 371(c)(1), (2) Date May 6, 2019,
PCT Pub. No. WO2018/083231, PCT Pub. Date May 11, 2018.
Claims priority of application No. 1618743 (GB), filed on Nov. 7, 2016.
Prior Publication US 2019/0284638 A1, Sep. 19, 2019
Int. Cl. A01N 43/00 (2006.01); A01N 43/46 (2006.01); A61K 31/55 (2006.01); C12Q 1/6886 (2018.01); G01N 33/574 (2006.01); C12N 5/071 (2010.01); C12M 1/12 (2006.01)
CPC C12Q 1/6886 (2013.01) [C12M 25/14 (2013.01); C12N 5/0631 (2013.01); G01N 33/57415 (2013.01); C12N 2502/30 (2013.01); C12N 2533/90 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/136 (2013.01); C12Q 2600/158 (2013.01)] 13 Claims
 
1. A method for determining one or more properties of a tumour in a patient, the method comprising:
seeding a 3-dimensional cell-free scaffold obtained from the tumour in the patient with cancer cells, wherein the cancer cells are not taken from the tumour in the patient;
culturing the cancer cells in the scaffold;
assaying the cultured cancer cells for the presence of target molecules indicative of the expression of one or more genes in the cells; and
determining one or more properties of the tumour from which the 3-dimensional cell-free scaffold was obtained based on the presence of target molecules indicative of the expression of one or more genes in the cells in the assay; and wherein the one or more genes are selected from the group consisting of:
ACTN1; AIFM1; ALDH2; ALDOA; ANXA1; AP1B1; AP2B1; ATM; ATXN1; BAG2; BAG3; BHLHE40; BIRC5; BTBD2; BYSL; C3; CAMK2B; CAMK4; CARD11; CASP3; CAV1; CEACAM1; CHD3; COL17A1; CRCT1; DAPK1; DMD; DPYSL2; DYSF; E2F1; EGFR; EIF2AK3; EP300; EPOR; ERBB3; ESR1; FANCC; FEN1; FHIT; FKBP5; FN1; FOS; FRMD6; GADD45A; GADD45G; GOLM1; GSN; GSTP1; HCK; HDAC5; HSPB1; HSPD1; IGF1R; IL4R; ITGA6; ITGB4; JAK1; JUN; KAT2B; KIF15; KRT18; KRT8; LYST; LRP1; LRPS; MAP2; MAP3K14; MAP3K5; MAPK3; MAPKAPK3; MST1R; NDRG1; NME1-NME2; NOS3; NPAS2; NPHP1; NQO1; NR3C; PIK3CG; PAEP; PAK1; PARK2; PARP1; PDE4D; PFN2; PIM1; PTN; PKD1; PLA2G4A; PLD1; PPARGC1A; PPL; PPM1A; PPP1R15A; PPP2R1B; PRKCA; PRNP; PSG9; PSME3; RABAC1; RAC2; RASA1; RBL1; RGS2; RPS6KA3; RUNX1T1; SH2B3; SH3GL3; SLC9A3R1; SMAD4; SNX9; SORBS2; SOX9;SP1; SPG7; SREBF1; STUB1; SUMO4; SVIL; TGFB1 11; TH; TNFAIP3; TNFRSF14; TNIK; TP73; TPD52L1; TRIO; TUBA1A; VIM; WEE1; XPO5;YAP1; and ZNF259.