Novel Markers for Detecting Microsatellite Instability in Cancer and Determining Synthetic Lethality with Inhibition of the DNA Base Excision Repair Pathway

Abstract

Described are mismatch repair (MMR−) deficient tumors. Markers are presented herein having a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods and materials are provided for diagnosing microsatellite instability of a tumor. Such a method comprises determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample.

1 .- 29 . (canceled) 
     
     
         30 . A method of detecting alterations in homopolymer lengths in a human tumor sample, the method comprising:
 performing primer-based amplification of DNA on a sample of the tumor, and   detecting lengths of at least three homopolymers that differ from the reference lengths of the at least three homopolymers;   wherein the at least three homopolymers and the reference lengths are selected from the group consisting of the homopolymers of 7 to 12 consecutive adenines or of 7 to 12 consecutive thymidines as listed in Tables 1 and 2.   
     
     
         31 . The method according to  claim 30 , wherein the primer-based amplification of DNA is a multiplex assay. 
     
     
         32 . The method according to  claim 30 , wherein the at least three homopolymers are homopolymers selected from Table 3. 
     
     
         33 . The method according to  claim 30 , wherein the at least three homopolymers are homopolymers selected from
 8 consecutive adenines in the gene DDX27 at position 47858504 of chromosome 20,   8 consecutive thymidines in the gene EXOSC9 at position 122723894 of chromosome 4,   10 consecutive adenines in the gene FAM111B at position 58892377 of chromosome 11,   8 consecutive adenines in the gene GRIK2 at position 102503432 of chromosome 6,   9 consecutive thymidines in the gene KIAA1919 at position 111587361 of chromosome 6,   11 consecutive thymidines in the gene MYL1 at position 211179766 of chromosome 2,   8 consecutive adenines in the gene PHF2 at position 96422612 of chromosome 9,   9 consecutive thymidines in the gene SEC31A at position 83785565 of chromosome 4,   9 consecutive thymidines in the gene TMEM60 at position 77423460 of chromosome 7,   9 consecutive adenines in the gene TTK at position 80751897 of chromosome 6,   11 consecutive thymidines in the gene ABAT at position 8876793 of chromosome 16,   10 consecutive adenines in the gene AKIRIN1 at position 39471673 of chromosome 1,   11 consecutive thymidines in the gene ARFIP1 at position 153832103 of chromosome 4,   10 consecutive thymidines in the gene ARL10 at position 175800427 of chromosome 5,   8 consecutive thymidines in the gene BMPR2 at position 203426177 of chromosome 2,   12 consecutive adenines in the gene BTBD7 at position 93708031 of chromosome 14,   10 consecutive adenines in the gene C15orf2 at position 24927892 of chromosome 15,   8 consecutive thymidines in the gene C17orf96 at position 36829266 of chromosome 17,   10 consecutive thymidines in the gene CCDC89 at position 85395560 of chromosome 11,   10 consecutive adenines in the gene CCND1 at position 69466274 of chromosome 11,   11 consecutive adenines in the gene DIDO1 at position 61536692 of chromosome 20,   10 consecutive thymidines in the gene EDEM1 at position 5260541 of chromosome 3,   11 consecutive adenines in the gene ENTPD4 at position 23289681 of chromosome 8,   11 consecutive adenines in the gene FGFBP3 at position 93666831 of chromosome 10,   11 consecutive adenines in the gene FMO2 at position 171178336 of chromosome 1,   10 consecutive thymidines in the gene FOXN2 at position 48603080 of chromosome 2,   9 consecutive adenines in the gene HDAC4 at position 239974110 of chromosome 2,   10 consecutive adenines in the gene HUS1B at position 656080 of chromosome 6,   11 consecutive thymidines in the gene KDM5A at position 393805 of chromosome 12,   10 consecutive thymidines in the gene KIF5C at position 149879666 of chromosome 2,   9 consecutive thymidines in the gene LANCL1 at position 211297866 of chromosome 2,   10 consecutive adenines in the gene LRCH1 at position 47325657 of chromosome 13,   10 consecutive adenines in the gene MKLN1 at position 131175981 of chromosome 7,   10 consecutive thymidines in the gene PCDHB3 at position 140482944 of chromosome 5,   10 consecutive thymidines in the gene PPM1A at position 60761434 of chromosome 14,   9 consecutive adenines in the gene PURB at position 44920831 of chromosome 7,   9 consecutive thymidines in the gene RYBP at position 72424550 of chromosome 3,   10 consecutive adenines in the gene RYR3 at position 34157542 of chromosome 15,   10 consecutive adenines in the gene ST7L at position 113067471 of chromosome 1,   10 consecutive adenines in the gene TMC7 at position 19073948 of chromosome 16,   11 consecutive adenines in the gene TMEM65 at position 125325218 of chromosome 8,   10 consecutive thymidines in the gene TSR2 at position 54471046 of chromosome X,   12 consecutive thymidines in the gene UBA6 at position 68481878 of chromosome 4,   11 consecutive adenines in the gene UBE2Z at position 47005702 of chromosome 17,   9 consecutive adenines in the gene USP14 at position 212030 of chromosome 18,   11 consecutive adenines in the gene WHSC1L1 at position 38175280 of chromosome 8,   9 consecutive thymidines in the gene ZNF287 at position 16454420 of chromosome 17,   9 consecutive adenines in the gene CEPT1 at position 111690319 of chromosome 1,   11 consecutive adenines in the gene ESCO1 at position 19164371 of chromosome 18,   9 consecutive adenines in the gene GRIA2 at position 158142151 of chromosome 4,   9 consecutive adenines in the gene ZXDA at position 57936947 of chromosome X, and   10 consecutive adenines in the gene SULF2 at position 46286320 of chromosome 20.   
     
     
         34 . The method according to  claim 30 , wherein the tumor is colorectal cancer, endometrial cancer, ovarian cancer, gastric cancer, or a tumor of Lynch syndrome. 
     
     
         35 . The method according to  claim 30 , wherein the detecting comprises detection with an oligonucleotide. 
     
     
         36 . The method according to  claim 31  wherein the multiplex assay is a single base pair extension assay, a DNA hybridization assay, and/or a melting curve assay. 
     
     
         37 . The method according to  claim 30  wherein the difference between a detected length and a reference length is one nucleotide base. 
     
     
         38 . The method according to  claim 30  wherein the difference between a detected length and a reference length is two nucleotide bases. 
     
     
         39 . The method according to  claim 30  wherein the at least three homopolymers are homopolymers selected from the group consisting of:
 the homopolymer of 11 consecutive thymidines in the gene ABAT at position 8876793 of chromosome 16, 
 the homopolymer of 10 consecutive thymidines in the gene ARL10 at position 175800427 of chromosome 5, 
 the homopolymer of 12 consecutive adenines in the gene BTBD7 at position 93708031 of chromosome 14, 
 the homopolymer of 11 consecutive adenines in the gene DIDO1 at position 61536692 of chromosome 20, 
 the homopolymer of 11 consecutive thymidines in the gene KDMSA at position 393805 of chromosome 12, 
 the homopolymer of 10 consecutive thymidines in the gene PPM1A at position 60761434 of chromosome 14, 
 the homopolymer of 10 consecutive adenines in the gene RYR3 at position 34157542 of chromosome 15, 
 the homopolymer of 10 consecutive adenines in the gene TMC7 at position 19073948 of chromosome 16, 
 the homopolymer of 11 consecutive adenines in the gene TMEM65 at position 125325218 of chromosome 8, 
 the homopolymer of 12 consecutive thymidines in the gene UBA6 at position 68481878 of chromosome 4, 
 the homopolymer of 11 consecutive adenines in the gene UBE2Z at position 47005702 of chromosome 17, and 
 the homopolymer of 10 consecutive adenines in the gene SULF2 at position 46286320 of chromosome 20. 
 
     
     
         40 . A kit for determining microsatellite instability in at least 3 microsatellite regions of a tumor or cancer sample, the kit comprising:
 labeled oligonucleotides specific to at least 3 microsatellite regions selected from the group consisting of the homopolymers of 7 to 12 consecutive adenines or of 7 to 12 consecutive thymidines as listed in Tables 1 and 2,   wherein each of the labeled oligonucleotides comprises a sequence specifically hybridizing to one of the microsatellite regions; wherein the maximal amount of the labeled oligonucleotides the kit comprises is limited to the number necessary to specifically detect 3 to 100 microsatellite regions; and   wherein the label of the labeled oligonucleotides is a non-nucleic acid label.   
     
     
         41 . A kit for determining microsatellite instability in at least 3 microsatellite regions of a tumor or cancer sample, the kit comprising:
 labeled oligonucleotides specific to at least 3 microsatellite regions selected from the group consisting of the homopolymers of 7 to 12 consecutive adenines or of 7 to 12 consecutive thymidines as listed in Tables 1 and 2,   wherein the labeled oligonucleotides are at least 3 microsatellite region-specific primer and probe sets;   wherein at least one primer or probe of each set comprises a sequence specifically hybridizing to one of the microsatellite regions;   wherein at least one of the primer or probe of each set is labeled;   wherein the maximal amount of the labeled oligonucleotides the kit comprises is limited to the number necessary to specifically detect 3 to 100 microsatellite regions; and   wherein the label of the labeled oligonucleotides is a non-nucleic acid label.   
     
     
         42 . The kit of  claim 40  further comprising labeled oligonucleotides specific to the microsatellite instability markers of a Bethesda panel or extended Bethesda panel. 
     
     
         43 . The kit of  claim 41  further comprising labeled oligonucleotides specific to the microsatellite instability markers of a Bethesda panel or extended Bethesda panel.