GENE EXPRESSION ASSAY FOR MEASUREMENT OF DNA MISMATCH REPAIR DEFICIENCY
The present disclosure relates to methods using gene expression measurements to identify mismatch repair deficiency, microsatellite instability and hypermutation in a subject.
1 . A method of identifying mismatch repair deficiency in a subject comprising
a) measuring the gene expression level of at least one gene comprising MLH1, MSH2, MSH6 or PMS2 in a tumor sample from the subject;
b) determining for each of the at least one gene a score Z, wherein Z=(x−μ 1 )/σ 1 , wherein x is the log-transformed normalized expression of the at least one gene, μ 1 is the mean of the log-transformed normalized expression of the at least one gene in non-hypermutated samples, and σ 1 is the standard deviation of the log-transformed normalized expression of the at least one gene in non-hypermutated samples;
c) determining a score MLS, wherein MLS=(Z m +c 1 )/c 2 , wherein Z m is the minimum Z score of the at least one gene, and wherein
c 1 is 0 and c 2 is 1 when one gene is used,
c 1 is 0.56 and c 2 is 0.83 when two genes are used,
c 1 is 0.85 and c 2 is 0.75 when three genes are used, or
c 1 is 1.03 and c 2 is 0.70 when four genes are used;
d) measuring the gene expression level of at least one gene comprising EPM2AIP1, TTC30A, SMAP1, RNLS, WNT11, SFXN1, SREBF1, TYMS, EIF5AL1, or WDR76 in a tumor sample from the subject;
e) determining a score HPS, wherein HPS=(y−μ 2 )/σ 2 , wherein y=Σ i=1 10 y i w i , wherein y i is the log-transformed normalized expression of the at least one gene i in the tumor sample and w i is the prespecified weight for gene i, μ 2 is the mean of the linear combination of the log-transformed normalized expression of the at least one gene in non-hypermutated samples, and σ 2 is the standard deviation of the linear combination of the log-transformed normalized expression of the at least one gene in non-hypermutated samples;
f
)
determining
a
score
MPS
wherein
MPS
=
(
max
(
H
P
S
,
0
)
2
+
min
(
MLS
,
0
)
2
)
1
/
2
;
g) comparing the MPS score with a predetermined cutoff value, wherein the cutoff value identifies mismatch repair deficiency in a subject with at least 95% specificity; and
h) identifying the presence of mismatch repair deficiency in the subject when the MPS score is equal to or greater than the predetermined cutoff value or identifying the absence of mismatch repair deficiency in the subject when the MPS score is less than the predetermined cutoff value.
2 . The method of claim 1 , wherein the weight w i for the at least one gene is
Gene
Weight
EPM2AIP1
−0.31218
TTC30A
−0.19894
SMAP1
−0.1835
RNLS
−0.19023
WNT11
−0.11515
SFXN1
0.214676
SREBF1
0.194835
TYMS
0.206972
EIF5AL1
0.194935
WDR76
0.188582
3 . The method of claim 1 , wherein the cutoff value identifies mismatch repair deficiency in a subject with at least 99% specificity.
4 . The method of claim 1 , wherein the cutoff value identifies mismatch repair deficiency in a subject with at least 99.5% specificity.
5 . The method of claim 1 , wherein the cutoff value is 2.058.
6 . The method of claim 3 , wherein the cutoff value is 2.699.
7 . The method of claim 4 , wherein the cutoff value is 2.939.
8 . The method of claim 1 , wherein the at least one gene in a) comprises MLH1.
9 . The method of claim 1 , wherein the at least one gene in a) comprises each of MLH1, MSH2, MSH6 and PMS2.
10 . The method of claim 1 , wherein the at least one gene in d) comprises each of EPM2AIP1, TTC30A, SMAP1, RNLS, WNT11, SFXN1, SREBF1, TYMS, EIF5AL1 and WDR76
11 . The method of claim 1 , wherein the at least one gene in a) comprises MLH1 and the at least one gene in d) comprises each of EPM2AIP1, TTC30A, SMAP1, RNLS, WNT11, SFXN1, SREBF1, TYMS, EIF5AL1 and WDR76.
12 . The method of claim 1 , wherein the at least one gene in a) comprises each of MLH1, MSH2, MSH6 and PMS2 and the at least one gene in d) comprises each of EPM2AIP1, TTC30A, SMAP1, RNLS, WNT11, SFXN1, SREBF1, TYMS, EIF5AL1 and WDR76.
13 . The method of claim 1 , wherein identifying the presence of mismatch repair deficiency further identifies the subject as having cancer.
14 . The method of claim 13 , wherein identifying the presence of mismatch repair deficiency further identifies the subject for treatment with an anti-cancer therapy.
15 . The method of claim 14 , further comprising administering a treatment to a subject identified as having mismatch repair deficiency.
16 . The method of claim 14 , wherein the treatment comprises administering to the subject an immunotherapy.
17 . The method of claim 14 , wherein the treatment comprises administering to the subject a checkpoint inhibitor therapy.
18 . The method of claim 14 , wherein the treatment comprises administering to the subject an anti-PD1 antibody, an anti-PDL1 antibody, or an anti-CTLA4 antibody.
19 . The method of claim 18 , wherein the anti-PD1 antibody or the anti-PDL1 antibody comprises pembrolizumab, nivolumab, atezolizumab, avelumab, durvalumab, pidilizumab, REGN2810, AMP-224, MEDI0680, PDR001, or CT-001.
20 . The method of claim 18 , wherein the CTLA4 antibody comprises ipilimumab, tremelimumab, or a combination thereof.