US2022403474A1PendingUtilityA1
Targeted measure of transcriptional activity related to hormone receptors
Est. expiryApr 29, 2036(~9.8 yrs left)· nominal 20-yr term from priority
A61K 31/565C12Q 2600/158A61K 45/06C12Q 2600/106A61K 31/5685C07K 14/705A61P 35/04G16B 25/10C12Q 1/6886A61K 31/566C07K 14/575C12Q 2600/118A61K 31/519G16B 25/00G16B 25/20A61K 31/436A61P 35/00C12Q 2600/112A61K 31/4196A61K 31/138G01N 33/5758G01N 33/57515G16B 10/00
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Claims
Abstract
Provided herein are methods of determining tumoral sensitivity to hormonal (endocrine) therapy based upon an index of estrogen receptor (ER)- and progesterone receptor (PR)-related genes, referred to as the sensitivity to endocrine therapy index (SETER/PR index), and may have additional consideration for the proportion of ER gene (ESR1) RNA transcripts that contain a mutation relative to the value of the SETER/PR index. Further provided are methods of treating breast cancer patients determined to be sensitive to an endocrine therapy by the SETER/PR index.
Claims
exact text as granted — not AI-modified1 . A kit for determining a Set index of a sample from a subject, the kit comprising:
(a) at least 3 probes for detecting mRNA expression levels of at least three ESR1 or PGR associated genes selected from: i) MAPT, CD2, and QDPR; or ii) MAPT, CD2 and PDZK1; and (b) at least one probe for detecting mRNA expression levels of at least one reference gene selected from: LDHA, ATP5J2, VDAC2, DARS, UGP2, UBE2Z, AK2, WIPF2, APPBP2, and TRIM2; and a package insert comprising instructions for using the kit.
2 . The kit of claim 1 , wherein the kit further comprises at least one additional probe for detecting at least one additional ESR1 or PGR associated gene(s) selected from the group consisting of STC2, KCNE4, CD3D, and AZGP1.
3 . The kit of claim 1 , wherein the kit further comprises at least one additional probe for detecting at least one additional ESR1 or PGR associated gene(s) selected from the group consisting of SLC39A6, STC2, CA12, ESR1, NPYIR, AZGPI, ABAT, ADCYI, CD3D, NATI, MRPS30, DNAJC12, SCUBE2 and KCNE4.
4 . The kit of claim 1 , wherein the kit further comprises at least 10 probes for detecting ESR1 or PGR associated gene(s) and the additional probes are selected from the group consisting of SLC39A6, STC2, CA12, ESR1, ABAT, ADCY1, NAT1, MRPS30, DNAJC12, and SCUBE2.
5 . The kit of claim 1 , wherein the kit further comprises at least 10 probes for detecting ESR1 or PGR associated gene(s) and the additional probes are selected from the group consisting of SLC39A6, STC2, CA12, ESR1, PDZK1, NPY1R, CD2, MAPT, QDPR, AZGP1, ABAT, ADCY1, CD3D, NAT1, MRPS30, DNAJC12, SCUBE2, and KCNE4.
6 . The kit of claim 1 , wherein the at least 3 probes in (a) consist of a set of 18 probes for detecting the ESR1 or PGR associated gene(s) selected from the group consisting of SLC39A6, STC2, CA12, ESR1, PDZK1, NPY1R, CD2, MAPT, QDPR, AZGP1, ABAT, ADCY1, CD3D, NAT1, MRPS30, DNAJC12, SCUBE2, and KCNE4.
7 . The kit of claim 1 , wherein the kit further comprises a plurality of probes for detecting mRNA expression levels of a plurality of reference genes selected from the group consisting of LDHA, ATP5J2, VDAC2, DARS, UCP2, UBE2Z, AK2, WIPF2, APPBP2, and TRIM2.
8 . The kit of claim 1 , wherein the at least 1 probe in (b) consist of a set of 10 probes for detecting mRNA expression levels of reference genes selected from the group consisting of LDHA, ATP5J2, VDAC2, DARS, UCP2, UBE2Z, AK2, WIPF2, APPBP2, and TRIM2.
9 . The kit of claim 1 , wherein the Set index is a SET ER/PR index.
10 . The kit of claim 9 , wherein the package insert comprising instructions for using the kit provides instructions for calculating a Set index that employs the formula
SET
ER
/
PR
=
Σ
i
=
1
1
8
T
i
1
8
-
Σ
j
=
1
1
0
R
j
1
0
+
2
,
where T i is the expression of the ith of the set of genes and R j the expression of the jth of the set of reference genes.
11 . The kit of claim 9 , wherein an index greater than 0, 0.5, or 1 identifies the subject as a subject afflicted with a breast cancer that is sensitive to endocrine therapy.
12 . The kit of claim 10 , wherein the breast cancer is metastatic breast cancer.
13 . The kit of claim 10 , wherein the breast cancer is hormone receptor positive.
14 . The kit of claim 12 , wherein the hormone receptor is an estrogen receptor (ER).
15 . The kit of claim 1 , wherein the at least 3 probes in (a) are configured for determining the mRNA expression levels of said at least three ESR1 or PGR associated genes via reverse transcription-quantitative real-time PCR (RT-qPCR), microarray analysis, amplification-free nucleic acid analysis, picodroplet targeting and reverse transcription, or RNA sequencing.
16 . The kit of claim 15 , wherein the at least 3 probes in (a) are configured for determining the mRNA expression levels of said at least three ESR1 or PGR associated genes via reverse transcription-quantitative real-time PCR (RT-qPCR).
17 . The kit of claim 1 , wherein the at least 1 probe in (b) is configured for determining the expression level of the at least one reference gene via reverse transcription-quantitative real-time PCR (RT-qPCR), microarray analysis, amplification-free nucleic acid analysis, picodroplet targeting and reverse transcription, or RNA sequencing.
18 . The kit of claim 17 , wherein the at least 1 probe in (b) is configured for determining the expression level of the at least one reference gene via reverse transcription-quantitative real-time PCR (RT-qPCR).
19 . The kit of claim 1 , wherein the probes in (a) and (b) are configured for detection of said genes via reverse transcription-quantitative real-time PCR (RT-qPCR).
20 . The kit of claim 1 , wherein the probes in (a) and (b) are configured as primers.Join the waitlist — get patent alerts
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