Devices and methods for prognosis prediction for melanoma cancer
The invention relates to prognostic markers and prognostic signatures, and compositions and methods for determining the prognosis of cancer in a patient, particularly for melanoma. Specifically, the invention relates to the use of genetic and protein markers for the prediction of the risk of progression of a cancer, such as melanoma, based on markers and signatures of markers. In various aspects, the invention provides methods, compositions, kits, and devices based on prognostic cancer markers, specifically melanoma prognostic markers, to aid in the prognosis and treatment of cancer.
1. (Allowed) A kit for determining prognosis of melanoma cancer, comprising:
forward and reverse oligonucleotide primers for each of the genes:
milk fat globule EGF factor 8 protein (MFGE8);
isocitrate dehydrogenase 1 (NADPH+soluble (IDH1);
paired immunoglobin-like type 2 receptor alpha (PILRA);
major histocompatibility complex class 1E (HLA-E); and
thioredoxin domain containing 5 (TXNDC5); and
a labeled oligonucleotide probe for each of said genes;
for MFGE8, said forward primer consisting of the sequence of SEQ ID NO.11, said reverse primer consisting of the sequence of SEQ ID NO.12;
for IDH1, said forward primer consisting of the sequence of SEQ ID NO.13, said reverse primer consisting of the sequence of SEQ ID NO.14;
for PILRA, said forward primer consisting of the sequence of SEQ ID NO.3, said reverse primer consisting of the sequence of SEQ ID NO.4;
for HLA-E, said forward probe consisting of the sequence of SEQ ID NO.5, said reverse primer consisting of the sequence of SEQ ID No.6; and
for TXNDC5, said forward primer consisting of the sequence of SEQ ID NO.1, said reverse primer consisting of the sequence of SEQ ID NO.2.
2. A method for predicting the prognosis of a melanoma in a patient with stage IIIB or stage IIIC cutaneous melanoma after lymphadenectomy, comprising:
measuring from a tumor sample from said patient, expression of mRNA for the genes:
milk fat globule EGF factor 8 protein (MFGE8);
isocitrate dehydrogenase 1 (NADPH+soluble (IDH1);
paired immunoglobin-like type 2 receptor alpha (PILRA);
major histocompatibility complex class 1E (HLA-E); and
thioredoxin domain containing 5 (TXNDC5); where
said expression of each of said genes from a sample from a patient is determined using qPCR to quantify mRNA expression; and
calculating a score (“qPS”) according to the formula:
qPS=−[ 1328.15−187.42( IDH 1)+137.10( MFGE 8)+73.61( PILRA )+211.22( HLA - E )+143.94( TXNDC 5)],
where in said formula, IDH1 means ΔΔC t for isocitrate dehydrogenase 1, MFGE8 means ΔΔC t for milk fat globule EGF factor 8 protein, PILRA means ΔΔC t for paired immunoglobin-like type 2 receptor alpha, HLA-E means ΔΔC t for major histocompatibility complex, class 1E, and TXHDC5 means ΔΔC t for thioredoxin domain containing 5;
wherein a qPS score of less than zero indicates poor prognosis with respect to time to progression and overall survival and a qPS score of greater than zero indicates good prognosis with respect to time to progression and overall survival; and
where the expression of MFGE8 is measured using:
a forward oligonucleotide primer for MFGE8 having the sequence of SEQ ID NO.11; and
a reverse oligonucleotide primer for MFGE8 having the sequence of SEQ ID NO.12.
3. The method of claim 2 , wherein the expression of IDH1 is measured using:
a forward oligonucleotide primer for IDH1 having the sequence of SEQ ID NO.1, and
a reverse oligonucleotide primer for IDH1 having the sequence of SEQ ID NO.2.
4. The method of claim 2 , wherein the expression of PILRA is measured using:
a forward oligonucleotide primer for PILRA having the sequence of SEQ ID NO.3, and
a reverse oligonucleotide primer for PILRA having the sequence of SEQ ID NO.4.
5. The method of claim 2 , wherein the expression of HLA-E is measured using:
a forward oligonucleotide primer for HLA-E having the sequence of SEQ ID NO.5, and
a reverse oligonucleotide primer for HLA-E having the sequence of SEQ ID NO.6.
6. The method of claim 2 , where the expression of TXNDC5 is measured using:
a forward oligonucleotide primer for TXNDC5 having the sequence of SEQ ID NO.13, and
a reverse oligonucleotide primer for TXNDC5 having the sequence of SEQ ID NO.14.