Compositions and methods for the detection and treatment of cervical cancer and cervical intraepithelial neoplasia

Abstract

Described herein are biomarkers for HPV-associated pre-cancers and cancers such as cervical cancer and cervical intraepithelial neoplasia. The RNA binding protein (RBP) and long-noncoding RNA (lnc-RNA) biomarkers can be detected and used to diagnose HPV-associated pre-cancers and cancers. In addition, early diagnosis of HPV-associated pre-cancers and cancers can facilitate therapeutic intervention in patients, particularly in the pre-cancer stage which can delay or prevent progression to cancer.

1 . A method of quantitating an expression level of a lnc-FANCI-2 polynucleotide in a sample containing cells from a test patient's cervix with one or more first polynucleotides that hybridizes to the lnc-FANCI-2 polynucleotide, the method comprising
 contacting the sample containing cells from the test patient's cervix with the one or more first polynucleotides, and   detecting the level of hybridization of the one or more first polynucleotides to the lnc-FANCI-2polynucleotide,   comparing the level of hybridization in the sample containing cells from the test patient's cervix to a control level of hybridization in a control sample of normal cervical tissues, and   determining differential expression of the lnc-FANCI-2polynucleotidein the sample containing cells from the test patient's cervix when the level of hybridization for the sample containing cells from the test patient's cervix is at least about 300% of the control level of hybridization in the control sample,   wherein the one or more first polynucleotides comprises a forward primer comprising 10-40 nucleotides of SEQ ID NO: 76, a probe comprising 10-40 nucleotides of SEQ ID NO: 77, and a reverse primer complementary to 10-40 nucleotides of SEQ ID NO: 77, wherein the probe and the reverse primer comprise non-overlapping sequences.   
     
     
         2 . The method of  claim 1 , wherein detecting the level of hybridization of the one or more first polynucleotides to the lnc-FANCI-2polynucleotide is done with real-time RT-PCR. 
     
     
         3 . The method of  claim 1 , wherein the sample containing cells from the test patient's cervix comprises a PAP smear, a vaginal wash, or a cervical biopsy sample. 
     
     
         4 . A method of classifying a patient as having a normal cervix, having stage 2-3 CIN, or having cervical cancer, the method comprising
 contacting a sample containing cells from the test patient's cervix with one or more first polynucleotides that hybridizes to the lnc-FANCI-2polynucleotide, and   detecting the level of hybridization of the one or more first polynucleotides to the lnc-FANCI-2polynucleotide,   comparing the level of hybridization in the sample containing cells from the test patient's cervix to a control level of hybridization in a control sample of normal cervical tissues, and   determining a normal cervix in the subject when the level of hybridization is comparable to the control sample of normal cervical tissues,   determining stage 2-3 CIN in the subject when the level of hybridization is at least about 300% to at least about 700% of the control level of hybridization in the control sample, and   determining stage 2-3 CIN in the subject when the level of hybridization is at least about 1000% of the control level of hybridization in the control sample,   wherein the one or more first polynucleotides comprises a forward primer comprising 10-40 nucleotides of SEQ ID NO: 76, a probe comprising 10-40 nucleotides of SEQ ID NO: 77, and a reverse primer complementary to 10-40 nucleotides of SEQ ID NO: 77, wherein the probe and the reverse primer comprise non-overlapping sequences.   
     
     
         5 . The method of  claim 4 , wherein detecting the level of hybridization of the one or more first polynucleotides to lnc-FANCI-2polynucleotide is done with real-time RT-PCR. 
     
     
         6 . The method of  claim 4 , wherein the sample containing cells from the test patient's cervix comprises a PAP smear, a vaginal wash, or a cervical biopsy sample.