Methods and compositions for modulating lncRNAs and methods of treatment based on lncRNA expression

1. A method of treating a subject having cancer expressing RAMS11, the method comprising:

providing a biological sample from the subject, the biological sample comprising long noncoding RNA associated with metastasis (RAMS);

measuring a level of RAMS11 (SEQ ID NO: 1) in the biological sample;

administering to the subject, when the measured level of RAMS11 is overexpressed compared to a control sample, a treatment comprising at least one antisense oligonucleotide (ASO) selected from CAACTTCCAGCAAGAT (SEQ ID NO: 41) and AGAACTGCTAAAAGTG (SEQ ID NO: 42); and

wherein the cancer expressing RAMS11 is selected from the group consisting of colorectal cancer (CRC), lung cancer, head or neck cancer, and kidney cancer.

2. The method of claim 1 , wherein the subject is not treated with a topoisomerase inhibitor.

3. The method of claim 1 , wherein the subject is further administered a therapeutically effective amount of: a kinase inhibitor, an alkylating agent, an antineoplastic antibiotic, or an anthracycline antibiotic.

4. The method of claim 1 , wherein the ASO reduces expression of one or more RAMS11 exons selected from the group consisting of:

 (SEQ ID NO: 2)

AGAATGCCAAAGAGCAGCAGGATGGATCCAGCATCCTCTCCTGATAAAAG

AGGGCTAGAAGACGGGAGGCTCCGGGAAGTCTACTGG;

(SEQ ID NO: 3)

AGTCATGAAGACACTGAAAAGTGATGAATCCACATAACCATGACACTGGA

AATGAAGTTTGAGTGGCAGTCAGAATCTGGGAGGAAGCATTGCTAAGTGA

AAATCTTATGGAGCTTGACTAAAAATCCCTGTCAGGAACCGTCAAAAGCT

GTGTCCCTGACATGAAAAATCTTGCTGGAAGTTGAGAGAGGTTTATGCCT

ACTCCGTGATCCGGGAACACAAGACCTTTACCAACCAAAAAAGTGGATAG

CTGTTCTTCTGCTGTGAAGGTTAATAAAG;

(SEQ ID NO: 4)

AACGCCAGAAGTGCCAAGCAATTAACAACCCCAGAAGCAACCCTTAACCA

ATGATTAAATAAAGTGGATGATTACATACCCAAGCTCCTTCAACTCCCAG

GGACATAATTCTGAG;

 (SEQ ID NO: 5)

GGATGGAAAACAAACTGAAACTGGCTCAAGTGAATGCTCACTGGAAGGCT

TACTGGAAAACTTACTGGAAGGATGTGAGGACATGTTCGGGAATCTATTT

GCAGAAAACATATTCAG; 

and

 (SEQ ID NO: 6)

CCCTGTCCACCACAGCCAGCTGGCTGAAGAGCTCAAAAGGCAAGAAATCA

GCAAGAGAGAGAGATGAAGCATGAGAAATGAGCAAAAAACACCCAGCACA

TCATAATCTTGGACAGTTTAGCAGTACATGAAAATAGATGGTCCTCGCCC

CAAGGGACTGCAGTAACCCTGAATAAACAGGATGTCTCTCACTTTTAGCA

GTTCTTTCTGTGCTAGTATTGGGGAAATATATTTTTGGCTGCATGCAAAA

TGGTAAAAGACATCTATTAAGAAAATGAAAACAATGCTTCTGTTTTAGAC

GAAGCTTTTGAAGGTTTAAGGATCACCTATTTATTGACAAAATTGTTTCC

GTGGCTTAAAA.

5. The method of claim 1 , wherein the biological sample comprises tumor cells, circulating tumor cells (CTCs), or formalin-fixed paraffin-embedded (FFPE) tissue, or frozen tissue.

6. The method of claim 1 , wherein the biological sample comprises tumor long noncoding RNAs (lncRNAs).

7. The method of claim 1 , wherein the biological sample is tumor tissue.

8. The method of claim 1 , wherein the biological sample is a biopsy sample.

9. The method of claim 1 , wherein the cancer is selected from the group consisting of: colorectal adenocarcinoma, lung adenocarcinoma, lung squamous cell carcinoma, head and neck squamous cell carcinoma (HNSC), and kidney renal papillary cell carcinoma (KIRP).

10. The method of claim 1 , wherein overexpressed RAMS11, indicates a bad outcome.

11. The method of claim 1 , wherein overexpressed RAMS11 indicates aggressive CRC.

12. The method of claim 1 , wherein overexpressed RAMS11 indicates a poor prognosis.

13. The method of claim 1 , wherein RAMS11 is detected by qPCR.