Non-coding rna for detection of cancer

Abstract

The present disclosure relates generally to detection of non-coding RNAS molecules in a sample or diagnosis of subject based upon detection or quantification of non-coding nucleic acid sequences in a sample, specifically to identify and use of molecular biomarkers for cancer including breast cancer.

1 . A method of diagnosing a subject with a benign, pre-malignant, or malignant hyperproliferative cell comprising:
 detecting the presence, absence, and/or quantity of at least one non-coding RNA or functional fragment thereof in a sample.   
     
     
         2 . The method of  claim 1 , wherein the subject is a human diagnosed with or suspected as having a breast cancer. 
     
     
         3 . The method of  claim 1 , wherein the step of detecting comprises:
 a) contacting the sample with one or a plurality of probes specific for the at least one non-coding RNA or functional fragment thereof, and normalizing the quantity in the sample with a measurement taken from a control sample;   b) contacting total RNA of the sample to at least one probe complementary to T3p;   c) contacting the total RNA of the sample to at least one probe complementary to one or a combination of nucleic acid sequences comprising any of the sequences in Tables 1, 2, and/or 3; and/or   d) using a chemiluminescent probe, fluorescent probe, and/or fluorescence microscopy.   
     
     
         4 . The method of  claim 1  further comprising exposing a sample from a subject to at least one nucleic acid molecule complementary to one or a combination of non-coding RNAs chosen from: SEQ ID NO:1 through SEQ ID NO:201 or one or combination of non-coding nucleic acid sequences that comprise at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence homology to any nucleic acid of Tables 1, 2, and/or 
     
     
         5 . The method of  claim 1 , wherein the at least one non-coding RNA is T3p or a functional fragment thereof. 
     
     
         6 - 7 . (canceled) 
     
     
         8 . The method of  claim 1 , further comprising correlating the amount of at least one non-coding RNA or homologous sequence thereof in the sample to the probability or likelihood the subject has a benign, pre-malignant, or malignant growth, relative to a measurement of the amount of at least one non-coding RNA or homologous sequence thereof in a control sample. 
     
     
         9 . The method of  claim 1 , wherein the benign, pre-malignant, or malignant hyperproliferative cell is from breast tissue. 
     
     
         10 . The method of  claim 1 , wherein the sample comprises:
 a) blood or serum from a subject;   b) RNA taken from a culture of cells seeded or inoculated by at least one cell from a subject;   c) human tissue sample comprising a tissue or liquid sample from a plasma, serum or blood draw, brushing, biopsy, or surgical resection of a subject; or   d) a cell that is freshly obtained, formalin fixed, alcohol-fixed and/or paraffin embedded.   
     
     
         11 - 12 . (canceled) 
     
     
         13 . The method of  claim 1 , further comprising culturing at least one biopsy from the subject with a culture medium under conditions and for a time period sufficient to grow at least one cell from a subject's breast tissue. 
     
     
         14 . The method of  claim 1 , wherein the step of measuring the quantity of at least one non-coding RNA or a functional fragment thereof in a sample comprises one or a combination of: digitally imaging a sample; exposing a sample to a known amount of labeled antibody specific for an epitope of non-coding RNA or a functional fragment thereof, exposing a sample to one or a plurality of dyes of specific for non-coding RNA or a functional fragment thereof, exposing a sample to at least one labeled probe complementary to a sequence of the non-coding RNA or a functional fragment thereof, exposing a sample to chromatography, isolating total RNA of a sample and exposing the total RNA to sequencing analysis and/or exposing the sample to mass spectrometry, and, optionally, further comprising analyzing morphology of cells from the sample. 
     
     
         15 . The method of  claim 1 , comprising:
 a) contacting one or a plurality of probes specific for the at least one non-coding RNA or functional fragment thereof with the sample;   b) quantifying the presence, absence, or quantity of the at least one non-coding RNA or functional fragment thereof in the sample;   c) calculating one or more scores based upon the presence, absence, or quantity of the at least one non-coding RNA or functional fragment thereof;   d) correlating the one or more scores to the presence, absence, or quantity of the at least one non-coding RNA or functional fragment thereof, such that, if the amount of the at least one non-coding RNA or functional fragment thereof is greater than the quantity of the at least one non-coding RNA or functional fragment thereof in a control sample, the correlating step comprises diagnosing the subject with the benign, pre-malignant, or malignant hyperproliferative cell.   
     
     
         16 - 20 . (canceled) 
     
     
         21 . A method of detecting a cancer cell in a subject comprising:
 detecting whether a non-coding RNA is present in a sample of the subject by contacting the sample with an amount of one or a combination of probes complementary to one or a combination of non-coding RNA sequences.   
     
     
         22 . The method of  claim 21 , wherein the step of detecting is preceded by a step of obtaining RNA from the sample of the subject. 
     
     
         23 . The method of  claim 21 , wherein the method further comprises:
 calculating one or more scores based upon the presence, absence, or quantity of one non-coding RNA and/or a homologous sequence thereof; and   correlating the one or more scores to the presence, absence, or quantity of non-coding RNA and/or functional fragment thereof, such that, if the amount of non-coding RNA and/or functional fragment thereof is greater than the quantity of non-coding RNA and/or functional fragment thereof in a control sample; or, if the amount of non-coding RNA and/or functional fragment thereof is substantially equal to the quantity of non-coding RNA and/or functional fragment thereof in a sample taken from a subject known to have cancer then the subject is diagnosed as having cancer.   
     
     
         24 . The method of  claim 21 , further comprising detecting a presence or quantifying two or more non-coding RNAs chosen from those nucleic acid sequences of Tables 1, 2, and/or 3 or one or combination of nucleic acids sequences that comprise at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% sequence homology to any of the sequences of Tables 1, 2 and/or 3. 
     
     
         25 . The method of  claim 21 , wherein the sample:
 a) is a human tissue sample comprising a tissue from a serum or plasma or blood draw, brushing, biopsy, or surgical resection of the subject;   b) comprises total RNA from a cell that is freshly obtained, formalin fixed, alcohol-fixed and/or paraffin embedded; or   c) is plasma, blood or serum.   
     
     
         26 - 27 . (canceled) 
     
     
         28 . The method of  claim 21 , wherein the probe complementary to is an RNA sequence that is T3p. 
     
     
         29 - 38 . (canceled) 
     
     
         39 . A method of treating a subject in need thereof diagnosed with or suspected of having breast cancer, comprising:
 (a) contacting one or a plurality of probes specific for one or a combination of non-coding RNA and/or a homologous sequence thereof with a sample;   (b) quantifying the presence, absence or amount of non-coding RNA and/or a homologous sequence thereof in the sample;   (c) calculating one or more scores based upon the presence, absence, or quantity of non-coding RNA and/or a homologous sequence thereof;   (d) correlating the one or more scores to the presence, absence, or quantity of non-coding RNA and/or a homologous sequence thereof, such that, if the amount of non-coding RNA and/or a homologous sequence thereof is greater than the quantity of non-coding RNA and/or a homologous sequence thereof in a control sample, the correlating step comprises diagnosing a subject with breast cancer; and   (e) administering to the subject a therapeutically effective amount of treatment for the breast cancer.   
     
     
         40 . (canceled) 
     
     
         41 . The method of  claim 39 , wherein the probe is one or a plurality of nucleic acid sequences complementary to a nucleic acid sequence chosen from one or a combination of sequences of Table 1, Table 2 and/or Table 3. 
     
     
         42 . The method of  claim 39 , wherein the one or plurality of probes comprise a fluorophore, a chemiluminescent agent, and/or a quenching agent. 
     
     
         43 - 48 . (canceled)